From 74cbffba447288613056549559d9aa91c28a6bf2 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Thu, 3 Aug 2017 20:07:36 -0400 Subject: [PATCH 01/18] add timing script and files --- .gitignore | 1 + ...ses-test_task-linebisection_events.tsv.swp | Bin 0 -> 16384 bytes timing.py | 29 ++++++++++++++++++ timing_sub-03_ses-retest_Correct_Task.1D | 1 + timing_sub-03_ses-retest_Incorrect_Task.1D | 1 + ...g_sub-03_ses-retest_No_Response_Control.1D | 1 + timing_sub-03_ses-retest_No_Response_Task.1D | 1 + timing_sub-03_ses-retest_Response_Control.1D | 1 + timing_sub-03_ses-test_Correct_Task.1D | 1 + timing_sub-03_ses-test_Incorrect_Task.1D | 1 + timing_sub-03_ses-test_No_Response_Control.1D | 1 + timing_sub-03_ses-test_No_Response_Task.1D | 1 + timing_sub-03_ses-test_Response_Control.1D | 1 + 13 files changed, 40 insertions(+) create mode 100644 .gitignore create mode 100644 sub-03/ses-test/func/.sub-03_ses-test_task-linebisection_events.tsv.swp create mode 100644 timing.py create mode 100644 timing_sub-03_ses-retest_Correct_Task.1D create mode 100644 timing_sub-03_ses-retest_Incorrect_Task.1D create mode 100644 timing_sub-03_ses-retest_No_Response_Control.1D create mode 100644 timing_sub-03_ses-retest_No_Response_Task.1D create mode 100644 timing_sub-03_ses-retest_Response_Control.1D create mode 100644 timing_sub-03_ses-test_Correct_Task.1D create mode 100644 timing_sub-03_ses-test_Incorrect_Task.1D create mode 100644 timing_sub-03_ses-test_No_Response_Control.1D create mode 100644 timing_sub-03_ses-test_No_Response_Task.1D create mode 100644 timing_sub-03_ses-test_Response_Control.1D diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b6308a3 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +*.tsv diff --git a/sub-03/ses-test/func/.sub-03_ses-test_task-linebisection_events.tsv.swp b/sub-03/ses-test/func/.sub-03_ses-test_task-linebisection_events.tsv.swp new file mode 100644 index 0000000000000000000000000000000000000000..9b9f05f6f36c5dd41cf0befdb97f128159547847 GIT binary patch literal 16384 zcmeI2Ux*|}9mhNI?sSduPYx0!1U3I|>uKrbhYy0=BIVtbn{Pe09vf%UXqB#51(a+v_<;Hg-}G~0I65<4 z`_ynY5T_^O(QG)Fh@J5RjqAQbgXM3_0xN!oyEbecyMdBJ-vTzcQ_iH98L#2v*CEOH8?*Q&8A{D zJ>R%(K9D1jBd{NVYYU^*zSZA%%gw7tue&S9B}X7fAV(laAV(laAV(laAV(la;QuHB zvvXG$5A(cNFP?dC@qN|O_gfZ!-?sRUX?8qsaX5eF2;>Ol2;>Ol2;>Ol2;>Ol2;>Ol z2;>Ol2;>O-7e-+FR8hR0e!V_V7@v&Pj^CBeYz2) zv99y}r4yC*3wd+2GoDQNJ;>H)_V7(+ofqy$}UZcQ2IE6^)`(WvQ#lP&7m_&SgpdMx2>bEgQ$EurP+k` zLfJmO6i)W(R`@c;tEG7(wC<6Wa49a$t5p!ec3-W$FjB|K(Y#zrVS+2$CXWtYRL)iH z1Fb_PlNLu2aOwD9MYw0B~I+naA{CUTe6Av6&_4#y;bk< zpKF^WS9(-d_%C#>54tR|VCeL(#-i5t=^88c=?Xh0{b0o65~gvi(;*IIW1zLG@MWJ~ z;?1PD-@;d>-dimgk##x{O>$Xa# zG~%x?t*!cWR&Ud%TdY~d@oVpb#-ZtymM*ZEs~+74eA=g1c(sbtq}hJSYHnm)Jq~tp ze>(7QO~@cSy{_=Gb$vRkx$4u6P*tDKdT!bV@k;mbu@6167uxm6r6^U8Y(=PgbW>qZ z8yAs-u}d=y2U~4BC#k~4mG9G8+-=g^Z^0Tb`%l5szO-$FoI0vm?|Iu;{P$|k6Ya2Y zpKh>mpN?6jZJS4_3)13e-@3Xeyv~24)^$KhmV1@7r44Yx@$brZXB1IFD6(WKxQ%TQ&iw#-Xgm91mMv z#xxa zU&CW?0k&WRJ_y&qOXT-|h9}{B@G$Ja2CPB>m&xxh!A1BYd=5SYH^9Hh?JvVK@Hl)E z9)!Cfz>V;4^84rESMYuKGJGBaycb@h&wqh=-+wXhfBxhM;yfc-lg#?owp)|>QfCb;+~Rcz@xMHZe)PIaxMTtoSK z@dRz5Cmo}>U3OM{Y$+*j_vj?LUM9Wu78IwcyLI1!O(mzxSj%Z|f=vaVPH9XKN(I!n z`*cZhJL#>ru Date: Thu, 3 Aug 2017 21:28:10 -0400 Subject: [PATCH 02/18] add experiment 1 script --- Exp-1.sh | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 Exp-1.sh diff --git a/Exp-1.sh b/Exp-1.sh new file mode 100644 index 0000000..d9f39df --- /dev/null +++ b/Exp-1.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +# 1. Threshold the stats at p <.05 +3dmerge -1zscore -1thresh 1.96 -1noneg \ +-prefix stats.test.thresh \ +'subject_results/group.test/subj.sub_03/sub_03.results/stats.sub_03+tlrc[17]' + +3dmerge -1zscore -1thresh 1.96 -1noneg \ +-prefix stats.retest.thresh \ +'subject_results/group.retest/subj.sub_03/sub_03.results/stats.sub_03+tlrc[17]' + +# 2. Calculate a mask that contains overlapping regions of the brain in both sessions +3dmask_tool -input subject_results/group.*/subj.sub_03/sub_03.results/mask_group+tlrc.HEAD -frac 1.0 -prefix mask + +# 3. Binarize the thresholded images +3dcalc -a stats.test.thresh+tlrc -prefix stats.test.bin -expr 'astep(a,.1)' +3dcalc -a stats.retest.thresh+tlrc -prefix stats.retest.bin -expr 'astep(a,.1)' + +# 4. Calculate the Dice coefficient +3ddot -mask mask+tlrc -dodice stats.test.bin+tlrc stats.retest.bin+tlrc \ No newline at end of file From c4efe30bea81327ba5d041cce8374bd160308599 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Thu, 3 Aug 2017 21:49:09 -0400 Subject: [PATCH 03/18] add afni auto-generated scripts for exp-1 --- .../subj.sub_03/.orig.cmd.ap.sub_03 | 49 + .../subj.sub_03/.orig.cmd.usubj.sub_03 | 30 + .../subj.sub_03/.orig.proc.sub_03 | 494 +++++++++ .../group.retest/subj.sub_03/cmd.ap.sub_03 | 49 + .../subj.sub_03/output.cmd.ap.sub_03 | 21 + .../subj.sub_03/output.proc.sub_03 | 956 +++++++++++++++++ .../group.retest/subj.sub_03/proc.sub_03 | 494 +++++++++ .../subj.sub_03/sub_03.results/stats.REML_cmd | 5 + .../subj.sub_03/.orig.cmd.ap.sub_03 | 49 + .../subj.sub_03/.orig.cmd.usubj.sub_03 | 30 + .../group.test/subj.sub_03/.orig.proc.sub_03 | 493 +++++++++ .../group.test/subj.sub_03/cmd.ap.sub_03 | 49 + .../subj.sub_03/output.cmd.ap.sub_03 | 21 + .../group.test/subj.sub_03/output.proc.sub_03 | 966 ++++++++++++++++++ .../group.test/subj.sub_03/proc.sub_03 | 493 +++++++++ .../sub_03.results/3dDeconvolve.err | 4 + .../subj.sub_03/sub_03.results/stats.REML_cmd | 5 + 17 files changed, 4208 insertions(+) create mode 100755 Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 create mode 100644 Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 create mode 100755 Exp-1/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 create mode 100755 Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 create mode 100644 Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 create mode 100644 Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 create mode 100755 Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 create mode 100644 Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd create mode 100755 Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 create mode 100644 Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 create mode 100755 Exp-1/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 create mode 100755 Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 create mode 100644 Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 create mode 100644 Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 create mode 100755 Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 create mode 100644 Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err create mode 100644 Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 new file mode 100755 index 0000000..8122ad9 --- /dev/null +++ b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 @@ -0,0 +1,49 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.40 (March 30, 2017) +# creation date: Thu Aug 3 20:37:56 2017 + +# set data directories +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = $top_dir/sub-03/ses-retest/anat +set epi_dir = $top_dir/sub-03/ses-retest/func + +# set subject and group identifiers +set subj = sub_03 +set group_id = retest + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $anat_dir/sub-03_ses-retest_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ + -align_opts_aea -cost nmi \ + -tlrc_base MNI_avg152T1+tlrc \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 6.0 \ + -regress_stim_times \ + $top_dir/timing_sub-03_ses-retest_Correct_Task.1D \ + $top_dir/timing_sub-03_ses-retest_Incorrect_Task.1D \ + $top_dir/timing_sub-03_ses-retest_No_Response_Control.1D \ + $top_dir/timing_sub-03_ses-retest_No_Response_Task.1D \ + $top_dir/timing_sub-03_ses-retest_Response_Control.1D \ + -regress_stim_labels \ + Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ + Response_Control \ + -regress_basis 'GAM' \ + -regress_censor_motion 0.3 \ + -regress_censor_outliers 0.5 \ + -regress_apply_mot_types demean deriv \ + -regress_opts_3dD \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -glt_label 1 Landmark-Detection \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts \ + -regress_run_clustsim no + diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 new file mode 100644 index 0000000..7361497 --- /dev/null +++ b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 @@ -0,0 +1,30 @@ +uber_subject.py \ + -cvar subj_dir subject_results/group.retest/subj.sub_03 \ + -svar align_cost nmi \ + -svar anat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ + \ + -svar blur_size 6.0 \ + -svar epi \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ + \ + -svar gid retest \ + -svar gltsym '0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -svar gltsym_label Landmark-Detection \ + -svar outlier_limit 0.5 \ + -svar regress_mot_deriv yes \ + -svar run_clustsim no \ + -svar sid sub_03 \ + -svar stim \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ + \ + -svar stim_basis 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' \ + -svar stim_label Correct_Task Incorrect_Task No_Response_Control \ + No_Response_Task Response_Control \ + -svar stim_type times times times times times \ + -svar tlrc_base MNI_avg152T1+tlrc diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 new file mode 100755 index 0000000..04545b4 --- /dev/null +++ b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 @@ -0,0 +1,494 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Aug 3 20:38:10 2017" +echo "(version 5.15, April 25, 2017)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + +# =========================== auto block: setup ============================ +# script setup + +# take note of the AFNI version +afni -ver + +# check that the current AFNI version is recent enough +afni_history -check_date 23 Sep 2016 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 23 Sep 2016)" + echo " (consider: @update.afni.binaries -defaults)" + exit +endif + +# the user may specify a single subject to run with +if ( $#argv > 0 ) then + set subj = $argv[1] +else + set subj = sub_03 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ + $output_dir/sub-03_ses-retest_T1w + +# ============================ auto block: tcat ============================ +# apply 3dTcat to copy input dsets to results dir, while +# removing the first 0 TRs +3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 238 ) + +# ------------------------------------------------------- +# enter the results directory (can begin processing data) +cd $output_dir + + +# ========================== auto block: outcount ========================== +# data check: compute outlier fraction for each volume +touch out.pre_ss_warn.txt +foreach run ( $runs ) + 3dToutcount -automask -fraction -polort 4 -legendre \ + pb00.$subj.r$run.tcat+orig > outcount.r$run.1D + + # censor outlier TRs per run, ignoring the first 0 TRs + # - censor when more than 0.5 of automask voxels are outliers + # - step() defines which TRs to remove via censoring + 1deval -a outcount.r$run.1D -expr "1-step(a-0.5)" > rm.out.cen.r$run.1D + + # outliers at TR 0 might suggest pre-steady state TRs + if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then + echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ + >> out.pre_ss_warn.txt + endif +end + +# catenate outlier counts into a single time series +cat outcount.r*.1D > outcount_rall.1D + +# catenate outlier censor files into a single time series +cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D + +# ================================= tshift ================================= +# time shift data so all slice timing is the same +foreach run ( $runs ) + 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + pb00.$subj.r$run.tcat+orig +end + +# -------------------------------- +# extract volreg registration base +3dbucket -prefix vr_base pb01.$subj.r01.tshift+orig"[2]" + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-03_ses-retest_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask \ + -cost nmi \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-retest_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-03_ses-retest_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-03_ses-retest_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base vr_base+orig \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg/epi2anat/tlrc xforms + cat_matvec -ONELINE \ + sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform: volreg/epi2anat/tlrc + 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc mask_epi_extents + +# and apply the extents mask to the EPI data +# (delete any time series with missing data) +foreach run ( $runs ) + 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc \ + -expr 'a*b' -prefix pb02.$subj.r$run.volreg +end + +# warp the volreg base EPI dataset to make a final version +cat_matvec -ONELINE \ + sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I > \ + mat.basewarp.aff12.1D + +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input vr_base+orig \ + -1Dmatrix_apply mat.basewarp.aff12.1D \ + -mast_dxyz 4 \ + -prefix final_epi_vr_base + +# create an anat_final dataset, aligned with stats +3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.$subj + +# record final registration costs +3dAllineate -base final_epi_vr_base+tlrc -allcostX \ + -input anat_final.$subj+tlrc |& tee out.allcostX.txt + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-03_ses-retest_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== blur ================================== +# blur each volume of each run +foreach run ( $runs ) + 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.$subj.r$run.blur \ + pb02.$subj.r$run.volreg+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc +end + +# create union of inputs, output type is byte +3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj + +# ---- create subject anatomy mask, mask_anat.$subj+tlrc ---- +# (resampled from tlrc anat) +3dresample -master full_mask.$subj+tlrc -input sub-03_ses-retest_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute overlaps between anat and EPI masks +3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_overlap.txt + +# note Dice coefficient of masks, as well +3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_dice.txt + +# ---- create group anatomy mask, mask_group+tlrc ---- +# (resampled from tlrc base anat, MNI_avg152T1+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/monicali/abin/MNI_avg152T1+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= scale ================================== +# scale each voxel time series to have a mean of 100 +# (be sure no negatives creep in) +# (subject to a range of [0,200]) +foreach run ( $runs ) + 3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.3 motion_${subj} + +# combine multiple censor files +1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \ + -expr "a*b" > censor_${subj}_combined_2.1D + +# note TRs that were not censored +set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ + -show_trs_uncensored encoded` + +# ------------------------------ +# run the regression analysis +3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ + -censor censor_${subj}_combined_2.1D \ + -polort 4 \ + -num_stimts 17 \ + -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D 'GAM' \ + -stim_label 1 Correct_Task \ + -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D 'GAM' \ + -stim_label 2 Incorrect_Task \ + -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D \ + 'GAM' \ + -stim_label 3 No_Response_Control \ + -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D 'GAM' \ + -stim_label 4 No_Response_Task \ + -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D 'GAM' \ + -stim_label 5 Response_Control \ + -stim_file 6 motion_demean.1D'[0]' -stim_base 6 -stim_label 6 roll_01 \ + -stim_file 7 motion_demean.1D'[1]' -stim_base 7 -stim_label 7 pitch_01 \ + -stim_file 8 motion_demean.1D'[2]' -stim_base 8 -stim_label 8 yaw_01 \ + -stim_file 9 motion_demean.1D'[3]' -stim_base 9 -stim_label 9 dS_01 \ + -stim_file 10 motion_demean.1D'[4]' -stim_base 10 -stim_label 10 dL_01 \ + -stim_file 11 motion_demean.1D'[5]' -stim_base 11 -stim_label 11 dP_01 \ + -stim_file 12 motion_deriv.1D'[0]' -stim_base 12 -stim_label 12 roll_02 \ + -stim_file 13 motion_deriv.1D'[1]' -stim_base 13 -stim_label 13 pitch_02 \ + -stim_file 14 motion_deriv.1D'[2]' -stim_base 14 -stim_label 14 yaw_02 \ + -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ + -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ + -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -glt_label 1 Landmark-Detection \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc"[$ktrs]" +3dcalc -a rm.signal.all+tlrc \ + -b rm.noise.all+tlrc \ + -c full_mask.$subj+tlrc \ + -expr 'c*a/b' -prefix TSNR.$subj + +# --------------------------------------------------- +# compute and store GCOR (global correlation average) +# (sum of squares of global mean of unit errts) +3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[5]' > ideal_Correct_Task.1D +1dcat X.nocensor.xmat.1D'[6]' > ideal_Incorrect_Task.1D +1dcat X.nocensor.xmat.1D'[7]' > ideal_No_Response_Control.1D +1dcat X.nocensor.xmat.1D'[8]' > ideal_No_Response_Task.1D +1dcat X.nocensor.xmat.1D'[9]' > ideal_Response_Control.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]" + +# also, create a stimulus-only X-matrix, for easy review +1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D + +# ============================ blur estimation ============================= +# compute blur estimates +touch blur_est.$subj.1D # start with empty file + +# create directory for ACF curve files +mkdir files_ACF + +# -- estimate blur for each run in epits -- +touch blur.epits.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +echo average epits FWHM blurs: $blurs +echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +echo average epits ACF blurs: $blurs +echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D + +# -- estimate blur for each run in errts -- +touch blur.errts.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +echo average errts FWHM blurs: $blurs +echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +echo average errts ACF blurs: $blurs +echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ +# -align_opts_aea -cost nmi -tlrc_base MNI_avg152T1+tlrc -volreg_align_to \ +# third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 \ +# -regress_stim_times \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ +# -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ +# 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ +# -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 \ +# Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ +# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 new file mode 100755 index 0000000..8122ad9 --- /dev/null +++ b/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 @@ -0,0 +1,49 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.40 (March 30, 2017) +# creation date: Thu Aug 3 20:37:56 2017 + +# set data directories +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = $top_dir/sub-03/ses-retest/anat +set epi_dir = $top_dir/sub-03/ses-retest/func + +# set subject and group identifiers +set subj = sub_03 +set group_id = retest + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $anat_dir/sub-03_ses-retest_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ + -align_opts_aea -cost nmi \ + -tlrc_base MNI_avg152T1+tlrc \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 6.0 \ + -regress_stim_times \ + $top_dir/timing_sub-03_ses-retest_Correct_Task.1D \ + $top_dir/timing_sub-03_ses-retest_Incorrect_Task.1D \ + $top_dir/timing_sub-03_ses-retest_No_Response_Control.1D \ + $top_dir/timing_sub-03_ses-retest_No_Response_Task.1D \ + $top_dir/timing_sub-03_ses-retest_Response_Control.1D \ + -regress_stim_labels \ + Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ + Response_Control \ + -regress_basis 'GAM' \ + -regress_censor_motion 0.3 \ + -regress_censor_outliers 0.5 \ + -regress_apply_mot_types demean deriv \ + -regress_opts_3dD \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -glt_label 1 Landmark-Detection \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts \ + -regress_run_clustsim no + diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 new file mode 100644 index 0000000..89d2fea --- /dev/null +++ b/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 @@ -0,0 +1,21 @@ +-- applying orig view as +orig +-- tcat: reps is now 238 +++ updating polort to 4, from run len 595.0 s +-- volreg: using base dset vr_base+orig +++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 4 mm tlrc voxels +-- applying anat warps to 1 dataset(s): sub-03_ses-retest_T1w +-- masking: group anat = 'MNI_avg152T1+tlrc', exists = 1 +-- have 1 ROI dict entries ... +-- will apply motion types: demean, deriv +-- using default: will not apply EPI Automask + (see 'MASKING NOTE' from the -help for details) + +------------------------------------- +** warning have only 1 run to analyze +------------------------------------- + +--> script is file: proc.sub_03 + consider the script execution command: + + tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 new file mode 100644 index 0000000..0b46bf7 --- /dev/null +++ b/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 @@ -0,0 +1,956 @@ +echo auto-generated by afni_proc.py, Thu Aug 3 20:38:10 2017 +auto-generated by afni_proc.py, Thu Aug 3 20:38:10 2017 +echo (version 5.15, April 25, 2017) +(version 5.15, April 25, 2017) +echo execution started: `date` +date +execution started: Thu Aug 3 20:45:11 EDT 2017 +afni -ver +Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) +afni_history -check_date 23 Sep 2016 +-- is current: afni_history as new as: 23 Sep 2016 + most recent entry is: 21 Jul 2017 +if ( 0 ) then +if ( 0 > 0 ) then +set subj = sub_03 +endif +set output_dir = sub_03.results +if ( -d sub_03.results ) then +set runs = ( `count -digits 2 1 1` ) +count -digits 2 1 1 +mkdir sub_03.results +mkdir sub_03.results/stimuli +cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D sub_03.results/stimuli +3dcopy /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz sub_03.results/sub-03_ses-retest_T1w +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] +++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ elapsed time = 1.4 s +set tr_counts = ( 238 ) +cd sub_03.results +touch out.pre_ss_warn.txt +foreach run ( 01 ) +3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig +++ 3dToutcount: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. +++ 18031 voxels passed mask/clip +1deval -a outcount.r01.1D -expr 1-step(a-0.5) +if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then +1deval -a outcount.r01.1D{0} -expr step(a-0.4) +echo ** TR #0 outliers: possible pre-steady state TRs in run 01 +endif +end +cat outcount.r01.1D +cat rm.out.cen.r01.1D +foreach run ( 01 ) +3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig +++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. +*+ WARNING: dataset is already aligned in time! +*+ WARNING: ==>> output dataset is just a copy of input dataset +end +3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] +++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -cost nmi -volreg off -tshift off +#++ align_epi_anat version: 1.57 +#++ turning off volume registration +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./sub-03_ses-retest_T1w+orig +#++ Multi-cost is nmi +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-retest_T1w* +#Script is running (command trimmed): + 3dcopy ./sub-03_ses-retest_T1w+orig ./__tt_sub-03_ses-retest_T1w+orig +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ Removing skull from anat data +#Script is running (command trimmed): + 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-retest_T1w+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-retest_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-retest_T1w+orig.BRIK is 7.491219 degrees from plumb. +#Script is running (command trimmed): + 3dinfo ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' +#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig is ***oblique**** +#Script is running (command trimmed): + 3dAttribute DELTA ./__tt_sub-03_ses-retest_T1w_ns+orig +#++ Spacing for anat to oblique epi alignment is 1.000000 +#++ Matching obliquity of anat to epi +#Script is running (command trimmed): + 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-retest_T1w_ns_obla2e_mat.1D +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Deobliquing original dataset before obliquing +++ Combining oblique transformations +++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.BRIK +#++ using 0th sub-brick because only one found +#Script is running (command trimmed): + 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' +++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ resampling epi to match anat data +#Script is running (command trimmed): + 3dresample -master ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_vr_base_ts+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_vr_base_ts+orig.BRIK is 4.947676 degrees from plumb. +#++ removing skull or area outside brain +#Script is running (command trimmed): + 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig +++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset ./__tt_vr_base_ts_rs+orig +++ Forming automask + + Fixed clip level = 708.019226 + + Used gradual clip level = 621.023193 .. 754.463989 + + Number voxels above clip level = 1151758 + + Clustering voxels ... + + Largest cluster has 1151071 voxels + + Clustering voxels ... + + Largest cluster has 1150607 voxels + + Filled 381 voxels in small holes; now have 1150988 voxels + + Filled 16522 voxels in large holes; now have 1167510 voxels + + Clustering voxels ... + + Largest cluster has 1167476 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 14352028 voxels + + Mask now has 1167476 voxels +++ 1167476 voxels in the mask [out of 15519504: 7.52%] +++ first 64 x-planes are zero [from R] +++ last 68 x-planes are zero [from L] +++ first 30 y-planes are zero [from A] +++ last 22 y-planes are zero [from P] +++ first 107 z-planes are zero [from I] +++ last 48 z-planes are zero [from S] +++ applying mask to original data +++ Writing masked data +++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK +++ CPU time = 3.950000 sec +#++ Computing weight mask +#Script is running (command trimmed): + 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1728.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#Script is running (command trimmed): + 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1728.000000))' +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK +#++ Aligning anat data to epi data +#Script is running (command trimmed): + 3dAllineate -nmi -wtprefix ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets +++ 1356008 voxels in -source_automask+4 +++ Zero-pad: not needed +++ 1167476 voxels [7.5%] in weight mask +++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal+orig.BRIK +++ Number of points for matching = 1167476 +++ shift param auto-range: -84.4..84.4 -70.6..70.6 -85.1..85.1 + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 + + 12 free parameters +++ Normalized convergence radius = 0.001000 +++ OpenMP thread count = 4 +++ ======= Allineation of 1 sub-bricks using Normalized MI [H(b,s)/(H(b)+H(s))] ======= +++ ========== sub-brick #0 ========== [total CPU to here=9.1 s] +++ *** Fine pass begins *** + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - copying weight image + + - using 1167476 points from base image [use_all=0] + + * Exit alignment setup routine + + - histogram: source clip 165.643 .. 715.741; base clip 487.29 .. 1872 + + - versus source range 0 .. 622.496; base range 0 .. 2253.55 + + - Initial cost = 0.997070 + + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +*********************** + + - Finalish cost = 0.995066 ; 154 funcs + + - histogram: source clip 151.975 .. 656.684; base clip 487.29 .. 1872 + + - versus source range 0 .. 622.496; base range 0 .. 2253.55 +************************ + + - Final cost = 0.994952 ; 236 funcs + + Final fine fit Parameters: + x-shift= 0.5215 y-shift= 3.9495 z-shift= 4.8067 + z-angle= 0.0062 x-angle=-0.1182 y-angle=-0.0256 + x-scale= 1.0011 y-scale= 1.1245 z-scale= 0.9636 + y/x-shear= 0.0006 z/x-shear=-0.0029 z/y-shear=-0.0016 + + - Fine net CPU time = 31.6 s +++ Computing output image +++ image warp: parameters = 0.5215 3.9495 4.8067 0.0062 -0.1182 -0.0256 1.0011 1.1245 0.9636 0.0006 -0.0029 -0.0016 +++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk+orig.BRIK +++ Wrote -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D +++ 3dAllineate: total CPU time = 43.0 sec Elapsed = 27.6 +++ ########################################################### +++ # Please check results visually for alignment quality # +++ ########################################################### +#Script is running (command trimmed): + cat_matvec -ONELINE ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D ./__tt_sub-03_ses-retest_T1w_ns_obla2e_mat.1D -I > ./sub-03_ses-retest_T1w_al_junk_mat.aff12.1D +#++ Combining anat to epi and oblique transformations +#Script is running (command trimmed): + 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-retest_T1w_al_junk -input ./__tt_sub-03_ses-retest_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +++ Source dataset: ./__tt_sub-03_ses-retest_T1w_ns+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +++ ========== sub-brick #0 ========== [total CPU to here=0.1 s] + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - no weight image + + - using 11 points from base image [use_all=0] + + * Exit alignment setup routine +++ using -1Dmatrix_apply +++ Computing output image +++ image warp: parameters = 1.0006 0.0454 -0.0079 -2.2618 -0.0238 1.1231 -0.0270 -21.1278 0.0100 0.0568 0.9630 8.6870 +++ Output dataset ./sub-03_ses-retest_T1w_al_junk+orig.BRIK +++ 3dAllineate: total CPU time = 2.1 sec Elapsed = 1.8 +++ ########################################################### +#++ Creating final output: skullstripped anat data +copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig +#Script is running (command trimmed): + 3dcopy ./__tt_sub-03_ses-retest_T1w_ns+orig sub-03_ses-retest_T1w_ns +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ Creating final output: anat data aligned to epi +# copy is not necessary +#++ Saving history +#Script is running (command trimmed): + 3dNotes -h "align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ + -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask -cost nmi -volreg off -tshift off" \ + ./sub-03_ses-retest_T1w_al_junk+orig + +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-retest_T1w* + +# Finished alignment successfully + +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-retest_T1w_ns+orig -no_ss +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +Center distance of 26.068730 mm +Padding ... +++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK +Resampling ... +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__ats_tmp__resamp_step+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 7.491219 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +Clipping -0.000100 1013.000100 ... +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./__ats_tmp___rs_sub-03_ses-retest_T1w_ns+tlrc.BRIK +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-retest_T1w_ns+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Registration (linear final interpolation) ... +++ 3dWarpDrive: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Initial scale factor set to 0.30/247.56=8.3e+02 +RMS[0] = 0.364249 0.163911 ITER = 6/137 +0.364249 + +Warping has converged. + +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +++ 7.491219 degrees from plumb. +*+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations +Applying brain mask +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.BRIK +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK +Unpadding ... +++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ output dataset: ./__ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig.BRIK +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig +*+ WARNING: Changing the space of an ORIG view dataset may cause confusion! +*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space). +*+ WARNING: Consider changing the view of the dataset to TLRC view also +++ 3drefit processed 1 datasets +Changing view of transformed anatomy +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Setting parent with 3drefit -wset sub-03_ses-retest_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc +++ 3drefit processed 1 datasets +++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Warning: ignoring +tlrc on new_prefix. +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc.HEAD -> sub-03_ses-retest_T1w_ns+tlrc.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc.BRIK -> sub-03_ses-retest_T1w_ns+tlrc.BRIK +Cleanup ... +cat_matvec sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I +if ( ! -f sub-03_ses-retest_T1w_ns+tlrc.HEAD ) then +foreach run ( 01 ) +3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig +++ 3dvolreg: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 4.947676 degrees from plumb. +++ Reading in base dataset ./vr_base+orig.BRIK +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 4.947676 degrees from plumb. +++ Reading input dataset ./pb01.sub_03.r01.tshift+orig.BRIK +++ Edging: x=3 y=3 z=2 +++ Creating mask for -maxdisp + + Automask has 19058 voxels + + 3364 voxels left in -maxdisp mask after erosion +++ Initializing alignment base +++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. +++ CPU time for realignment=7.19 s [=0.0302 s/sub-brick] +++ Min : roll=-0.200 pitch=-0.367 yaw=-0.118 dS=-1.139 dL=-0.157 dP=-0.055 +++ Mean: roll=-0.094 pitch=-0.011 yaw=+0.456 dS=-0.124 dL=+0.184 dP=+0.074 +++ Max : roll=+0.027 pitch=+0.449 yaw=+0.935 dS=+0.523 dL=+0.640 dP=+0.245 +++ Max displacements (mm) for each sub-brick: + 1.41(0.00) 0.17(1.52) 0.00(0.17) 0.33(0.33) 0.34(0.10) 0.45(0.12) 0.41(0.06) 0.20(0.28) 0.21(0.16) 0.22(0.05) 0.31(0.29) 0.37(0.19) 0.50(0.19) 0.61(0.12) 0.87(0.29) 0.94(0.10) 1.05(0.18) 1.12(0.12) 1.07(0.11) 0.82(0.28) 0.67(0.28) 0.69(0.13) 0.57(0.16) 0.70(0.22) 0.67(0.04) 0.75(0.13) 0.63(0.15) 0.68(0.19) 0.59(0.12) 0.66(0.09) 0.67(0.04) 0.78(0.19) 0.61(0.19) 0.59(0.05) 0.51(0.16) 0.62(0.22) 0.63(0.12) 0.66(0.12) 0.70(0.10) 0.69(0.04) 0.70(0.03) 0.77(0.07) 0.70(0.16) 0.65(0.14) 0.72(0.10) 0.74(0.16) 0.71(0.08) 0.68(0.10) 0.74(0.12) 0.70(0.13) 0.74(0.19) 0.60(0.21) 0.54(0.09) 0.50(0.12) 0.46(0.11) 0.45(0.08) 0.44(0.09) 0.50(0.23) 0.46(0.11) 0.50(0.15) 0.49(0.11) 0.56(0.15) 0.52(0.11) 0.57(0.17) 0.63(0.15) 0.56(0.12) 0.69(0.13) 0.64(0.26) 0.67(0.18) 0.62(0.07) 0.68(0.18) 0.76(0.27) 0.58(0.33) 0.80(0.22) 0.67(0.15) 0.65(0.08) 0.70(0.08) 0.77(0.08) 0.70(0.12) 0.70(0.14) 0.66(0.08) 0.68(0.12) 0.83(0.18) 0.74(0.22) 0.64(0.22) 0.72(0.14) 0.74(0.13) 0.81(0.14) 0.75(0.10) 0.72(0.07) 0.73(0.07) 0.69(0.16) 0.69(0.12) 0.69(0.17) 0.70(0.13) 0.64(0.16) 0.68(0.16) 0.65(0.10) 0.73(0.17) 0.74(0.06) 0.69(0.10) 0.67(0.05) 0.65(0.15) 0.72(0.12) 0.63(0.25) 0.70(0.15) 0.68(0.14) 0.70(0.17) 0.63(0.21) 0.60(0.07) 0.64(0.08) 0.76(0.16) 0.72(0.14) 0.69(0.15) 0.57(0.24) 0.58(0.06) 0.59(0.04) 0.63(0.08) 0.58(0.07) 0.60(0.07) 0.67(0.10) 0.67(0.25) 0.81(0.23) 0.79(0.06) 0.72(0.11) 0.74(0.04) 0.68(0.15) 0.71(0.14) 0.69(0.04) 0.69(0.09) 0.70(0.11) 0.68(0.11) 0.75(0.16) 0.70(0.12) 0.81(0.19) 0.73(0.10) 0.85(0.14) 0.78(0.10) 0.85(0.07) 0.84(0.05) 0.84(0.04) 0.77(0.09) 0.78(0.09) 0.80(0.06) 0.81(0.03) 0.77(0.11) 0.86(0.13) 0.80(0.16) 0.91(0.15) 0.86(0.10) 0.90(0.07) 0.98(0.08) 1.10(0.14) 1.13(0.06) 1.03(0.12) 1.14(0.17) 1.06(0.09) 1.18(0.12) 1.10(0.11) 1.13(0.07) 1.08(0.14) 1.18(0.15) 1.23(0.07) 1.07(0.19) 1.17(0.13) 1.14(0.10) 1.18(0.07) 1.20(0.05) 1.22(0.07) 1.20(0.07) 1.14(0.13) 1.22(0.14) 1.14(0.14) 1.29(0.18) 1.19(0.11) 1.32(0.17) 1.27(0.10) 1.34(0.16) 1.38(0.05) 1.28(0.19) 1.31(0.09) 1.33(0.05) 1.37(0.10) 1.36(0.05) 1.42(0.14) 1.39(0.10) 1.40(0.06) 1.36(0.08) 1.36(0.03) 1.49(0.13) 1.42(0.09) 1.48(0.10) 1.30(0.24) 1.20(0.16) 1.24(0.10) 1.23(0.11) 1.25(0.03) 1.24(0.08) 1.19(0.11) 1.25(0.11) 1.18(0.08) 1.19(0.04) 1.21(0.06) 1.40(0.25) 1.31(0.26) 1.36(0.14) 1.47(0.11) 1.51(0.07) 1.53(0.06) 1.58(0.06) 1.60(0.08) 1.58(0.11) 1.65(0.10) 1.64(0.11) 1.65(0.13) 1.72(0.09) 1.79(0.07) 1.76(0.09) 1.80(0.13) 1.96(0.20) 1.94(0.03) 1.82(0.16) 1.72(0.20) 1.55(0.33) 1.60(0.32) 1.57(0.14) 1.37(0.21) 1.38(0.20) 1.14(0.38) 1.18(0.25) 1.21(0.30) 0.70(0.63) 0.81(0.24) 0.91(0.13) 1.00(0.10) 1.12(0.13) 1.02(0.23) 1.19(0.19) +++ Max displacement in automask = 1.96 (mm) at sub-brick 219 +++ Max delta displ in automask = 1.52 (mm) at sub-brick 1 +++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK +3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +*+ WARNING: input 'a' is not used in the expression +++ Output dataset ./rm.epi.all1+orig.BRIK +cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb01.sub_03.r01.tshift+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 4.947676 degrees from plumb. +++ Source dataset: ./pb01.sub_03.r01.tshift+orig.HEAD +++ Base dataset: ./sub-03_ses-retest_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 238 sub-bricks ========== +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 5.9 sec Elapsed = 4.3 +++ ########################################################### +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./rm.epi.all1+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./rm.epi.all1+orig.BRIK is 4.947676 degrees from plumb. +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ Output dataset ./rm.epi.1.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 3.4 +3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.epi.min.r01+tlrc.BRIK +end +cat dfile.r01.1D +3dcopy rm.epi.min.r01+tlrc mask_epi_extents +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +foreach run ( 01 ) +3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK +end +cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 4.947676 degrees from plumb. +++ Source dataset: ./vr_base+orig.HEAD +++ Base dataset: ./sub-03_ses-retest_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.1 +++ ########################################################### +3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.sub_03 +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc +tee out.allcostX.txt +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./anat_final.sub_03+tlrc.HEAD +++ Base dataset: ./final_epi_vr_base+tlrc.HEAD +++ Loading datasets +++ 222503 voxels in source_automask+0 +++ Zero-pad: xbot=2 xtop=3 +++ Zero-pad: ybot=3 ytop=4 +++ Zero-pad: zbot=0 ztop=2 +++ Computing -autobox +++ 128372 voxels [89.6%] in weight mask +++ Number of points for matching = 60334 +++ Local correlation: blok type = 'RHDD(14.76)' +*+ WARNING: No output dataset will be calculated +++ OpenMP thread count = 4 +volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +++ allcost output: init #0 + ls = 0.334584 + sp = 0.421822 + mi = -0.363941 + crM = 0.239215 + nmi = 0.905608 + je = 3.4917 + hel = -0.0669546 + crA = 0.489691 + crU = 0.465557 + lss = 0.665416 + lpc = 0.0927771 + lpa = 0.907223 + lpc+ = 0.413355 + ncd = 0.996623 +++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 +++ ########################################################### +3dAllineate -source sub-03_ses-retest_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w+orig.BRIK is 7.491219 degrees from plumb. +++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers +++ Source dataset: ./sub-03_ses-retest_T1w+orig.HEAD +++ Base dataset: (not given) +++ Loading datasets +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ð++ wsinc5 interpolation setup: + + taper function = Min sidelobe 3 term + + taper cut point = 0.000 + + window radius = 5 voxels + + window shape = Cubical + + The above can be altered via the AFNI_WSINC5_* environment variables. + + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + + wsinc5 CUBE(5) mask has 1000 points +++ Output dataset ./anat_w_skull_warped+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.2 +++ ########################################################### +foreach run ( 01 ) +3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc +++ 3dmerge: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ default -1dindex = 0 +++ default -1tindex = 1 +Program 3dmerge +3dmerge: edit and combine 3D datasets, by RW Cox +++ editing input dataset in memory (49.6 MB) +..............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK + +end +foreach run ( 01 ) +3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc +++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset pb03.sub_03.r01.blur+tlrc +++ Forming automask + + Fixed clip level = 698.280457 + + Used gradual clip level = 635.212769 .. 744.364258 + + Number voxels above clip level = 31922 + + Clustering voxels ... + + Largest cluster has 31922 voxels + + Clustering voxels ... + + Largest cluster has 31863 voxels + + Filled 53 voxels in small holes; now have 31916 voxels + + Clustering voxels ... + + Largest cluster has 31916 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 77434 voxels + + Mask now has 31916 voxels +++ Dilating automask + + Clustering voxels ... + + Largest cluster has 71995 voxels +++ 37355 voxels in the mask [out of 109350: 34.16%] +++ first 4 x-planes are zero [from L] +++ last 2 x-planes are zero [from R] +++ first 0 y-planes are zero [from P] +++ last 0 y-planes are zero [from A] +++ first 6 z-planes are zero [from I] +++ last 2 z-planes are zero [from S] +++ Output dataset ./rm.mask_r01+tlrc.BRIK +++ CPU time = 0.280000 sec +end +3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 +++ processing 1 input datasets... +++ padding all datasets by 0 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 37355 survived, 71995 were zero +++ writing result full_mask.sub_03... +++ Output dataset ./full_mask.sub_03+tlrc.BRIK +3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-retest_T1w_ns+tlrc -prefix rm.resam.anat +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30574 survived, 78776 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_anat.sub_03... +++ Output dataset ./mask_anat.sub_03+tlrc.BRIK +3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_overlap.txt +++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK +#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) +37355 30574 42077 25852 11503 4722 30.7937 15.4445 0.8844 0.6939 1.0830 +3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_dice.txt +0.761148 +3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30980 survived, 78370 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_group... +++ Output dataset ./mask_group+tlrc.BRIK +foreach run ( 01 ) +3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.mean_r01+tlrc.BRIK +3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK +end +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_sub_03 +total number of censored TRs (simple form) = 4 +1deval -a motion_sub_03_censor.1D -b outcount_sub_03_censor.1D -expr a*b +set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D + -show_trs_uncensored encoded` +1d_tool.py -infile censor_sub_03_combined_2.1D -show_trs_uncensored encoded +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor censor_sub_03_combined_2.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: B. Douglas Ward, et al. +++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD +++ STAT automask has 94004 voxels (out of 109350 = 86.0%) +++ Skipping check for initial transients +++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ +++ -stim_times using TR=2.5 s for stimulus timing conversion +++ -stim_times using TR=2.5 s for any -iresp output datasets +++ [you can alter the -iresp TR via the -TR_times option] +++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise +++ ** GUESSED ** -stim_times 1 using LOCAL times +++ ** GUESSED ** -stim_times 2 using LOCAL times +++ ** GUESSED ** -stim_times 3 using LOCAL times +++ ** GUESSED ** -stim_times 4 using LOCAL times +++ ** GUESSED ** -stim_times 5 using LOCAL times +------------------------------------------------------------ +GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task': + 0 0 0 0 0 0.333 0.333 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 + +++ Number of time points: 238 (before censor) ; 234 (after) + + Number of parameters: 22 [17 baseline ; 5 signal] +++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) +++ Wrote matrix image to file X.jpg +++ Wrote matrix values to file X.xmat.1D +++ ========= Things you can do with the matrix file ========= +++ (a) Linear regression with ARMA(1,1) modeling of serial correlation: + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb + +++ N.B.: 3dREMLfit command above written to file stats.REML_cmd +++ (b) Visualization/analysis of the matrix via ExamineXmat.R +++ (c) Synthesis of sub-model datasets using 3dSynthesize +++ ========================================================== +++ Wrote matrix values to file X.nocensor.xmat.1D +++ ----- Signal+Baseline matrix condition [X] (234x22): 5.25117 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (234x5): 1.40108 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (234x17): 5.14998 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (234x12): 3.86898 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (234x5): 1.04487 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 2.53435e-15 ++ VERY GOOD ++ +++ Matrix setup time = 0.59 s +++ Calculations starting; elapsed time=1.081 +++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. +++ Calculations finished; elapsed time=15.587 +++ Smallest FDR q [0 Full_Fstat] = 1.80302e-13 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 3.17479e-12 +++ Smallest FDR q [3 Correct_Task_Fstat] = 3.17424e-12 +++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 2.29951e-05 +++ Smallest FDR q [6 Incorrect_Task_Fstat] = 2.29984e-05 +++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.00105465 +++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.00105469 +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 0.000818031 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.000818027 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 5.9968e-13 +++ Smallest FDR q [15 Response_Control_Fstat] = 5.99731e-13 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.00156636 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.00156632 +++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + + created 13 FDR curves in bucket header +++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK +++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK +++ #Flops=4.28212e+10 Average Dot Product=37.4548 +if ( 0 != 0 ) then +1d_tool.py -show_cormat_warnings -infile X.xmat.1D +tee out.cormat_warn.txt + +Warnings regarding Correlation Matrix: X.xmat.1D + + severity correlation cosine regressor pair + -------- ----------- ------ ---------------------------------------- + medium: 0.446 0.539 ( 5 vs. 6) Correct_Task#0 vs. Incorrect_Task#0 + +3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD +++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ elapsed time = 0.8 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..229,232..237] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.signal.all+tlrc.BRIK +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..229,232..237] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.noise.all+tlrc.BRIK +3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./TSNR.sub_03+tlrc.BRIK +3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc +++ 3dTnorm: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Output dataset ./rm.errts.unit+tlrc.BRIK +3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc +++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++++ 37355 voxels survive the mask +3dTstat -sos -prefix - gmean.errts.unit.1D' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo -- GCOR = `cat out.gcor.1D` +cat out.gcor.1D +-- GCOR = 0.104389 +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./rm.DP+tlrc.BRIK +3dTstat -sum -prefix corr_brain rm.DP+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./corr_brain+tlrc.BRIK +1dcat X.nocensor.xmat.1D[5] +1dcat X.nocensor.xmat.1D[6] +1dcat X.nocensor.xmat.1D[7] +1dcat X.nocensor.xmat.1D[8] +1dcat X.nocensor.xmat.1D[9] +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +++ Output dataset ./sum_ideal.1D +1dcat X.nocensor.xmat.1D[5..9] +touch blur_est.sub_03.1D +mkdir files_ACF +touch blur.epits.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 2..229,232..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..229,232..237] +++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 37355 +*+ WARNING: removed 272 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 234 time points + + detrending done (2.77 CPU s thus far) +++ start ACF calculations out to radius = 28.27 mm + + ACF done (75.10 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits FWHM blurs: 0 0 0 0 +average epits FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # epits FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits ACF blurs: 0.64237 5.36951 13.6925 13.7381 +average epits ACF blurs: 0.64237 5.36951 13.6925 13.7381 +echo 0.64237 5.36951 13.6925 13.7381 # epits ACF blur estimates +touch blur.errts.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 2..229,232..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..229,232..237] +++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 37355 +*+ WARNING: removed 272 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 234 time points + + detrending done (2.71 CPU s thus far) +++ start ACF calculations out to radius = 27.79 mm + + ACF done (68.58 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts FWHM blurs: 0 0 0 0 +average errts FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # errts FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts ACF blurs: 0.694349 5.35765 13.035 13.4143 +average errts ACF blurs: 0.694349 5.35765 13.035 13.4143 +echo 0.694349 5.35765 13.035 13.4143 # errts ACF blur estimates +gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD +gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 +++ writing ss review basic: @ss_review_basic +++ writing ss review driver: @ss_review_driver +++ writing ss review drive commands: @ss_review_driver_commands +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.out.cen.r01.1D rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +tee out.ss_review.sub_03.txt +if ( -e @ss_review_basic ) ./@ss_review_basic +./@ss_review_basic + +subject ID : sub_03 +TRs removed (per run) : 0 +num stim classes provided : 5 +final anatomy dset : anat_final.sub_03+tlrc.HEAD +final stats dset : stats.sub_03+tlrc.HEAD +final voxel resolution : 4.000000 4.000000 4.000000 + +motion limit : 0.3 +num TRs above mot limit : 2 +average motion (per TR) : 0.0937926 +average censored motion : 0.0872231 +max motion displacement : 1.69106 +max censored displacement : 1.69012 +outlier limit : 0.5 +average outlier frac (TR) : 0.00559353 +num TRs above out limit : 1 + +num runs found : 1 +num TRs per run : 238 +num TRs per run (applied) : 234 +num TRs per run (censored): 4 +fraction censored per run : 0.0168067 +TRs total (uncensored) : 238 +TRs total : 234 +degrees of freedom used : 22 +degrees of freedom left : 212 + +TRs censored : 4 +censor fraction : 0.016807 +num regs of interest : 5 +num TRs per stim (orig) : 78 56 46 19 79 +num TRs censored per stim : 0 0 0 0 0 +fraction TRs censored : 0.000 0.000 0.000 0.000 0.000 +ave mot per sresp (orig) : 0.086607 0.082908 0.080591 0.071212 0.078827 +ave mot per sresp (cens) : 0.086607 0.082908 0.080591 0.071212 0.078827 + +TSNR average : 231.468 +global correlation (GCOR) : 0.104389 +anat/EPI mask Dice coef : 0.761148 +maximum F-stat (masked) : 48.4589 +blur estimates (ACF) : 0.694349 5.35765 13.035 +blur estimates (FWHM) : 0 0 0 + +** TR #0 outliers: possible pre-steady state TRs in run 01 + +cd .. +echo execution finished: `date` +date +execution finished: Thu Aug 3 20:49:40 EDT 2017 diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 new file mode 100755 index 0000000..04545b4 --- /dev/null +++ b/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 @@ -0,0 +1,494 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Aug 3 20:38:10 2017" +echo "(version 5.15, April 25, 2017)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + +# =========================== auto block: setup ============================ +# script setup + +# take note of the AFNI version +afni -ver + +# check that the current AFNI version is recent enough +afni_history -check_date 23 Sep 2016 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 23 Sep 2016)" + echo " (consider: @update.afni.binaries -defaults)" + exit +endif + +# the user may specify a single subject to run with +if ( $#argv > 0 ) then + set subj = $argv[1] +else + set subj = sub_03 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ + $output_dir/sub-03_ses-retest_T1w + +# ============================ auto block: tcat ============================ +# apply 3dTcat to copy input dsets to results dir, while +# removing the first 0 TRs +3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 238 ) + +# ------------------------------------------------------- +# enter the results directory (can begin processing data) +cd $output_dir + + +# ========================== auto block: outcount ========================== +# data check: compute outlier fraction for each volume +touch out.pre_ss_warn.txt +foreach run ( $runs ) + 3dToutcount -automask -fraction -polort 4 -legendre \ + pb00.$subj.r$run.tcat+orig > outcount.r$run.1D + + # censor outlier TRs per run, ignoring the first 0 TRs + # - censor when more than 0.5 of automask voxels are outliers + # - step() defines which TRs to remove via censoring + 1deval -a outcount.r$run.1D -expr "1-step(a-0.5)" > rm.out.cen.r$run.1D + + # outliers at TR 0 might suggest pre-steady state TRs + if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then + echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ + >> out.pre_ss_warn.txt + endif +end + +# catenate outlier counts into a single time series +cat outcount.r*.1D > outcount_rall.1D + +# catenate outlier censor files into a single time series +cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D + +# ================================= tshift ================================= +# time shift data so all slice timing is the same +foreach run ( $runs ) + 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + pb00.$subj.r$run.tcat+orig +end + +# -------------------------------- +# extract volreg registration base +3dbucket -prefix vr_base pb01.$subj.r01.tshift+orig"[2]" + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-03_ses-retest_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask \ + -cost nmi \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-retest_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-03_ses-retest_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-03_ses-retest_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base vr_base+orig \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg/epi2anat/tlrc xforms + cat_matvec -ONELINE \ + sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform: volreg/epi2anat/tlrc + 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc mask_epi_extents + +# and apply the extents mask to the EPI data +# (delete any time series with missing data) +foreach run ( $runs ) + 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc \ + -expr 'a*b' -prefix pb02.$subj.r$run.volreg +end + +# warp the volreg base EPI dataset to make a final version +cat_matvec -ONELINE \ + sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I > \ + mat.basewarp.aff12.1D + +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input vr_base+orig \ + -1Dmatrix_apply mat.basewarp.aff12.1D \ + -mast_dxyz 4 \ + -prefix final_epi_vr_base + +# create an anat_final dataset, aligned with stats +3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.$subj + +# record final registration costs +3dAllineate -base final_epi_vr_base+tlrc -allcostX \ + -input anat_final.$subj+tlrc |& tee out.allcostX.txt + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-03_ses-retest_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== blur ================================== +# blur each volume of each run +foreach run ( $runs ) + 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.$subj.r$run.blur \ + pb02.$subj.r$run.volreg+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc +end + +# create union of inputs, output type is byte +3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj + +# ---- create subject anatomy mask, mask_anat.$subj+tlrc ---- +# (resampled from tlrc anat) +3dresample -master full_mask.$subj+tlrc -input sub-03_ses-retest_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute overlaps between anat and EPI masks +3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_overlap.txt + +# note Dice coefficient of masks, as well +3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_dice.txt + +# ---- create group anatomy mask, mask_group+tlrc ---- +# (resampled from tlrc base anat, MNI_avg152T1+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/monicali/abin/MNI_avg152T1+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= scale ================================== +# scale each voxel time series to have a mean of 100 +# (be sure no negatives creep in) +# (subject to a range of [0,200]) +foreach run ( $runs ) + 3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.3 motion_${subj} + +# combine multiple censor files +1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \ + -expr "a*b" > censor_${subj}_combined_2.1D + +# note TRs that were not censored +set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ + -show_trs_uncensored encoded` + +# ------------------------------ +# run the regression analysis +3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ + -censor censor_${subj}_combined_2.1D \ + -polort 4 \ + -num_stimts 17 \ + -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D 'GAM' \ + -stim_label 1 Correct_Task \ + -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D 'GAM' \ + -stim_label 2 Incorrect_Task \ + -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D \ + 'GAM' \ + -stim_label 3 No_Response_Control \ + -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D 'GAM' \ + -stim_label 4 No_Response_Task \ + -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D 'GAM' \ + -stim_label 5 Response_Control \ + -stim_file 6 motion_demean.1D'[0]' -stim_base 6 -stim_label 6 roll_01 \ + -stim_file 7 motion_demean.1D'[1]' -stim_base 7 -stim_label 7 pitch_01 \ + -stim_file 8 motion_demean.1D'[2]' -stim_base 8 -stim_label 8 yaw_01 \ + -stim_file 9 motion_demean.1D'[3]' -stim_base 9 -stim_label 9 dS_01 \ + -stim_file 10 motion_demean.1D'[4]' -stim_base 10 -stim_label 10 dL_01 \ + -stim_file 11 motion_demean.1D'[5]' -stim_base 11 -stim_label 11 dP_01 \ + -stim_file 12 motion_deriv.1D'[0]' -stim_base 12 -stim_label 12 roll_02 \ + -stim_file 13 motion_deriv.1D'[1]' -stim_base 13 -stim_label 13 pitch_02 \ + -stim_file 14 motion_deriv.1D'[2]' -stim_base 14 -stim_label 14 yaw_02 \ + -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ + -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ + -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -glt_label 1 Landmark-Detection \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc"[$ktrs]" +3dcalc -a rm.signal.all+tlrc \ + -b rm.noise.all+tlrc \ + -c full_mask.$subj+tlrc \ + -expr 'c*a/b' -prefix TSNR.$subj + +# --------------------------------------------------- +# compute and store GCOR (global correlation average) +# (sum of squares of global mean of unit errts) +3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[5]' > ideal_Correct_Task.1D +1dcat X.nocensor.xmat.1D'[6]' > ideal_Incorrect_Task.1D +1dcat X.nocensor.xmat.1D'[7]' > ideal_No_Response_Control.1D +1dcat X.nocensor.xmat.1D'[8]' > ideal_No_Response_Task.1D +1dcat X.nocensor.xmat.1D'[9]' > ideal_Response_Control.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]" + +# also, create a stimulus-only X-matrix, for easy review +1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D + +# ============================ blur estimation ============================= +# compute blur estimates +touch blur_est.$subj.1D # start with empty file + +# create directory for ACF curve files +mkdir files_ACF + +# -- estimate blur for each run in epits -- +touch blur.epits.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +echo average epits FWHM blurs: $blurs +echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +echo average epits ACF blurs: $blurs +echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D + +# -- estimate blur for each run in errts -- +touch blur.errts.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +echo average errts FWHM blurs: $blurs +echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +echo average errts ACF blurs: $blurs +echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ +# -align_opts_aea -cost nmi -tlrc_base MNI_avg152T1+tlrc -volreg_align_to \ +# third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 \ +# -regress_stim_times \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ +# -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ +# 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ +# -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 \ +# Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ +# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd new file mode 100644 index 0000000..ff98bd9 --- /dev/null +++ b/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd @@ -0,0 +1,5 @@ +# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor censor_sub_03_combined_2.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb $* diff --git a/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 new file mode 100755 index 0000000..2787c4b --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 @@ -0,0 +1,49 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.40 (March 30, 2017) +# creation date: Thu Aug 3 20:35:15 2017 + +# set data directories +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = $top_dir/sub-03/ses-test/anat +set epi_dir = $top_dir/sub-03/ses-test/func + +# set subject and group identifiers +set subj = sub_03 +set group_id = test + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $anat_dir/sub-03_ses-test_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $epi_dir/sub-03_ses-test_task-linebisection_bold.nii.gz \ + -align_opts_aea -cost nmi \ + -tlrc_base MNI_avg152T1+tlrc \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 6.0 \ + -regress_stim_times \ + $top_dir/timing_sub-03_ses-test_Correct_Task.1D \ + $top_dir/timing_sub-03_ses-test_Incorrect_Task.1D \ + $top_dir/timing_sub-03_ses-test_No_Response_Control.1D \ + $top_dir/timing_sub-03_ses-test_No_Response_Task.1D \ + $top_dir/timing_sub-03_ses-test_Response_Control.1D \ + -regress_stim_labels \ + Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ + Response_Control \ + -regress_basis 'GAM' \ + -regress_censor_motion 0.3 \ + -regress_censor_outliers 0.5 \ + -regress_apply_mot_types demean deriv \ + -regress_opts_3dD \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -glt_label 1 Landmark-Detection \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts \ + -regress_run_clustsim no + diff --git a/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 new file mode 100644 index 0000000..dc380fd --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 @@ -0,0 +1,30 @@ +uber_subject.py \ + -cvar subj_dir subject_results/group.test/subj.sub_03 \ + -svar align_cost nmi \ + -svar anat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ + \ + -svar blur_size 6.0 \ + -svar epi \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ + \ + -svar gid test \ + -svar gltsym '0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -svar gltsym_label Landmark-Detection \ + -svar outlier_limit 0.5 \ + -svar regress_mot_deriv yes \ + -svar run_clustsim no \ + -svar sid sub_03 \ + -svar stim \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ + \ + -svar stim_basis 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' \ + -svar stim_label Correct_Task Incorrect_Task No_Response_Control \ + No_Response_Task Response_Control \ + -svar stim_type times times times times times \ + -svar tlrc_base MNI_avg152T1+tlrc diff --git a/Exp-1/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 new file mode 100755 index 0000000..e3af51b --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 @@ -0,0 +1,493 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Aug 3 20:35:22 2017" +echo "(version 5.15, April 25, 2017)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + +# =========================== auto block: setup ============================ +# script setup + +# take note of the AFNI version +afni -ver + +# check that the current AFNI version is recent enough +afni_history -check_date 23 Sep 2016 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 23 Sep 2016)" + echo " (consider: @update.afni.binaries -defaults)" + exit +endif + +# the user may specify a single subject to run with +if ( $#argv > 0 ) then + set subj = $argv[1] +else + set subj = sub_03 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ + $output_dir/sub-03_ses-test_T1w + +# ============================ auto block: tcat ============================ +# apply 3dTcat to copy input dsets to results dir, while +# removing the first 0 TRs +3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 238 ) + +# ------------------------------------------------------- +# enter the results directory (can begin processing data) +cd $output_dir + + +# ========================== auto block: outcount ========================== +# data check: compute outlier fraction for each volume +touch out.pre_ss_warn.txt +foreach run ( $runs ) + 3dToutcount -automask -fraction -polort 4 -legendre \ + pb00.$subj.r$run.tcat+orig > outcount.r$run.1D + + # censor outlier TRs per run, ignoring the first 0 TRs + # - censor when more than 0.5 of automask voxels are outliers + # - step() defines which TRs to remove via censoring + 1deval -a outcount.r$run.1D -expr "1-step(a-0.5)" > rm.out.cen.r$run.1D + + # outliers at TR 0 might suggest pre-steady state TRs + if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then + echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ + >> out.pre_ss_warn.txt + endif +end + +# catenate outlier counts into a single time series +cat outcount.r*.1D > outcount_rall.1D + +# catenate outlier censor files into a single time series +cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D + +# ================================= tshift ================================= +# time shift data so all slice timing is the same +foreach run ( $runs ) + 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + pb00.$subj.r$run.tcat+orig +end + +# -------------------------------- +# extract volreg registration base +3dbucket -prefix vr_base pb01.$subj.r01.tshift+orig"[2]" + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-03_ses-test_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask \ + -cost nmi \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-test_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-03_ses-test_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base vr_base+orig \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg/epi2anat/tlrc xforms + cat_matvec -ONELINE \ + sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform: volreg/epi2anat/tlrc + 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc mask_epi_extents + +# and apply the extents mask to the EPI data +# (delete any time series with missing data) +foreach run ( $runs ) + 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc \ + -expr 'a*b' -prefix pb02.$subj.r$run.volreg +end + +# warp the volreg base EPI dataset to make a final version +cat_matvec -ONELINE \ + sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I > \ + mat.basewarp.aff12.1D + +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input vr_base+orig \ + -1Dmatrix_apply mat.basewarp.aff12.1D \ + -mast_dxyz 4 \ + -prefix final_epi_vr_base + +# create an anat_final dataset, aligned with stats +3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.$subj + +# record final registration costs +3dAllineate -base final_epi_vr_base+tlrc -allcostX \ + -input anat_final.$subj+tlrc |& tee out.allcostX.txt + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-03_ses-test_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== blur ================================== +# blur each volume of each run +foreach run ( $runs ) + 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.$subj.r$run.blur \ + pb02.$subj.r$run.volreg+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc +end + +# create union of inputs, output type is byte +3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj + +# ---- create subject anatomy mask, mask_anat.$subj+tlrc ---- +# (resampled from tlrc anat) +3dresample -master full_mask.$subj+tlrc -input sub-03_ses-test_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute overlaps between anat and EPI masks +3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_overlap.txt + +# note Dice coefficient of masks, as well +3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_dice.txt + +# ---- create group anatomy mask, mask_group+tlrc ---- +# (resampled from tlrc base anat, MNI_avg152T1+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/monicali/abin/MNI_avg152T1+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= scale ================================== +# scale each voxel time series to have a mean of 100 +# (be sure no negatives creep in) +# (subject to a range of [0,200]) +foreach run ( $runs ) + 3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.3 motion_${subj} + +# combine multiple censor files +1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \ + -expr "a*b" > censor_${subj}_combined_2.1D + +# note TRs that were not censored +set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ + -show_trs_uncensored encoded` + +# ------------------------------ +# run the regression analysis +3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ + -censor censor_${subj}_combined_2.1D \ + -polort 4 \ + -num_stimts 17 \ + -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D 'GAM' \ + -stim_label 1 Correct_Task \ + -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D 'GAM' \ + -stim_label 2 Incorrect_Task \ + -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D 'GAM' \ + -stim_label 3 No_Response_Control \ + -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D 'GAM' \ + -stim_label 4 No_Response_Task \ + -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D 'GAM' \ + -stim_label 5 Response_Control \ + -stim_file 6 motion_demean.1D'[0]' -stim_base 6 -stim_label 6 roll_01 \ + -stim_file 7 motion_demean.1D'[1]' -stim_base 7 -stim_label 7 pitch_01 \ + -stim_file 8 motion_demean.1D'[2]' -stim_base 8 -stim_label 8 yaw_01 \ + -stim_file 9 motion_demean.1D'[3]' -stim_base 9 -stim_label 9 dS_01 \ + -stim_file 10 motion_demean.1D'[4]' -stim_base 10 -stim_label 10 dL_01 \ + -stim_file 11 motion_demean.1D'[5]' -stim_base 11 -stim_label 11 dP_01 \ + -stim_file 12 motion_deriv.1D'[0]' -stim_base 12 -stim_label 12 roll_02 \ + -stim_file 13 motion_deriv.1D'[1]' -stim_base 13 -stim_label 13 pitch_02 \ + -stim_file 14 motion_deriv.1D'[2]' -stim_base 14 -stim_label 14 yaw_02 \ + -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ + -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ + -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -glt_label 1 Landmark-Detection \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc"[$ktrs]" +3dcalc -a rm.signal.all+tlrc \ + -b rm.noise.all+tlrc \ + -c full_mask.$subj+tlrc \ + -expr 'c*a/b' -prefix TSNR.$subj + +# --------------------------------------------------- +# compute and store GCOR (global correlation average) +# (sum of squares of global mean of unit errts) +3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[5]' > ideal_Correct_Task.1D +1dcat X.nocensor.xmat.1D'[6]' > ideal_Incorrect_Task.1D +1dcat X.nocensor.xmat.1D'[7]' > ideal_No_Response_Control.1D +1dcat X.nocensor.xmat.1D'[8]' > ideal_No_Response_Task.1D +1dcat X.nocensor.xmat.1D'[9]' > ideal_Response_Control.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]" + +# also, create a stimulus-only X-matrix, for easy review +1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D + +# ============================ blur estimation ============================= +# compute blur estimates +touch blur_est.$subj.1D # start with empty file + +# create directory for ACF curve files +mkdir files_ACF + +# -- estimate blur for each run in epits -- +touch blur.epits.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +echo average epits FWHM blurs: $blurs +echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +echo average epits ACF blurs: $blurs +echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D + +# -- estimate blur for each run in errts -- +touch blur.errts.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +echo average errts FWHM blurs: $blurs +echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +echo average errts ACF blurs: $blurs +echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ +# -align_opts_aea -cost nmi -tlrc_base MNI_avg152T1+tlrc -volreg_align_to \ +# third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 \ +# -regress_stim_times \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ +# -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ +# 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ +# -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 \ +# Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ +# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 new file mode 100755 index 0000000..2787c4b --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 @@ -0,0 +1,49 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.40 (March 30, 2017) +# creation date: Thu Aug 3 20:35:15 2017 + +# set data directories +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = $top_dir/sub-03/ses-test/anat +set epi_dir = $top_dir/sub-03/ses-test/func + +# set subject and group identifiers +set subj = sub_03 +set group_id = test + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $anat_dir/sub-03_ses-test_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $epi_dir/sub-03_ses-test_task-linebisection_bold.nii.gz \ + -align_opts_aea -cost nmi \ + -tlrc_base MNI_avg152T1+tlrc \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 6.0 \ + -regress_stim_times \ + $top_dir/timing_sub-03_ses-test_Correct_Task.1D \ + $top_dir/timing_sub-03_ses-test_Incorrect_Task.1D \ + $top_dir/timing_sub-03_ses-test_No_Response_Control.1D \ + $top_dir/timing_sub-03_ses-test_No_Response_Task.1D \ + $top_dir/timing_sub-03_ses-test_Response_Control.1D \ + -regress_stim_labels \ + Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ + Response_Control \ + -regress_basis 'GAM' \ + -regress_censor_motion 0.3 \ + -regress_censor_outliers 0.5 \ + -regress_apply_mot_types demean deriv \ + -regress_opts_3dD \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -glt_label 1 Landmark-Detection \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts \ + -regress_run_clustsim no + diff --git a/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 new file mode 100644 index 0000000..5ce52e3 --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 @@ -0,0 +1,21 @@ +-- applying orig view as +orig +-- tcat: reps is now 238 +++ updating polort to 4, from run len 595.0 s +-- volreg: using base dset vr_base+orig +++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 4 mm tlrc voxels +-- applying anat warps to 1 dataset(s): sub-03_ses-test_T1w +-- masking: group anat = 'MNI_avg152T1+tlrc', exists = 1 +-- have 1 ROI dict entries ... +-- will apply motion types: demean, deriv +-- using default: will not apply EPI Automask + (see 'MASKING NOTE' from the -help for details) + +------------------------------------- +** warning have only 1 run to analyze +------------------------------------- + +--> script is file: proc.sub_03 + consider the script execution command: + + tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + diff --git a/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 new file mode 100644 index 0000000..9ad2393 --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 @@ -0,0 +1,966 @@ +echo auto-generated by afni_proc.py, Thu Aug 3 20:35:22 2017 +auto-generated by afni_proc.py, Thu Aug 3 20:35:22 2017 +echo (version 5.15, April 25, 2017) +(version 5.15, April 25, 2017) +echo execution started: `date` +date +execution started: Thu Aug 3 20:39:28 EDT 2017 +afni -ver +Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) +afni_history -check_date 23 Sep 2016 +-- is current: afni_history as new as: 23 Sep 2016 + most recent entry is: 21 Jul 2017 +if ( 0 ) then +if ( 0 > 0 ) then +set subj = sub_03 +endif +set output_dir = sub_03.results +if ( -d sub_03.results ) then +set runs = ( `count -digits 2 1 1` ) +count -digits 2 1 1 +mkdir sub_03.results +mkdir sub_03.results/stimuli +cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D sub_03.results/stimuli +3dcopy /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz sub_03.results/sub-03_ses-test_T1w +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[0..$] +++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ elapsed time = 1.7 s +set tr_counts = ( 238 ) +cd sub_03.results +touch out.pre_ss_warn.txt +foreach run ( 01 ) +3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig +++ 3dToutcount: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. +++ 17837 voxels passed mask/clip +1deval -a outcount.r01.1D -expr 1-step(a-0.5) +if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then +1deval -a outcount.r01.1D{0} -expr step(a-0.4) +echo ** TR #0 outliers: possible pre-steady state TRs in run 01 +endif +end +cat outcount.r01.1D +cat rm.out.cen.r01.1D +foreach run ( 01 ) +3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig +++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. +*+ WARNING: dataset is already aligned in time! +*+ WARNING: ==>> output dataset is just a copy of input dataset +end +3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] +++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -cost nmi -volreg off -tshift off +#++ align_epi_anat version: 1.57 +#++ turning off volume registration +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./sub-03_ses-test_T1w+orig +#++ Multi-cost is nmi +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-test_T1w* +#Script is running (command trimmed): + 3dcopy ./sub-03_ses-test_T1w+orig ./__tt_sub-03_ses-test_T1w+orig +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ Removing skull from anat data +#Script is running (command trimmed): + 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-test_T1w+orig -prefix ./__tt_sub-03_ses-test_T1w_ns +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-test_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. +#Script is running (command trimmed): + 3dinfo ./__tt_sub-03_ses-test_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' +#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig is ***oblique**** +#Script is running (command trimmed): + 3dAttribute DELTA ./__tt_sub-03_ses-test_T1w_ns+orig +#++ Spacing for anat to oblique epi alignment is 1.000000 +#++ Matching obliquity of anat to epi +#Script is running (command trimmed): + 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-test_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Deobliquing original dataset before obliquing +++ Combining oblique transformations +++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob+orig.BRIK +#++ using 0th sub-brick because only one found +#Script is running (command trimmed): + 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' +++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ resampling epi to match anat data +#Script is running (command trimmed): + 3dresample -master ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_vr_base_ts+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_vr_base_ts+orig.BRIK is 6.153038 degrees from plumb. +#++ removing skull or area outside brain +#Script is running (command trimmed): + 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig +++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset ./__tt_vr_base_ts_rs+orig +++ Forming automask + + Fixed clip level = 722.140930 + + Used gradual clip level = 624.995605 .. 827.664490 + + Number voxels above clip level = 1139938 + + Clustering voxels ... + + Largest cluster has 1138291 voxels + + Clustering voxels ... + + Largest cluster has 1137874 voxels + + Filled 374 voxels in small holes; now have 1138248 voxels + + Filled 17631 voxels in large holes; now have 1155879 voxels + + Clustering voxels ... + + Largest cluster has 1155874 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 15251279 voxels + + Mask now has 1155874 voxels +++ 1155874 voxels in the mask [out of 16407153: 7.04%] +++ first 71 x-planes are zero [from R] +++ last 75 x-planes are zero [from L] +++ first 33 y-planes are zero [from A] +++ last 17 y-planes are zero [from P] +++ first 123 z-planes are zero [from I] +++ last 36 z-planes are zero [from S] +++ applying mask to original data +++ Writing masked data +++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK +++ CPU time = 3.580000 sec +#++ Computing weight mask +#Script is running (command trimmed): + 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1890.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#Script is running (command trimmed): + 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1890.000000))' +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK +#++ Aligning anat data to epi data +#Script is running (command trimmed): + 3dAllineate -nmi -wtprefix ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns_ob+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets +++ 1350442 voxels in -source_automask+4 +++ Zero-pad: not needed +++ 1155874 voxels [7.0%] in weight mask +++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal+orig.BRIK +++ Number of points for matching = 1155874 +++ shift param auto-range: -89.2..89.2 -69.3..69.3 -86.7..86.7 + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 + + 12 free parameters +++ Normalized convergence radius = 0.001000 +++ OpenMP thread count = 4 +++ ======= Allineation of 1 sub-bricks using Normalized MI [H(b,s)/(H(b)+H(s))] ======= +++ ========== sub-brick #0 ========== [total CPU to here=9.7 s] +++ *** Fine pass begins *** + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - copying weight image + + - using 1155874 points from base image [use_all=0] + + * Exit alignment setup routine + + - histogram: source clip 184.345 .. 796.556; base clip 497.178 .. 2090 + + - versus source range 0 .. 698.5; base range 0 .. 2299.05 + + - Initial cost = 0.997036 + + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +************************************************* + + - Finalish cost = 0.995029 ; 213 funcs + + - histogram: source clip 172.628 .. 745.927; base clip 497.178 .. 2090 + + - versus source range 0 .. 698.5; base range 0 .. 2299.05 +* + + - Final cost = 0.995029 ; 120 funcs + + Final fine fit Parameters: + x-shift= 1.8095 y-shift= 3.5058 z-shift= 2.8843 + z-angle=-0.3971 x-angle= 0.2785 y-angle= 2.8435 + x-scale= 0.9263 y-scale= 1.1929 z-scale= 0.9578 + y/x-shear=-0.0128 z/x-shear=-0.0069 z/y-shear= 0.0283 + + - Fine net CPU time = 26.1 s +++ Computing output image +++ image warp: parameters = 1.8095 3.5058 2.8843 -0.3971 0.2785 2.8435 0.9263 1.1929 0.9578 -0.0128 -0.0069 0.0283 +++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk+orig.BRIK +++ Wrote -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D +++ 3dAllineate: total CPU time = 37.9 sec Elapsed = 26.5 +++ ########################################################### +++ # Please check results visually for alignment quality # +++ ########################################################### +#Script is running (command trimmed): + cat_matvec -ONELINE ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D -I > ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D +#++ Combining anat to epi and oblique transformations +#Script is running (command trimmed): + 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-test_T1w_al_junk -input ./__tt_sub-03_ses-test_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +++ ========== sub-brick #0 ========== [total CPU to here=0.1 s] + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - no weight image + + - using 11 points from base image [use_all=0] + + * Exit alignment setup routine +++ using -1Dmatrix_apply +++ Computing output image +++ image warp: parameters = 0.9251 -0.0819 -0.0018 2.8288 0.0321 1.1915 -0.0102 -33.9090 0.0054 -0.0269 0.9581 18.1316 +++ Output dataset ./sub-03_ses-test_T1w_al_junk+orig.BRIK +++ 3dAllineate: total CPU time = 2.1 sec Elapsed = 1.7 +++ ########################################################### +#++ Creating final output: skullstripped anat data +copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig +#Script is running (command trimmed): + 3dcopy ./__tt_sub-03_ses-test_T1w_ns+orig sub-03_ses-test_T1w_ns +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ Creating final output: anat data aligned to epi +# copy is not necessary +#++ Saving history +#Script is running (command trimmed): + 3dNotes -h "align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ + -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask -cost nmi -volreg off -tshift off" \ + ./sub-03_ses-test_T1w_al_junk+orig + +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-test_T1w* + +# Finished alignment successfully + +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-test_T1w_ns+orig -no_ss +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. + +*********** Warning ************* +Dataset centers are 52.843487 mm +apart. If registration fails, or if +parts of the original anatomy gets +cropped, try adding option + -init_xform AUTO_CENTER +to your @auto_tlrc command. + +********************************* + +Padding ... +++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK +Resampling ... +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__ats_tmp__resamp_step+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 6.455733 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +Clipping -0.000100 1158.000100 ... +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./__ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.BRIK +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Registration (linear final interpolation) ... +++ 3dWarpDrive: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Initial scale factor set to 0.30/273.95=9.2e+02 +RMS[0] = 0.384861 0.16449 ITER = 6/137 +0.384861 + +Warping has converged. + +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ 6.455733 degrees from plumb. +*+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations +Applying brain mask +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.BRIK +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK +Unpadding ... +++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ output dataset: ./__ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.BRIK +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig +*+ WARNING: Changing the space of an ORIG view dataset may cause confusion! +*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space). +*+ WARNING: Consider changing the view of the dataset to TLRC view also +++ 3drefit processed 1 datasets +Changing view of transformed anatomy +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Setting parent with 3drefit -wset sub-03_ses-test_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc +++ 3drefit processed 1 datasets +++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Warning: ignoring +tlrc on new_prefix. +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.HEAD -> sub-03_ses-test_T1w_ns+tlrc.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.BRIK -> sub-03_ses-test_T1w_ns+tlrc.BRIK +Cleanup ... +cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I +if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then +foreach run ( 01 ) +3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig +++ 3dvolreg: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 6.153038 degrees from plumb. +++ Reading in base dataset ./vr_base+orig.BRIK +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 6.153038 degrees from plumb. +++ Reading input dataset ./pb01.sub_03.r01.tshift+orig.BRIK +++ Edging: x=3 y=3 z=2 +++ Creating mask for -maxdisp + + Automask has 18932 voxels + + 3319 voxels left in -maxdisp mask after erosion +++ Initializing alignment base +++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. +++ CPU time for realignment=9.71 s [=0.0408 s/sub-brick] +++ Min : roll=-0.125 pitch=-0.838 yaw=-0.100 dS=-1.314 dL=-0.122 dP=-0.602 +++ Mean: roll=+0.244 pitch=-0.353 yaw=+1.492 dS=+1.594 dL=+0.625 dP=-0.273 +++ Max : roll=+0.752 pitch=+0.977 yaw=+2.780 dS=+2.627 dL=+1.582 dP=+0.307 +++ Max displacements (mm) for each sub-brick: + 1.52(0.00) 0.25(1.43) 0.00(0.25) 0.40(0.40) 0.85(0.46) 0.73(0.21) 0.34(0.44) 0.80(0.50) 0.82(0.05) 0.97(0.22) 0.87(0.11) 1.14(0.27) 1.23(0.16) 1.37(0.28) 1.26(0.16) 1.40(0.16) 1.34(0.10) 1.53(0.22) 1.37(0.18) 1.47(0.12) 1.43(0.07) 1.39(0.23) 1.43(0.08) 1.54(0.12) 1.51(0.07) 1.54(0.05) 1.54(0.05) 1.63(0.10) 1.61(0.10) 1.65(0.10) 1.58(0.17) 1.71(0.19) 1.62(0.17) 1.77(0.19) 1.79(0.08) 1.95(0.18) 1.92(0.03) 2.10(0.19) 2.00(0.14) 2.23(0.27) 2.03(0.25) 2.26(0.23) 2.09(0.31) 2.37(0.33) 2.12(0.35) 2.37(0.41) 2.24(0.24) 2.31(0.12) 2.16(0.21) 1.75(0.92) 1.69(0.29) 1.26(0.56) 0.82(1.06) 1.02(0.77) 1.77(1.06) 2.02(2.37) 2.06(0.37) 3.95(3.75) 3.32(0.64) 3.59(1.18) 3.39(0.23) 3.42(0.10) 3.04(0.50) 2.05(1.20) 2.22(0.39) 3.63(1.92) 1.23(3.45) 1.76(1.27) 2.43(0.95) 2.71(0.28) 2.77(0.09) 3.03(0.29) 2.84(0.35) 2.83(0.31) 2.96(0.54) 2.87(0.19) 2.94(0.08) 2.89(0.08) 2.81(0.17) 2.77(0.22) 2.81(0.14) 2.95(0.14) 2.95(0.08) 3.06(0.14) 3.10(0.07) 3.01(0.16) 3.28(0.30) 3.28(0.02) 3.43(0.18) 3.45(0.06) 3.56(0.13) 3.57(0.06) 3.65(0.08) 3.70(0.08) 3.59(0.15) 3.66(0.17) 3.19(0.76) 3.37(0.22) 3.17(0.24) 3.47(0.52) 3.40(0.19) 3.40(0.24) 3.00(0.74) 3.66(1.10) 3.60(0.37) 3.73(0.37) 3.84(0.14) 3.89(0.14) 3.87(0.11) 3.89(0.14) 3.80(0.15) 3.73(0.12) 3.58(0.20) 3.69(0.13) 3.73(0.21) 3.94(0.25) 3.97(0.12) 4.13(0.21) 4.09(0.08) 4.18(0.13) 4.31(0.20) 4.11(0.27) 4.31(0.31) 4.13(0.23) 3.87(0.38) 3.82(0.12) 3.71(0.29) 3.74(0.07) 3.87(0.25) 3.89(0.04) 4.03(0.17) 4.19(0.19) 4.11(0.13) 4.27(0.21) 4.04(0.40) 4.27(0.29) 4.15(0.16) 4.26(0.14) 4.45(0.22) 4.07(0.63) 4.50(0.54) 4.38(0.16) 4.90(0.59) 4.74(0.24) 4.66(0.13) 4.65(0.20) 4.60(0.17) 4.66(0.26) 4.53(0.16) 4.73(0.26) 4.77(0.11) 4.69(0.13) 4.51(0.35) 4.52(0.15) 4.72(0.22) 4.55(0.21) 4.72(0.18) 4.65(0.12) 4.70(0.06) 4.79(0.14) 5.04(0.26) 4.95(0.48) 5.70(1.30) 5.19(0.83) 5.18(0.35) 5.42(0.26) 5.61(0.36) 5.74(0.24) 5.78(0.09) 5.89(0.15) 5.83(0.13) 5.83(0.10) 5.80(0.06) 5.73(0.25) 5.59(0.28) 5.50(0.39) 5.51(0.31) 5.49(0.23) 5.37(0.20) 5.45(0.10) 5.55(0.10) 5.64(0.17) 5.69(0.08) 5.62(0.12) 5.73(0.14) 5.69(0.09) 5.45(0.51) 5.28(0.22) 5.59(0.71) 5.03(0.73) 4.43(0.85) 4.81(0.47) 5.08(0.37) 5.55(0.73) 5.80(0.42) 5.82(0.13) 5.79(0.07) 6.03(0.40) 5.85(0.36) 5.89(0.09) 5.76(0.31) 5.95(0.23) 6.06(0.14) 5.97(0.17) 6.01(0.08) 6.11(0.29) 6.11(0.07) 6.21(0.16) 6.12(0.24) 6.18(0.07) 6.15(0.16) 6.15(0.10) 6.11(0.10) 6.23(0.23) 6.11(0.23) 6.18(0.10) 6.13(0.07) 6.12(0.08) 6.14(0.15) 6.04(0.16) 6.16(0.16) 6.15(0.11) 5.93(0.28) 6.00(0.08) 5.90(0.20) 5.86(0.40) 5.77(0.25) 6.07(0.68) 6.04(0.20) 5.99(0.20) 6.28(0.40) 6.31(0.10) 6.35(0.22) 6.33(0.19) 6.10(0.42) 6.01(0.25) 6.16(0.24) 6.13(0.07) +++ Max displacement in automask = 6.35 (mm) at sub-brick 232 +++ Max delta displ in automask = 3.75 (mm) at sub-brick 57 +++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK +3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +*+ WARNING: input 'a' is not used in the expression +++ Output dataset ./rm.epi.all1+orig.BRIK +cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb01.sub_03.r01.tshift+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 6.153038 degrees from plumb. +++ Source dataset: ./pb01.sub_03.r01.tshift+orig.HEAD +++ Base dataset: ./sub-03_ses-test_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 238 sub-bricks ========== +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 5.8 sec Elapsed = 4.4 +++ ########################################################### +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./rm.epi.all1+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./rm.epi.all1+orig.BRIK is 6.153038 degrees from plumb. +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ Output dataset ./rm.epi.1.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.4 sec Elapsed = 3.1 +3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.epi.min.r01+tlrc.BRIK +end +cat dfile.r01.1D +3dcopy rm.epi.min.r01+tlrc mask_epi_extents +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +foreach run ( 01 ) +3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK +end +cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 6.153038 degrees from plumb. +++ Source dataset: ./vr_base+orig.HEAD +++ Base dataset: ./sub-03_ses-test_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.2 +++ ########################################################### +3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.sub_03 +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc +tee out.allcostX.txt +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./anat_final.sub_03+tlrc.HEAD +++ Base dataset: ./final_epi_vr_base+tlrc.HEAD +++ Loading datasets +++ 223015 voxels in source_automask+0 +++ Zero-pad: xbot=1 xtop=1 +++ Zero-pad: ybot=4 ytop=4 +++ Zero-pad: zbot=0 ztop=1 +++ Computing -autobox +++ 119923 voxels [89.5%] in weight mask +++ Number of points for matching = 56363 +++ Local correlation: blok type = 'RHDD(14.76)' +*+ WARNING: No output dataset will be calculated +++ OpenMP thread count = 4 +volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +++ allcost output: init #0 + ls = 0.319992 + sp = 0.392466 + mi = -0.430206 + crM = 0.204696 + nmi = 0.897455 + je = 3.76509 + hel = -0.0823942 + crA = 0.454393 + crU = 0.412241 + lss = 0.680008 + lpc = 0.12108 + lpa = 0.87892 + lpc+ = 0.416704 + ncd = 1 +++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 +++ ########################################################### +3dAllineate -source sub-03_ses-test_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. +++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers +++ Source dataset: ./sub-03_ses-test_T1w+orig.HEAD +++ Base dataset: (not given) +++ Loading datasets +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ð++ wsinc5 interpolation setup: + + taper function = Min sidelobe 3 term + + taper cut point = 0.000 + + window radius = 5 voxels + + window shape = Cubical + + The above can be altered via the AFNI_WSINC5_* environment variables. + + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + + wsinc5 CUBE(5) mask has 1000 points +++ Output dataset ./anat_w_skull_warped+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.2 +++ ########################################################### +foreach run ( 01 ) +3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc +++ 3dmerge: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ default -1dindex = 0 +++ default -1tindex = 1 +Program 3dmerge +3dmerge: edit and combine 3D datasets, by RW Cox +++ editing input dataset in memory (49.6 MB) +..............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK + +end +foreach run ( 01 ) +3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc +++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset pb03.sub_03.r01.blur+tlrc +++ Forming automask + + Fixed clip level = 710.685547 + + Used gradual clip level = 648.283936 .. 804.968506 + + Number voxels above clip level = 30766 + + Clustering voxels ... + + Largest cluster has 30766 voxels + + Clustering voxels ... + + Largest cluster has 30698 voxels + + Filled 56 voxels in small holes; now have 30754 voxels + + Clustering voxels ... + + Largest cluster has 30753 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 78597 voxels + + Mask now has 30753 voxels +++ Dilating automask + + Clustering voxels ... + + Largest cluster has 73337 voxels +++ 36013 voxels in the mask [out of 109350: 32.93%] +++ first 4 x-planes are zero [from L] +++ last 5 x-planes are zero [from R] +++ first 0 y-planes are zero [from P] +++ last 0 y-planes are zero [from A] +++ first 6 z-planes are zero [from I] +++ last 3 z-planes are zero [from S] +++ Output dataset ./rm.mask_r01+tlrc.BRIK +++ CPU time = 0.280000 sec +end +3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 +++ processing 1 input datasets... +++ padding all datasets by 0 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 36013 survived, 73337 were zero +++ writing result full_mask.sub_03... +++ Output dataset ./full_mask.sub_03+tlrc.BRIK +3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-test_T1w_ns+tlrc -prefix rm.resam.anat +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30704 survived, 78646 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_anat.sub_03... +++ Output dataset ./mask_anat.sub_03+tlrc.BRIK +3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_overlap.txt +++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK +#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) +36013 30704 40588 26129 9884 4575 27.4456 14.9003 1.0267 0.6317 1.1274 +3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_dice.txt +0.783279 +3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30980 survived, 78370 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_group... +++ Output dataset ./mask_group+tlrc.BRIK +foreach run ( 01 ) +3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.mean_r01+tlrc.BRIK +3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK +end +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_sub_03 +total number of censored TRs (simple form) = 44 +1deval -a motion_sub_03_censor.1D -b outcount_sub_03_censor.1D -expr a*b +set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D + -show_trs_uncensored encoded` +1d_tool.py -infile censor_sub_03_combined_2.1D -show_trs_uncensored encoded +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor censor_sub_03_combined_2.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: B. Douglas Ward, et al. +++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD +++ STAT automask has 93751 voxels (out of 109350 = 85.7%) +++ Skipping check for initial transients +++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ +++ -stim_times using TR=2.5 s for stimulus timing conversion +++ -stim_times using TR=2.5 s for any -iresp output datasets +++ [you can alter the -iresp TR via the -TR_times option] +++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise +++ ** GUESSED ** -stim_times 1 using LOCAL times +++ ** GUESSED ** -stim_times 2 using LOCAL times +++ ** GUESSED ** -stim_times 3 using LOCAL times +++ ** GUESSED ** -stim_times 4 using LOCAL times +++ ** GUESSED ** -stim_times 5 using LOCAL times +------------------------------------------------------------ +GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task': + 0 0 0 0 0 0.333 0.333 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 + +++ Number of time points: 238 (before censor) ; 194 (after) + + Number of parameters: 22 [17 baseline ; 5 signal] +++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) +++ Wrote matrix image to file X.jpg +++ Wrote matrix values to file X.xmat.1D +++ ========= Things you can do with the matrix file ========= +++ (a) Linear regression with ARMA(1,1) modeling of serial correlation: + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb + +++ N.B.: 3dREMLfit command above written to file stats.REML_cmd +++ (b) Visualization/analysis of the matrix via ExamineXmat.R +++ (c) Synthesis of sub-model datasets using 3dSynthesize +++ ========================================================== +++ Wrote matrix values to file X.nocensor.xmat.1D +++ ----- Signal+Baseline matrix condition [X] (194x22): 8.14751 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (194x5): 1.4614 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (194x17): 8.00108 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (194x12): 6.40992 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (194x5): 1.11242 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 1.22155e-14 ++ VERY GOOD ++ +++ Matrix setup time = 0.60 s +++ Calculations starting; elapsed time=1.217 +++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. +++ Calculations finished; elapsed time=13.567 +++ Smallest FDR q [0 Full_Fstat] = 1.14224e-12 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 3.09596e-09 +++ Smallest FDR q [3 Correct_Task_Fstat] = 3.09588e-09 +*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.312787 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.312288 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.300188 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [9 No_Response_Control_Fstat] = 0.299698 ==> few true single voxel detections +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 2.9327e-11 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 2.9328e-11 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 1.66531e-07 +++ Smallest FDR q [15 Response_Control_Fstat] = 1.66531e-07 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 2.95886e-08 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 2.95896e-08 +++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + + created 13 FDR curves in bucket header +++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK +++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK +++ #Flops=3.55203e+10 Average Dot Product=36.8509 +if ( 0 != 0 ) then +1d_tool.py -show_cormat_warnings -infile X.xmat.1D +tee out.cormat_warn.txt + +Warnings regarding Correlation Matrix: X.xmat.1D + + severity correlation cosine regressor pair + -------- ----------- ------ ---------------------------------------- + medium: 0.561 0.640 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 + +3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD +++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ elapsed time = 1.1 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.signal.all+tlrc.BRIK +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.noise.all+tlrc.BRIK +3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./TSNR.sub_03+tlrc.BRIK +3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc +++ 3dTnorm: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Output dataset ./rm.errts.unit+tlrc.BRIK +3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc +++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++++ 36013 voxels survive the mask +3dTstat -sos -prefix - gmean.errts.unit.1D' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo -- GCOR = `cat out.gcor.1D` +cat out.gcor.1D +-- GCOR = 0.140811 +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./rm.DP+tlrc.BRIK +3dTstat -sum -prefix corr_brain rm.DP+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./corr_brain+tlrc.BRIK +1dcat X.nocensor.xmat.1D[5] +1dcat X.nocensor.xmat.1D[6] +1dcat X.nocensor.xmat.1D[7] +1dcat X.nocensor.xmat.1D[8] +1dcat X.nocensor.xmat.1D[9] +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +++ Output dataset ./sum_ideal.1D +1dcat X.nocensor.xmat.1D[5..9] +touch blur_est.sub_03.1D +mkdir files_ACF +touch blur.epits.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237] +++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 36013 +*+ WARNING: removed 269 voxels from mask because they are constant in time +++ detrending start: 15 baseline funcs, 194 time points + + detrending done (1.90 CPU s thus far) +++ start ACF calculations out to radius = 28.03 mm + + ACF done (56.24 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits FWHM blurs: 0 0 0 0 +average epits FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # epits FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits ACF blurs: 0.656416 5.22886 14.4219 13.5135 +average epits ACF blurs: 0.656416 5.22886 14.4219 13.5135 +echo 0.656416 5.22886 14.4219 13.5135 # epits ACF blur estimates +touch blur.errts.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237] +++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 36013 +*+ WARNING: removed 269 voxels from mask because they are constant in time +++ detrending start: 15 baseline funcs, 194 time points + + detrending done (1.91 CPU s thus far) +++ start ACF calculations out to radius = 27.62 mm + + ACF done (53.59 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts FWHM blurs: 0 0 0 0 +average errts FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # errts FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts ACF blurs: 0.712442 5.22743 14.2881 13.2541 +average errts ACF blurs: 0.712442 5.22743 14.2881 13.2541 +echo 0.712442 5.22743 14.2881 13.2541 # errts ACF blur estimates +gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD +gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 +++ writing ss review basic: @ss_review_basic +++ writing ss review driver: @ss_review_driver +++ writing ss review drive commands: @ss_review_driver_commands +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.out.cen.r01.1D rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +tee out.ss_review.sub_03.txt +if ( -e @ss_review_basic ) ./@ss_review_basic +./@ss_review_basic + +subject ID : sub_03 +TRs removed (per run) : 0 +num stim classes provided : 5 +final anatomy dset : anat_final.sub_03+tlrc.HEAD +final stats dset : stats.sub_03+tlrc.HEAD +final voxel resolution : 4.000000 4.000000 4.000000 + +motion limit : 0.3 +num TRs above mot limit : 29 +average motion (per TR) : 0.179191 +average censored motion : 0.111049 +max motion displacement : 5.04394 +max censored displacement : 3.96802 +outlier limit : 0.5 +average outlier frac (TR) : 0.0152516 +num TRs above out limit : 1 + +num runs found : 1 +num TRs per run : 238 +num TRs per run (applied) : 194 +num TRs per run (censored): 44 +fraction censored per run : 0.184874 +TRs total (uncensored) : 238 +TRs total : 194 +degrees of freedom used : 22 +degrees of freedom left : 172 + +TRs censored : 44 +censor fraction : 0.184874 +num regs of interest : 5 +num TRs per stim (orig) : 71 43 64 28 79 +num TRs censored per stim : 5 0 19 9 17 +fraction TRs censored : 0.070 0.000 0.297 0.321 0.215 +ave mot per sresp (orig) : 0.124806 0.112975 0.230781 0.273948 0.190656 +ave mot per sresp (cens) : 0.113477 0.112975 0.095777 0.114754 0.093013 + +TSNR average : 202.889 +global correlation (GCOR) : 0.140811 +anat/EPI mask Dice coef : 0.783279 +maximum F-stat (masked) : 33.52 +blur estimates (ACF) : 0.712442 5.22743 14.2881 +blur estimates (FWHM) : 0 0 0 + +** TR #0 outliers: possible pre-steady state TRs in run 01 + +cd .. +echo execution finished: `date` +date +execution finished: Thu Aug 3 20:43:53 EDT 2017 diff --git a/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 new file mode 100755 index 0000000..e3af51b --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 @@ -0,0 +1,493 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Aug 3 20:35:22 2017" +echo "(version 5.15, April 25, 2017)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + +# =========================== auto block: setup ============================ +# script setup + +# take note of the AFNI version +afni -ver + +# check that the current AFNI version is recent enough +afni_history -check_date 23 Sep 2016 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 23 Sep 2016)" + echo " (consider: @update.afni.binaries -defaults)" + exit +endif + +# the user may specify a single subject to run with +if ( $#argv > 0 ) then + set subj = $argv[1] +else + set subj = sub_03 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ + $output_dir/sub-03_ses-test_T1w + +# ============================ auto block: tcat ============================ +# apply 3dTcat to copy input dsets to results dir, while +# removing the first 0 TRs +3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 238 ) + +# ------------------------------------------------------- +# enter the results directory (can begin processing data) +cd $output_dir + + +# ========================== auto block: outcount ========================== +# data check: compute outlier fraction for each volume +touch out.pre_ss_warn.txt +foreach run ( $runs ) + 3dToutcount -automask -fraction -polort 4 -legendre \ + pb00.$subj.r$run.tcat+orig > outcount.r$run.1D + + # censor outlier TRs per run, ignoring the first 0 TRs + # - censor when more than 0.5 of automask voxels are outliers + # - step() defines which TRs to remove via censoring + 1deval -a outcount.r$run.1D -expr "1-step(a-0.5)" > rm.out.cen.r$run.1D + + # outliers at TR 0 might suggest pre-steady state TRs + if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then + echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ + >> out.pre_ss_warn.txt + endif +end + +# catenate outlier counts into a single time series +cat outcount.r*.1D > outcount_rall.1D + +# catenate outlier censor files into a single time series +cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D + +# ================================= tshift ================================= +# time shift data so all slice timing is the same +foreach run ( $runs ) + 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + pb00.$subj.r$run.tcat+orig +end + +# -------------------------------- +# extract volreg registration base +3dbucket -prefix vr_base pb01.$subj.r01.tshift+orig"[2]" + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-03_ses-test_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask \ + -cost nmi \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-test_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-03_ses-test_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base vr_base+orig \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg/epi2anat/tlrc xforms + cat_matvec -ONELINE \ + sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform: volreg/epi2anat/tlrc + 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc mask_epi_extents + +# and apply the extents mask to the EPI data +# (delete any time series with missing data) +foreach run ( $runs ) + 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc \ + -expr 'a*b' -prefix pb02.$subj.r$run.volreg +end + +# warp the volreg base EPI dataset to make a final version +cat_matvec -ONELINE \ + sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I > \ + mat.basewarp.aff12.1D + +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input vr_base+orig \ + -1Dmatrix_apply mat.basewarp.aff12.1D \ + -mast_dxyz 4 \ + -prefix final_epi_vr_base + +# create an anat_final dataset, aligned with stats +3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.$subj + +# record final registration costs +3dAllineate -base final_epi_vr_base+tlrc -allcostX \ + -input anat_final.$subj+tlrc |& tee out.allcostX.txt + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-03_ses-test_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== blur ================================== +# blur each volume of each run +foreach run ( $runs ) + 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.$subj.r$run.blur \ + pb02.$subj.r$run.volreg+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc +end + +# create union of inputs, output type is byte +3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj + +# ---- create subject anatomy mask, mask_anat.$subj+tlrc ---- +# (resampled from tlrc anat) +3dresample -master full_mask.$subj+tlrc -input sub-03_ses-test_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute overlaps between anat and EPI masks +3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_overlap.txt + +# note Dice coefficient of masks, as well +3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_dice.txt + +# ---- create group anatomy mask, mask_group+tlrc ---- +# (resampled from tlrc base anat, MNI_avg152T1+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/monicali/abin/MNI_avg152T1+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= scale ================================== +# scale each voxel time series to have a mean of 100 +# (be sure no negatives creep in) +# (subject to a range of [0,200]) +foreach run ( $runs ) + 3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.3 motion_${subj} + +# combine multiple censor files +1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \ + -expr "a*b" > censor_${subj}_combined_2.1D + +# note TRs that were not censored +set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ + -show_trs_uncensored encoded` + +# ------------------------------ +# run the regression analysis +3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ + -censor censor_${subj}_combined_2.1D \ + -polort 4 \ + -num_stimts 17 \ + -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D 'GAM' \ + -stim_label 1 Correct_Task \ + -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D 'GAM' \ + -stim_label 2 Incorrect_Task \ + -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D 'GAM' \ + -stim_label 3 No_Response_Control \ + -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D 'GAM' \ + -stim_label 4 No_Response_Task \ + -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D 'GAM' \ + -stim_label 5 Response_Control \ + -stim_file 6 motion_demean.1D'[0]' -stim_base 6 -stim_label 6 roll_01 \ + -stim_file 7 motion_demean.1D'[1]' -stim_base 7 -stim_label 7 pitch_01 \ + -stim_file 8 motion_demean.1D'[2]' -stim_base 8 -stim_label 8 yaw_01 \ + -stim_file 9 motion_demean.1D'[3]' -stim_base 9 -stim_label 9 dS_01 \ + -stim_file 10 motion_demean.1D'[4]' -stim_base 10 -stim_label 10 dL_01 \ + -stim_file 11 motion_demean.1D'[5]' -stim_base 11 -stim_label 11 dP_01 \ + -stim_file 12 motion_deriv.1D'[0]' -stim_base 12 -stim_label 12 roll_02 \ + -stim_file 13 motion_deriv.1D'[1]' -stim_base 13 -stim_label 13 pitch_02 \ + -stim_file 14 motion_deriv.1D'[2]' -stim_base 14 -stim_label 14 yaw_02 \ + -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ + -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ + -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + -glt_label 1 Landmark-Detection \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc"[$ktrs]" +3dcalc -a rm.signal.all+tlrc \ + -b rm.noise.all+tlrc \ + -c full_mask.$subj+tlrc \ + -expr 'c*a/b' -prefix TSNR.$subj + +# --------------------------------------------------- +# compute and store GCOR (global correlation average) +# (sum of squares of global mean of unit errts) +3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[5]' > ideal_Correct_Task.1D +1dcat X.nocensor.xmat.1D'[6]' > ideal_Incorrect_Task.1D +1dcat X.nocensor.xmat.1D'[7]' > ideal_No_Response_Control.1D +1dcat X.nocensor.xmat.1D'[8]' > ideal_No_Response_Task.1D +1dcat X.nocensor.xmat.1D'[9]' > ideal_Response_Control.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]" + +# also, create a stimulus-only X-matrix, for easy review +1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D + +# ============================ blur estimation ============================= +# compute blur estimates +touch blur_est.$subj.1D # start with empty file + +# create directory for ACF curve files +mkdir files_ACF + +# -- estimate blur for each run in epits -- +touch blur.epits.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +echo average epits FWHM blurs: $blurs +echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +echo average epits ACF blurs: $blurs +echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D + +# -- estimate blur for each run in errts -- +touch blur.errts.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +echo average errts FWHM blurs: $blurs +echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +echo average errts ACF blurs: $blurs +echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ +# -align_opts_aea -cost nmi -tlrc_base MNI_avg152T1+tlrc -volreg_align_to \ +# third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 \ +# -regress_stim_times \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ +# -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ +# 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ +# -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 \ +# Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ +# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err new file mode 100644 index 0000000..b506101 --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err @@ -0,0 +1,4 @@ +*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.312787 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.312288 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.300188 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [9 No_Response_Control_Fstat] = 0.299698 ==> few true single voxel detections diff --git a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd new file mode 100644 index 0000000..f78bb04 --- /dev/null +++ b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd @@ -0,0 +1,5 @@ +# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor censor_sub_03_combined_2.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb $* From 8226a546dc5e4ae8706447ab8f307b40b906521a Mon Sep 17 00:00:00 2001 From: Monica Li Date: Thu, 3 Aug 2017 21:51:23 -0400 Subject: [PATCH 04/18] add more file extensions to .gitignore --- .gitignore | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.gitignore b/.gitignore index b6308a3..a4dadab 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,7 @@ *.tsv +*.1D +*.BRIK +*.HEAD +@* +*.txt +*.jpg From 389a3931393aca3d89f9d15106aa8ff937d4acd9 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Thu, 3 Aug 2017 22:50:18 -0400 Subject: [PATCH 05/18] update Exp-1 scripts fix -regress_censor_motion update directory in Exp-1.sh --- Exp-1.sh | 17 +- .../subj.sub_03/.orig.cmd.ap.sub_03 | 7 +- .../subj.sub_03/.orig.cmd.usubj.sub_03 | 3 +- .../subj.sub_03/.orig.proc.sub_03 | 12 +- .../group.retest/subj.sub_03/cmd.ap.sub_03 | 10 +- .../subj.sub_03/output.cmd.ap.sub_03 | 8 + .../subj.sub_03/output.proc.sub_03 | 314 +++++++++-------- .../group.retest/subj.sub_03/proc.sub_03 | 42 +-- .../subj.sub_03/sub_03.results/stats.REML_cmd | 2 +- .../subj.sub_03/.orig.cmd.ap.sub_03 | 7 +- .../subj.sub_03/.orig.cmd.usubj.sub_03 | 3 +- .../group.test/subj.sub_03/.orig.proc.sub_03 | 12 +- .../group.test/subj.sub_03/cmd.ap.sub_03 | 10 +- .../subj.sub_03/output.cmd.ap.sub_03 | 8 + .../group.test/subj.sub_03/output.proc.sub_03 | 318 +++++++++--------- .../group.test/subj.sub_03/proc.sub_03 | 42 +-- .../sub_03.results/3dDeconvolve.err | 8 +- .../subj.sub_03/sub_03.results/stats.REML_cmd | 2 +- 18 files changed, 399 insertions(+), 426 deletions(-) mode change 100644 => 100755 Exp-1.sh diff --git a/Exp-1.sh b/Exp-1.sh old mode 100644 new mode 100755 index d9f39df..487e5c6 --- a/Exp-1.sh +++ b/Exp-1.sh @@ -2,19 +2,20 @@ # 1. Threshold the stats at p <.05 3dmerge -1zscore -1thresh 1.96 -1noneg \ --prefix stats.test.thresh \ -'subject_results/group.test/subj.sub_03/sub_03.results/stats.sub_03+tlrc[17]' +-prefix Exp-1/stats.test.thresh \ +'Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.sub_03+tlrc[17]' 3dmerge -1zscore -1thresh 1.96 -1noneg \ --prefix stats.retest.thresh \ -'subject_results/group.retest/subj.sub_03/sub_03.results/stats.sub_03+tlrc[17]' +-prefix Exp-1/stats.retest.thresh \ +'Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.sub_03+tlrc[17]' # 2. Calculate a mask that contains overlapping regions of the brain in both sessions -3dmask_tool -input subject_results/group.*/subj.sub_03/sub_03.results/mask_group+tlrc.HEAD -frac 1.0 -prefix mask +3dmask_tool -input Exp-1/subject_results/group.*/subj.sub_03/sub_03.results/mask_group+tlrc.HEAD \ +-frac 1.0 -prefix Exp-1/mask # 3. Binarize the thresholded images -3dcalc -a stats.test.thresh+tlrc -prefix stats.test.bin -expr 'astep(a,.1)' -3dcalc -a stats.retest.thresh+tlrc -prefix stats.retest.bin -expr 'astep(a,.1)' +3dcalc -a Exp-1/stats.test.thresh+tlrc -prefix Exp-1/stats.test.bin -expr 'astep(a,.1)' +3dcalc -a Exp-1/stats.retest.thresh+tlrc -prefix Exp-1/stats.retest.bin -expr 'astep(a,.1)' # 4. Calculate the Dice coefficient -3ddot -mask mask+tlrc -dodice stats.test.bin+tlrc stats.retest.bin+tlrc \ No newline at end of file +3ddot -mask Exp-1/mask+tlrc -dodice Exp-1/stats.test.bin+tlrc Exp-1/stats.retest.bin+tlrc \ No newline at end of file diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 index 8122ad9..4726041 100755 --- a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 @@ -1,7 +1,7 @@ #!/usr/bin/env tcsh # created by uber_subject.py: version 0.40 (March 30, 2017) -# creation date: Thu Aug 3 20:37:56 2017 +# creation date: Thu Aug 3 22:03:06 2017 # set data directories set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground @@ -19,7 +19,6 @@ afni_proc.py -subj_id $subj \ -copy_anat $anat_dir/sub-03_ses-retest_T1w.nii.gz \ -tcat_remove_first_trs 0 \ -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ - -align_opts_aea -cost nmi \ -tlrc_base MNI_avg152T1+tlrc \ -volreg_align_to third \ -volreg_align_e2a \ @@ -40,8 +39,8 @@ afni_proc.py -subj_id $subj \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ - -glt_label 1 Landmark-Detection \ + +0.333*No_Response_Task -0.5*Response_Control \ + -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 index 7361497..e94908e 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 @@ -1,6 +1,5 @@ uber_subject.py \ -cvar subj_dir subject_results/group.retest/subj.sub_03 \ - -svar align_cost nmi \ -svar anat \ /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ \ @@ -10,7 +9,7 @@ uber_subject.py \ -svar gid retest \ -svar gltsym '0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ -svar gltsym_label Landmark-Detection \ -svar outlier_limit 0.5 \ -svar regress_mot_deriv yes \ diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 index 04545b4..e883f7a 100755 --- a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Thu Aug 3 20:38:10 2017" +echo "auto-generated by afni_proc.py, Thu Aug 3 22:03:22 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -115,7 +115,6 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ -save_skullstrip -suffix _al_junk \ -epi vr_base+orig -epi_base 0 \ -epi_strip 3dAutomask \ - -cost nmi \ -volreg off -tshift off # ================================== tlrc ================================== @@ -320,7 +319,7 @@ set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -476,9 +475,8 @@ echo "execution finished: `date`" # /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ # -tcat_remove_first_trs 0 -dsets \ # /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ -# -align_opts_aea -cost nmi -tlrc_base MNI_avg152T1+tlrc -volreg_align_to \ -# third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 \ -# -regress_stim_times \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ @@ -489,6 +487,6 @@ echo "execution finished: `date`" # -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ # -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ # 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ -# -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 \ +# -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 \ # Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ # -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 index 8122ad9..05ecd7d 100755 --- a/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 @@ -1,7 +1,7 @@ #!/usr/bin/env tcsh # created by uber_subject.py: version 0.40 (March 30, 2017) -# creation date: Thu Aug 3 20:37:56 2017 +# creation date: Thu Aug 3 22:03:06 2017 # set data directories set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground @@ -19,7 +19,6 @@ afni_proc.py -subj_id $subj \ -copy_anat $anat_dir/sub-03_ses-retest_T1w.nii.gz \ -tcat_remove_first_trs 0 \ -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ - -align_opts_aea -cost nmi \ -tlrc_base MNI_avg152T1+tlrc \ -volreg_align_to third \ -volreg_align_e2a \ @@ -35,13 +34,12 @@ afni_proc.py -subj_id $subj \ Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ Response_Control \ -regress_basis 'GAM' \ - -regress_censor_motion 0.3 \ - -regress_censor_outliers 0.5 \ + -regress_censor_motion 0.5 \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ - -glt_label 1 Landmark-Detection \ + +0.333*No_Response_Task -0.5*Response_Control \ + -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 index 89d2fea..26e0d70 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 @@ -1,3 +1,11 @@ +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat +set epi_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func +set subj = sub_03 +set group_id = retest +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control + -0.5*No_Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig -- tcat: reps is now 238 ++ updating polort to 4, from run len 595.0 s diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 index 0b46bf7..8498c74 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 @@ -1,10 +1,10 @@ -echo auto-generated by afni_proc.py, Thu Aug 3 20:38:10 2017 -auto-generated by afni_proc.py, Thu Aug 3 20:38:10 2017 +echo auto-generated by afni_proc.py, Thu Aug 3 22:21:05 2017 +auto-generated by afni_proc.py, Thu Aug 3 22:21:05 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Thu Aug 3 20:45:11 EDT 2017 +execution started: Thu Aug 3 22:24:53 EDT 2017 afni -ver Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) afni_history -check_date 23 Sep 2016 @@ -25,7 +25,7 @@ cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Corre ++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] 3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] ++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 1.4 s +++ elapsed time = 1.5 s set tr_counts = ( 238 ) cd sub_03.results touch out.pre_ss_warn.txt @@ -41,14 +41,12 @@ foreach run ( 01 ) See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. ++ 18031 voxels passed mask/clip -1deval -a outcount.r01.1D -expr 1-step(a-0.5) if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then 1deval -a outcount.r01.1D{0} -expr step(a-0.4) echo ** TR #0 outliers: possible pre-steady state TRs in run 01 endif end cat outcount.r01.1D -cat rm.out.cen.r01.1D foreach run ( 01 ) 3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig ++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -65,7 +63,7 @@ foreach run ( 01 ) end 3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] ++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -cost nmi -volreg off -tshift off +align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off #++ align_epi_anat version: 1.57 #++ turning off volume registration #Script is running (command trimmed): @@ -74,7 +72,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s 3dAttribute DELTA ./vr_base+orig #Script is running (command trimmed): 3dAttribute DELTA ./sub-03_ses-retest_T1w+orig -#++ Multi-cost is nmi +#++ Multi-cost is lpc #++ Removing all the temporary files #Script is running: \rm -f ./__tt_vr_base* @@ -96,7 +94,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Oblique dataset:./__tt_sub-03_ses-retest_T1w+orig.BRIK is 7.491219 degrees from plumb. #Script is running (command trimmed): 3dinfo ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' -#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig is ***oblique**** +#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig is ***oblique**** #Script is running (command trimmed): 3dAttribute DELTA ./__tt_sub-03_ses-retest_T1w_ns+orig #++ Spacing for anat to oblique epi alignment is 1.000000 @@ -155,11 +153,11 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ applying mask to original data ++ Writing masked data ++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK -++ CPU time = 3.950000 sec +++ CPU time = 4.220000 sec #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1728.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1728.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig #Script is running (command trimmed): 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1728.000000))' ++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -167,7 +165,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK #++ Aligning anat data to epi data #Script is running (command trimmed): - 3dAllineate -nmi -wtprefix ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass + 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass ++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.HEAD @@ -178,6 +176,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ 1167476 voxels [7.5%] in weight mask ++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal+orig.BRIK ++ Number of points for matching = 1167476 +++ Local correlation: blok type = 'RHDD(6.54321)' ++ shift param auto-range: -84.4..84.4 -70.6..70.6 -85.1..85.1 + Range param#4 [z-angle] = -6.000000 .. 6.000000 + Range param#5 [x-angle] = -6.000000 .. 6.000000 @@ -188,8 +187,8 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s + 12 free parameters ++ Normalized convergence radius = 0.001000 ++ OpenMP thread count = 4 -++ ======= Allineation of 1 sub-bricks using Normalized MI [H(b,s)/(H(b)+H(s))] ======= -++ ========== sub-brick #0 ========== [total CPU to here=9.1 s] +++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= +++ ========== sub-brick #0 ========== [total CPU to here=9.4 s] ++ *** Fine pass begins *** + * Enter alignment setup routine + - copying base image @@ -197,30 +196,30 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s + - copying weight image + - using 1167476 points from base image [use_all=0] + * Exit alignment setup routine - + - histogram: source clip 165.643 .. 715.741; base clip 487.29 .. 1872 - + - versus source range 0 .. 622.496; base range 0 .. 2253.55 - + - Initial cost = 0.997070 + + 1097666 total points stored in 2068 'RHDD(6.54321)' bloks + + - Initial cost = -0.053122 + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 -*********************** - + - Finalish cost = 0.995066 ; 154 funcs - + - histogram: source clip 151.975 .. 656.684; base clip 487.29 .. 1872 - + - versus source range 0 .. 622.496; base range 0 .. 2253.55 -************************ - + - Final cost = 0.994952 ; 236 funcs +********************************************************************************************************************************************** + + - Finalish cost = -0.295415 ; 350 funcs +********** + + - Final cost = -0.295420 ; 136 funcs + Final fine fit Parameters: - x-shift= 0.5215 y-shift= 3.9495 z-shift= 4.8067 - z-angle= 0.0062 x-angle=-0.1182 y-angle=-0.0256 - x-scale= 1.0011 y-scale= 1.1245 z-scale= 0.9636 - y/x-shear= 0.0006 z/x-shear=-0.0029 z/y-shear=-0.0016 - + - Fine net CPU time = 31.6 s + x-shift= 0.2981 y-shift=-0.5136 z-shift=-1.2234 + z-angle= 0.4394 x-angle= 1.9668 y-angle=-5.3161 + x-scale= 0.9674 y-scale= 0.9725 z-scale= 1.0191 + y/x-shear= 0.0000 z/x-shear= 0.0099 z/y-shear= 0.0534 + + - Fine net CPU time = 34.7 s ++ Computing output image -++ image warp: parameters = 0.5215 3.9495 4.8067 0.0062 -0.1182 -0.0256 1.0011 1.1245 0.9636 0.0006 -0.0029 -0.0016 +++ image warp: parameters = 0.2981 -0.5136 -1.2234 0.4394 1.9668 -5.3161 0.9674 0.9725 1.0191 0.0000 0.0099 0.0534 ++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk+orig.BRIK ++ Wrote -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 43.0 sec Elapsed = 27.6 +++ 3dAllineate: total CPU time = 46.5 sec Elapsed = 34.1 ++ ########################################################### ++ # Please check results visually for alignment quality # ++ ########################################################### +++ # '-autoweight' is recommended when using -lpc or -lpa # +++ # If your results are not good, please try again. # +++ ########################################################### #Script is running (command trimmed): cat_matvec -ONELINE ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D ./__tt_sub-03_ses-retest_T1w_ns_obla2e_mat.1D -I > ./sub-03_ses-retest_T1w_al_junk_mat.aff12.1D #++ Combining anat to epi and oblique transformations @@ -256,12 +255,12 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s + * Exit alignment setup routine ++ using -1Dmatrix_apply ++ Computing output image -++ image warp: parameters = 1.0006 0.0454 -0.0079 -2.2618 -0.0238 1.1231 -0.0270 -21.1278 0.0100 0.0568 0.9630 8.6870 +++ image warp: parameters = 0.9618 0.0448 -0.0985 14.5442 -0.0314 0.9711 -0.0538 -1.5252 0.0911 0.0281 1.0141 -11.6150 ++ Output dataset ./sub-03_ses-retest_T1w_al_junk+orig.BRIK -++ 3dAllineate: total CPU time = 2.1 sec Elapsed = 1.8 +++ 3dAllineate: total CPU time = 2.1 sec Elapsed = 5.2 ++ ########################################################### #++ Creating final output: skullstripped anat data -copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig +copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig #Script is running (command trimmed): 3dcopy ./__tt_sub-03_ses-retest_T1w_ns+orig sub-03_ses-retest_T1w_ns ++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -271,7 +270,7 @@ copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_resu #Script is running (command trimmed): 3dNotes -h "align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 \ - -epi_strip 3dAutomask -cost nmi -volreg off -tshift off" \ + -epi_strip 3dAutomask -volreg off -tshift off" \ ./sub-03_ses-retest_T1w_al_junk+orig #++ Removing all the temporary files @@ -436,7 +435,7 @@ foreach run ( 01 ) + 3364 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=7.19 s [=0.0302 s/sub-brick] +++ CPU time for realignment=7.04 s [=0.0296 s/sub-brick] ++ Min : roll=-0.200 pitch=-0.367 yaw=-0.118 dS=-1.139 dL=-0.157 dP=-0.055 ++ Mean: roll=-0.094 pitch=-0.011 yaw=+0.456 dS=-0.124 dL=+0.184 dP=+0.074 ++ Max : roll=+0.027 pitch=+0.449 yaw=+0.935 dS=+0.523 dL=+0.640 dP=+0.245 @@ -472,7 +471,7 @@ cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retes ++ OpenMP thread count = 4 ++ ========== Applying transformation to 238 sub-bricks ========== volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 5.9 sec Elapsed = 4.3 +++ 3dAllineate: total CPU time = 6.2 sec Elapsed = 5.3 ++ ########################################################### 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 ++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -488,7 +487,7 @@ volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20. ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (LPI); source=Left handed (RPI) ++ Output dataset ./rm.epi.1.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 3.4 +++ 3dAllineate: total CPU time = 3.4 sec Elapsed = 3.7 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc ++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox @@ -525,7 +524,7 @@ cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retes ++ OpenMP thread count = 4 ++ ========== Applying transformation to 1 sub-bricks ========== volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK -++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.1 +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.3 ++ ########################################################### 3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.sub_03 ++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -537,31 +536,31 @@ tee out.allcostX.txt ++ Base dataset: ./final_epi_vr_base+tlrc.HEAD ++ Loading datasets ++ 222503 voxels in source_automask+0 -++ Zero-pad: xbot=2 xtop=3 -++ Zero-pad: ybot=3 ytop=4 -++ Zero-pad: zbot=0 ztop=2 +++ Zero-pad: xbot=1 xtop=2 +++ Zero-pad: ybot=0 ytop=1 +++ Zero-pad: zbot=2 ztop=1 ++ Computing -autobox -++ 128372 voxels [89.6%] in weight mask -++ Number of points for matching = 60334 +++ 113297 voxels [89.4%] in weight mask +++ Number of points for matching = 53249 ++ Local correlation: blok type = 'RHDD(14.76)' *+ WARNING: No output dataset will be calculated ++ OpenMP thread count = 4 volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 ++ allcost output: init #0 - ls = 0.334584 - sp = 0.421822 - mi = -0.363941 - crM = 0.239215 - nmi = 0.905608 - je = 3.4917 - hel = -0.0669546 - crA = 0.489691 - crU = 0.465557 - lss = 0.665416 - lpc = 0.0927771 - lpa = 0.907223 - lpc+ = 0.413355 - ncd = 0.996623 + ls = 0.184126 + sp = 0.307224 + mi = -0.531581 + crM = 0.0790675 + nmi = 0.868615 + je = 3.51437 + hel = -0.106047 + crA = 0.2819 + crU = 0.301908 + lss = 0.815874 + lpc = 0.296009 + lpa = 0.703991 + lpc+ = 0.494411 + ncd = 1 ++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 ++ ########################################################### 3dAllineate -source sub-03_ses-retest_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped @@ -590,7 +589,7 @@ volume 0 + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + wsinc5 CUBE(5) mask has 1000 points ++ Output dataset ./anat_w_skull_warped+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.2 +++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 2.1 ++ ########################################################### foreach run ( 01 ) 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc @@ -609,30 +608,30 @@ foreach run ( 01 ) ++ Authored by: Emperor Zhark ++ Loading dataset pb03.sub_03.r01.blur+tlrc ++ Forming automask - + Fixed clip level = 698.280457 - + Used gradual clip level = 635.212769 .. 744.364258 - + Number voxels above clip level = 31922 + + Fixed clip level = 698.003235 + + Used gradual clip level = 617.152649 .. 742.589600 + + Number voxels above clip level = 28220 + Clustering voxels ... - + Largest cluster has 31922 voxels + + Largest cluster has 28219 voxels + Clustering voxels ... - + Largest cluster has 31863 voxels - + Filled 53 voxels in small holes; now have 31916 voxels + + Largest cluster has 28153 voxels + + Filled 52 voxels in small holes; now have 28205 voxels + Clustering voxels ... - + Largest cluster has 31916 voxels + + Largest cluster has 28205 voxels + Clustering non-brain voxels ... + Clustering voxels ... - + Largest cluster has 77434 voxels - + Mask now has 31916 voxels + + Largest cluster has 81145 voxels + + Mask now has 28205 voxels ++ Dilating automask + Clustering voxels ... - + Largest cluster has 71995 voxels -++ 37355 voxels in the mask [out of 109350: 34.16%] + + Largest cluster has 76109 voxels +++ 33241 voxels in the mask [out of 109350: 30.40%] ++ first 4 x-planes are zero [from L] -++ last 2 x-planes are zero [from R] -++ first 0 y-planes are zero [from P] -++ last 0 y-planes are zero [from A] -++ first 6 z-planes are zero [from I] -++ last 2 z-planes are zero [from S] +++ last 3 x-planes are zero [from R] +++ first 4 y-planes are zero [from P] +++ last 2 y-planes are zero [from A] +++ first 3 z-planes are zero [from I] +++ last 3 z-planes are zero [from S] ++ Output dataset ./rm.mask_r01+tlrc.BRIK ++ CPU time = 0.280000 sec end @@ -640,7 +639,7 @@ end ++ processing 1 input datasets... ++ padding all datasets by 0 (for dilations) ++ frac 0 over 1 volumes gives min count 0 -++ voxel limits: 0 clipped, 37355 survived, 71995 were zero +++ voxel limits: 0 clipped, 33241 survived, 76109 were zero ++ writing result full_mask.sub_03... ++ Output dataset ./full_mask.sub_03+tlrc.BRIK 3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-retest_T1w_ns+tlrc -prefix rm.resam.anat @@ -658,10 +657,10 @@ tee out.mask_ae_overlap.txt ++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] #A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK #A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) -37355 30574 42077 25852 11503 4722 30.7937 15.4445 0.8844 0.6939 1.0830 +33241 30574 35745 28070 5171 2504 15.5561 8.1900 0.9405 0.9263 0.9667 3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_dice.txt -0.761148 +0.87973 3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ no -frac option: defaulting to -union @@ -684,18 +683,17 @@ foreach run ( 01 ) end 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D -1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_sub_03 -total number of censored TRs (simple form) = 4 -1deval -a motion_sub_03_censor.1D -b outcount_sub_03_censor.1D -expr a*b -set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 +total number of censored TRs (simple form) = 2 +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D -show_trs_uncensored encoded` -1d_tool.py -infile censor_sub_03_combined_2.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor censor_sub_03_combined_2.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 ++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD -++ STAT automask has 94004 voxels (out of 109350 = 86.0%) +++ STAT automask has 100184 voxels (out of 109350 = 91.6%) ++ Skipping check for initial transients ++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ ++ -stim_times using TR=2.5 s for stimulus timing conversion @@ -709,10 +707,10 @@ set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D ++ ** GUESSED ** -stim_times 5 using LOCAL times ------------------------------------------------------------ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task': - 0 0 0 0 0 0.333 0.333 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control': + 0 0 0 0 0 0.333 0.333 -0.5 0.333 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 -++ Number of time points: 238 (before censor) ; 234 (after) +++ Number of time points: 238 (before censor) ; 236 (after) + Number of parameters: 22 [17 baseline ; 5 signal] ++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) ++ Wrote matrix image to file X.jpg @@ -729,34 +727,34 @@ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task ++ (c) Synthesis of sub-model datasets using 3dSynthesize ++ ========================================================== ++ Wrote matrix values to file X.nocensor.xmat.1D -++ ----- Signal+Baseline matrix condition [X] (234x22): 5.25117 ++ VERY GOOD ++ -++ ----- Signal-only matrix condition [X] (234x5): 1.40108 ++ VERY GOOD ++ -++ ----- Baseline-only matrix condition [X] (234x17): 5.14998 ++ VERY GOOD ++ -++ ----- stim_base-only matrix condition [X] (234x12): 3.86898 ++ VERY GOOD ++ -++ ----- polort-only matrix condition [X] (234x5): 1.04487 ++ VERY GOOD ++ -++ +++++ Matrix inverse average error = 2.53435e-15 ++ VERY GOOD ++ -++ Matrix setup time = 0.59 s -++ Calculations starting; elapsed time=1.081 +++ ----- Signal+Baseline matrix condition [X] (236x22): 5.23887 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (236x5): 1.40108 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (236x17): 5.1314 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (236x12): 3.87376 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (236x5): 1.05506 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 2.74977e-15 ++ VERY GOOD ++ +++ Matrix setup time = 0.64 s +++ Calculations starting; elapsed time=1.296 ++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=15.587 -++ Smallest FDR q [0 Full_Fstat] = 1.80302e-13 -++ Smallest FDR q [2 Correct_Task#0_Tstat] = 3.17479e-12 -++ Smallest FDR q [3 Correct_Task_Fstat] = 3.17424e-12 -++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 2.29951e-05 -++ Smallest FDR q [6 Incorrect_Task_Fstat] = 2.29984e-05 -++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.00105465 -++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.00105469 -++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 0.000818031 -++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.000818027 -++ Smallest FDR q [14 Response_Control#0_Tstat] = 5.9968e-13 -++ Smallest FDR q [15 Response_Control_Fstat] = 5.99731e-13 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.00156636 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.00156632 +++ Calculations finished; elapsed time=15.878 +++ Smallest FDR q [0 Full_Fstat] = 2.20611e-13 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 4.23368e-12 +++ Smallest FDR q [3 Correct_Task_Fstat] = 4.23389e-12 +++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 1.38672e-05 +++ Smallest FDR q [6 Incorrect_Task_Fstat] = 1.38678e-05 +++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.000272278 +++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.000272271 +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 0.00181556 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.0018156 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 7.47239e-13 +++ Smallest FDR q [15 Response_Control_Fstat] = 7.47258e-13 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.000154149 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.000154153 ++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + created 13 FDR curves in bucket header ++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK ++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK -++ #Flops=4.28212e+10 Average Dot Product=37.4548 +++ #Flops=4.31862e+10 Average Dot Product=37.4801 if ( 0 != 0 ) then 1d_tool.py -show_cormat_warnings -infile X.xmat.1D tee out.cormat_warn.txt @@ -765,16 +763,16 @@ Warnings regarding Correlation Matrix: X.xmat.1D severity correlation cosine regressor pair -------- ----------- ------ ---------------------------------------- - medium: 0.446 0.539 ( 5 vs. 6) Correct_Task#0 vs. Incorrect_Task#0 + medium: 0.447 0.539 ( 5 vs. 6) Correct_Task#0 vs. Incorrect_Task#0 3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD ++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 0.8 s -3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..229,232..237] +++ elapsed time = 1.2 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..237] ++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.signal.all+tlrc.BRIK -3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..229,232..237] +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..237] ++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.noise.all+tlrc.BRIK @@ -788,14 +786,14 @@ Warnings regarding Correlation Matrix: X.xmat.1D ++ Output dataset ./rm.errts.unit+tlrc.BRIK 3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc ++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -+++ 37355 voxels survive the mask ++++ 33241 voxels survive the mask 3dTstat -sos -prefix - gmean.errts.unit.1D' ++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D --- GCOR = 0.104389 +-- GCOR = 0.109705 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP ++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: A cast of thousands @@ -824,16 +822,16 @@ foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..229,232..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..229,232..237] +if ( 2..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..237] ++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 37355 -*+ WARNING: removed 272 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 234 time points - + detrending done (2.77 CPU s thus far) -++ start ACF calculations out to radius = 28.27 mm - + ACF done (75.10 CPU s thus far) +++ Number of voxels in mask = 33241 +*+ WARNING: removed 220 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 236 time points + + detrending done (2.52 CPU s thus far) +++ start ACF calculations out to radius = 27.83 mm + + ACF done (64.84 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: RWC et al. @@ -854,24 +852,24 @@ set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.64237 5.36951 13.6925 13.7381 -average epits ACF blurs: 0.64237 5.36951 13.6925 13.7381 -echo 0.64237 5.36951 13.6925 13.7381 # epits ACF blur estimates +echo average epits ACF blurs: 0.63099 5.37461 12.731 13.5951 +average epits ACF blurs: 0.63099 5.37461 12.731 13.5951 +echo 0.63099 5.37461 12.731 13.5951 # epits ACF blur estimates touch blur.errts.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..229,232..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..229,232..237] +if ( 2..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..237] ++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 37355 -*+ WARNING: removed 272 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 234 time points - + detrending done (2.71 CPU s thus far) -++ start ACF calculations out to radius = 27.79 mm - + ACF done (68.58 CPU s thus far) +++ Number of voxels in mask = 33241 +*+ WARNING: removed 220 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 236 time points + + detrending done (2.49 CPU s thus far) +++ start ACF calculations out to radius = 27.36 mm + + ACF done (64.46 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: RWC et al. @@ -892,15 +890,15 @@ set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.694349 5.35765 13.035 13.4143 -average errts ACF blurs: 0.694349 5.35765 13.035 13.4143 -echo 0.694349 5.35765 13.035 13.4143 # errts ACF blur estimates +echo average errts ACF blurs: 0.694841 5.25415 13.1837 13.2188 +average errts ACF blurs: 0.694841 5.25415 13.1837 13.2188 +echo 0.694841 5.25415 13.1837 13.2188 # errts ACF blur estimates gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD -gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 ++ writing ss review basic: @ss_review_basic ++ writing ss review driver: @ss_review_driver ++ writing ss review drive commands: @ss_review_driver_commands -rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.out.cen.r01.1D rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD tee out.ss_review.sub_03.txt if ( -e @ss_review_basic ) ./@ss_review_basic ./@ss_review_basic @@ -912,28 +910,28 @@ final anatomy dset : anat_final.sub_03+tlrc.HEAD final stats dset : stats.sub_03+tlrc.HEAD final voxel resolution : 4.000000 4.000000 4.000000 -motion limit : 0.3 -num TRs above mot limit : 2 +motion limit : 0.5 +num TRs above mot limit : 1 average motion (per TR) : 0.0937926 -average censored motion : 0.0872231 +average censored motion : 0.0889158 max motion displacement : 1.69106 max censored displacement : 1.69012 -outlier limit : 0.5 +outlier limit : 0.1 average outlier frac (TR) : 0.00559353 num TRs above out limit : 1 num runs found : 1 num TRs per run : 238 -num TRs per run (applied) : 234 -num TRs per run (censored): 4 -fraction censored per run : 0.0168067 +num TRs per run (applied) : 236 +num TRs per run (censored): 2 +fraction censored per run : 0.00840336 TRs total (uncensored) : 238 -TRs total : 234 +TRs total : 236 degrees of freedom used : 22 -degrees of freedom left : 212 +degrees of freedom left : 214 -TRs censored : 4 -censor fraction : 0.016807 +TRs censored : 2 +censor fraction : 0.008403 num regs of interest : 5 num TRs per stim (orig) : 78 56 46 19 79 num TRs censored per stim : 0 0 0 0 0 @@ -941,11 +939,11 @@ fraction TRs censored : 0.000 0.000 0.000 0.000 0.000 ave mot per sresp (orig) : 0.086607 0.082908 0.080591 0.071212 0.078827 ave mot per sresp (cens) : 0.086607 0.082908 0.080591 0.071212 0.078827 -TSNR average : 231.468 -global correlation (GCOR) : 0.104389 -anat/EPI mask Dice coef : 0.761148 -maximum F-stat (masked) : 48.4589 -blur estimates (ACF) : 0.694349 5.35765 13.035 +TSNR average : 234.187 +global correlation (GCOR) : 0.109705 +anat/EPI mask Dice coef : 0.87973 +maximum F-stat (masked) : 48.3344 +blur estimates (ACF) : 0.694841 5.25415 13.1837 blur estimates (FWHM) : 0 0 0 ** TR #0 outliers: possible pre-steady state TRs in run 01 @@ -953,4 +951,4 @@ blur estimates (FWHM) : 0 0 0 cd .. echo execution finished: `date` date -execution finished: Thu Aug 3 20:49:40 EDT 2017 +execution finished: Thu Aug 3 22:30:59 EDT 2017 diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 index 04545b4..2004341 100755 --- a/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Thu Aug 3 20:38:10 2017" +echo "auto-generated by afni_proc.py, Thu Aug 3 22:21:05 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -79,11 +79,6 @@ foreach run ( $runs ) 3dToutcount -automask -fraction -polort 4 -legendre \ pb00.$subj.r$run.tcat+orig > outcount.r$run.1D - # censor outlier TRs per run, ignoring the first 0 TRs - # - censor when more than 0.5 of automask voxels are outliers - # - step() defines which TRs to remove via censoring - 1deval -a outcount.r$run.1D -expr "1-step(a-0.5)" > rm.out.cen.r$run.1D - # outliers at TR 0 might suggest pre-steady state TRs if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ @@ -94,9 +89,6 @@ end # catenate outlier counts into a single time series cat outcount.r*.1D > outcount_rall.1D -# catenate outlier censor files into a single time series -cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D - # ================================= tshift ================================= # time shift data so all slice timing is the same foreach run ( $runs ) @@ -115,7 +107,6 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ -save_skullstrip -suffix _al_junk \ -epi vr_base+orig -epi_base 0 \ -epi_strip 3dAutomask \ - -cost nmi \ -volreg off -tshift off # ================================== tlrc ================================== @@ -280,20 +271,16 @@ end # create censor file motion_${subj}_censor.1D, for censoring motion 1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ -show_censor_count -censor_prev_TR \ - -censor_motion 0.3 motion_${subj} - -# combine multiple censor files -1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \ - -expr "a*b" > censor_${subj}_combined_2.1D + -censor_motion 0.5 motion_${subj} # note TRs that were not censored -set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -show_trs_uncensored encoded` # ------------------------------ # run the regression analysis 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ - -censor censor_${subj}_combined_2.1D \ + -censor motion_${subj}_censor.1D \ -polort 4 \ -num_stimts 17 \ -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D 'GAM' \ @@ -320,7 +307,7 @@ set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -449,7 +436,7 @@ gen_epi_review.py -script @epi_review.$subj \ # generate scripts to review single subject results # (try with defaults, but do not allow bad exit status) -gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 # ========================== auto block: finalize ========================== @@ -476,9 +463,8 @@ echo "execution finished: `date`" # /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ # -tcat_remove_first_trs 0 -dsets \ # /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ -# -align_opts_aea -cost nmi -tlrc_base MNI_avg152T1+tlrc -volreg_align_to \ -# third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 \ -# -regress_stim_times \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ @@ -486,9 +472,9 @@ echo "execution finished: `date`" # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ # -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ # No_Response_Task Response_Control -regress_basis GAM \ -# -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ -# -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ -# 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ -# -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 \ -# Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ -# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ +# -regress_opts_3dD -gltsym 'SYM: 0.333*Correct_Task \ +# +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control \ +# -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ +# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd index ff98bd9..a997d7b 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd +++ b/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd @@ -1,4 +1,4 @@ -# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor censor_sub_03_combined_2.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ diff --git a/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 index 2787c4b..70784fa 100755 --- a/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 @@ -1,7 +1,7 @@ #!/usr/bin/env tcsh # created by uber_subject.py: version 0.40 (March 30, 2017) -# creation date: Thu Aug 3 20:35:15 2017 +# creation date: Thu Aug 3 22:01:15 2017 # set data directories set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground @@ -19,7 +19,6 @@ afni_proc.py -subj_id $subj \ -copy_anat $anat_dir/sub-03_ses-test_T1w.nii.gz \ -tcat_remove_first_trs 0 \ -dsets $epi_dir/sub-03_ses-test_task-linebisection_bold.nii.gz \ - -align_opts_aea -cost nmi \ -tlrc_base MNI_avg152T1+tlrc \ -volreg_align_to third \ -volreg_align_e2a \ @@ -40,8 +39,8 @@ afni_proc.py -subj_id $subj \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ - -glt_label 1 Landmark-Detection \ + +0.333*No_Response_Task -0.5*Response_Control \ + -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 index dc380fd..8b80dbd 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 @@ -1,6 +1,5 @@ uber_subject.py \ -cvar subj_dir subject_results/group.test/subj.sub_03 \ - -svar align_cost nmi \ -svar anat \ /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ \ @@ -10,7 +9,7 @@ uber_subject.py \ -svar gid test \ -svar gltsym '0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ -svar gltsym_label Landmark-Detection \ -svar outlier_limit 0.5 \ -svar regress_mot_deriv yes \ diff --git a/Exp-1/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 index e3af51b..bb99a95 100755 --- a/Exp-1/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Thu Aug 3 20:35:22 2017" +echo "auto-generated by afni_proc.py, Thu Aug 3 22:01:23 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -115,7 +115,6 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ -save_skullstrip -suffix _al_junk \ -epi vr_base+orig -epi_base 0 \ -epi_strip 3dAutomask \ - -cost nmi \ -volreg off -tshift off # ================================== tlrc ================================== @@ -319,7 +318,7 @@ set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -475,9 +474,8 @@ echo "execution finished: `date`" # /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ # -tcat_remove_first_trs 0 -dsets \ # /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ -# -align_opts_aea -cost nmi -tlrc_base MNI_avg152T1+tlrc -volreg_align_to \ -# third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 \ -# -regress_stim_times \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ @@ -488,6 +486,6 @@ echo "execution finished: `date`" # -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ # -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ # 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ -# -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 \ +# -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 \ # Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ # -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 index 2787c4b..50f5fd0 100755 --- a/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 @@ -1,7 +1,7 @@ #!/usr/bin/env tcsh # created by uber_subject.py: version 0.40 (March 30, 2017) -# creation date: Thu Aug 3 20:35:15 2017 +# creation date: Thu Aug 3 22:01:15 2017 # set data directories set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground @@ -19,7 +19,6 @@ afni_proc.py -subj_id $subj \ -copy_anat $anat_dir/sub-03_ses-test_T1w.nii.gz \ -tcat_remove_first_trs 0 \ -dsets $epi_dir/sub-03_ses-test_task-linebisection_bold.nii.gz \ - -align_opts_aea -cost nmi \ -tlrc_base MNI_avg152T1+tlrc \ -volreg_align_to third \ -volreg_align_e2a \ @@ -35,13 +34,12 @@ afni_proc.py -subj_id $subj \ Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ Response_Control \ -regress_basis 'GAM' \ - -regress_censor_motion 0.3 \ - -regress_censor_outliers 0.5 \ + -regress_censor_motion 0.5 \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ - -glt_label 1 Landmark-Detection \ + +0.333*No_Response_Task -0.5*Response_Control \ + -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 index 5ce52e3..7e616bd 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 @@ -1,3 +1,11 @@ +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat +set epi_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func +set subj = sub_03 +set group_id = test +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control + -0.5*No_Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig -- tcat: reps is now 238 ++ updating polort to 4, from run len 595.0 s diff --git a/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 index 9ad2393..e668689 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 @@ -1,10 +1,10 @@ -echo auto-generated by afni_proc.py, Thu Aug 3 20:35:22 2017 -auto-generated by afni_proc.py, Thu Aug 3 20:35:22 2017 +echo auto-generated by afni_proc.py, Thu Aug 3 22:13:37 2017 +auto-generated by afni_proc.py, Thu Aug 3 22:13:37 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Thu Aug 3 20:39:28 EDT 2017 +execution started: Thu Aug 3 22:14:07 EDT 2017 afni -ver Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) afni_history -check_date 23 Sep 2016 @@ -25,7 +25,7 @@ cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct ++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] 3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[0..$] ++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 1.7 s +++ elapsed time = 1.5 s set tr_counts = ( 238 ) cd sub_03.results touch out.pre_ss_warn.txt @@ -41,14 +41,12 @@ foreach run ( 01 ) See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. ++ 17837 voxels passed mask/clip -1deval -a outcount.r01.1D -expr 1-step(a-0.5) if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then 1deval -a outcount.r01.1D{0} -expr step(a-0.4) echo ** TR #0 outliers: possible pre-steady state TRs in run 01 endif end cat outcount.r01.1D -cat rm.out.cen.r01.1D foreach run ( 01 ) 3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig ++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -65,7 +63,7 @@ foreach run ( 01 ) end 3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] ++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -cost nmi -volreg off -tshift off +align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off #++ align_epi_anat version: 1.57 #++ turning off volume registration #Script is running (command trimmed): @@ -74,7 +72,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf 3dAttribute DELTA ./vr_base+orig #Script is running (command trimmed): 3dAttribute DELTA ./sub-03_ses-test_T1w+orig -#++ Multi-cost is nmi +#++ Multi-cost is lpc #++ Removing all the temporary files #Script is running: \rm -f ./__tt_vr_base* @@ -96,7 +94,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ Oblique dataset:./__tt_sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. #Script is running (command trimmed): 3dinfo ./__tt_sub-03_ses-test_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' -#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig is ***oblique**** +#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig is ***oblique**** #Script is running (command trimmed): 3dAttribute DELTA ./__tt_sub-03_ses-test_T1w_ns+orig #++ Spacing for anat to oblique epi alignment is 1.000000 @@ -159,7 +157,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1890.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1890.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig #Script is running (command trimmed): 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1890.000000))' ++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -167,7 +165,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK #++ Aligning anat data to epi data #Script is running (command trimmed): - 3dAllineate -nmi -wtprefix ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass + 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass ++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns_ob+orig.HEAD @@ -178,6 +176,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ 1155874 voxels [7.0%] in weight mask ++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal+orig.BRIK ++ Number of points for matching = 1155874 +++ Local correlation: blok type = 'RHDD(6.54321)' ++ shift param auto-range: -89.2..89.2 -69.3..69.3 -86.7..86.7 + Range param#4 [z-angle] = -6.000000 .. 6.000000 + Range param#5 [x-angle] = -6.000000 .. 6.000000 @@ -188,7 +187,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf + 12 free parameters ++ Normalized convergence radius = 0.001000 ++ OpenMP thread count = 4 -++ ======= Allineation of 1 sub-bricks using Normalized MI [H(b,s)/(H(b)+H(s))] ======= +++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= ++ ========== sub-brick #0 ========== [total CPU to here=9.7 s] ++ *** Fine pass begins *** + * Enter alignment setup routine @@ -197,30 +196,30 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf + - copying weight image + - using 1155874 points from base image [use_all=0] + * Exit alignment setup routine - + - histogram: source clip 184.345 .. 796.556; base clip 497.178 .. 2090 - + - versus source range 0 .. 698.5; base range 0 .. 2299.05 - + - Initial cost = 0.997036 + + 1095215 total points stored in 2075 'RHDD(6.54321)' bloks + + - Initial cost = -0.096907 + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 -************************************************* - + - Finalish cost = 0.995029 ; 213 funcs - + - histogram: source clip 172.628 .. 745.927; base clip 497.178 .. 2090 - + - versus source range 0 .. 698.5; base range 0 .. 2299.05 -* - + - Final cost = 0.995029 ; 120 funcs +*************************************************************************************************************************************************************************************************************************************************************************************************** + + - Finalish cost = -0.235911 ; 645 funcs +** + + - Final cost = -0.235912 ; 97 funcs + Final fine fit Parameters: - x-shift= 1.8095 y-shift= 3.5058 z-shift= 2.8843 - z-angle=-0.3971 x-angle= 0.2785 y-angle= 2.8435 - x-scale= 0.9263 y-scale= 1.1929 z-scale= 0.9578 - y/x-shear=-0.0128 z/x-shear=-0.0069 z/y-shear= 0.0283 - + - Fine net CPU time = 26.1 s + x-shift= 0.2099 y-shift=-0.6560 z-shift=-1.7075 + z-angle=-0.6314 x-angle= 4.7459 y-angle=-1.0126 + x-scale= 0.9677 y-scale= 0.9751 z-scale= 1.0200 + y/x-shear=-0.0038 z/x-shear= 0.0093 z/y-shear= 0.0929 + + - Fine net CPU time = 50.4 s ++ Computing output image -++ image warp: parameters = 1.8095 3.5058 2.8843 -0.3971 0.2785 2.8435 0.9263 1.1929 0.9578 -0.0128 -0.0069 0.0283 +++ image warp: parameters = 0.2099 -0.6560 -1.7075 -0.6314 4.7459 -1.0126 0.9677 0.9751 1.0200 -0.0038 0.0093 0.0929 ++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk+orig.BRIK ++ Wrote -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 37.9 sec Elapsed = 26.5 +++ 3dAllineate: total CPU time = 62.5 sec Elapsed = 39.9 ++ ########################################################### ++ # Please check results visually for alignment quality # ++ ########################################################### +++ # '-autoweight' is recommended when using -lpc or -lpa # +++ # If your results are not good, please try again. # +++ ########################################################### #Script is running (command trimmed): cat_matvec -ONELINE ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D -I > ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D #++ Combining anat to epi and oblique transformations @@ -256,12 +255,12 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf + * Exit alignment setup routine ++ using -1Dmatrix_apply ++ Computing output image -++ image warp: parameters = 0.9251 -0.0819 -0.0018 2.8288 0.0321 1.1915 -0.0102 -33.9090 0.0054 -0.0269 0.9581 18.1316 +++ image warp: parameters = 0.9643 -0.0770 -0.0643 8.3030 0.0414 0.9701 -0.0701 -8.0767 0.0578 0.0003 1.0212 -4.7196 ++ Output dataset ./sub-03_ses-test_T1w_al_junk+orig.BRIK -++ 3dAllineate: total CPU time = 2.1 sec Elapsed = 1.7 +++ 3dAllineate: total CPU time = 2.4 sec Elapsed = 4.6 ++ ########################################################### #++ Creating final output: skullstripped anat data -copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig +copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig #Script is running (command trimmed): 3dcopy ./__tt_sub-03_ses-test_T1w_ns+orig sub-03_ses-test_T1w_ns ++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -271,7 +270,7 @@ copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/subject_resu #Script is running (command trimmed): 3dNotes -h "align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 \ - -epi_strip 3dAutomask -cost nmi -volreg off -tshift off" \ + -epi_strip 3dAutomask -volreg off -tshift off" \ ./sub-03_ses-test_T1w_al_junk+orig #++ Removing all the temporary files @@ -446,7 +445,7 @@ foreach run ( 01 ) + 3319 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=9.71 s [=0.0408 s/sub-brick] +++ CPU time for realignment=10 s [=0.0421 s/sub-brick] ++ Min : roll=-0.125 pitch=-0.838 yaw=-0.100 dS=-1.314 dL=-0.122 dP=-0.602 ++ Mean: roll=+0.244 pitch=-0.353 yaw=+1.492 dS=+1.594 dL=+0.625 dP=-0.273 ++ Max : roll=+0.752 pitch=+0.977 yaw=+2.780 dS=+2.627 dL=+1.582 dP=+0.307 @@ -482,7 +481,7 @@ cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1 ++ OpenMP thread count = 4 ++ ========== Applying transformation to 238 sub-bricks ========== volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 5.8 sec Elapsed = 4.4 +++ 3dAllineate: total CPU time = 6.4 sec Elapsed = 16.3 ++ ########################################################### 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 ++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -498,7 +497,7 @@ volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20. ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (LPI); source=Left handed (RPI) ++ Output dataset ./rm.epi.1.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.4 sec Elapsed = 3.1 +++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 4.3 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc ++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox @@ -547,32 +546,32 @@ tee out.allcostX.txt ++ Base dataset: ./final_epi_vr_base+tlrc.HEAD ++ Loading datasets ++ 223015 voxels in source_automask+0 -++ Zero-pad: xbot=1 xtop=1 -++ Zero-pad: ybot=4 ytop=4 -++ Zero-pad: zbot=0 ztop=1 +++ Zero-pad: xbot=2 xtop=2 +++ Zero-pad: ybot=0 ytop=1 +++ Zero-pad: zbot=1 ztop=1 ++ Computing -autobox -++ 119923 voxels [89.5%] in weight mask -++ Number of points for matching = 56363 +++ 113223 voxels [89.4%] in weight mask +++ Number of points for matching = 53214 ++ Local correlation: blok type = 'RHDD(14.76)' *+ WARNING: No output dataset will be calculated ++ OpenMP thread count = 4 volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 ++ allcost output: init #0 - ls = 0.319992 - sp = 0.392466 - mi = -0.430206 - crM = 0.204696 - nmi = 0.897455 - je = 3.76509 - hel = -0.0823942 - crA = 0.454393 - crU = 0.412241 - lss = 0.680008 - lpc = 0.12108 - lpa = 0.87892 - lpc+ = 0.416704 - ncd = 1 -++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 + ls = 0.183754 + sp = 0.30567 + mi = -0.534639 + crM = 0.0839806 + nmi = 0.868199 + je = 3.52175 + hel = -0.107071 + crA = 0.290078 + crU = 0.302909 + lss = 0.816246 + lpc = 0.339594 + lpa = 0.660406 + lpc+ = 0.540057 + ncd = 0.974675 +++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.5 ++ ########################################################### 3dAllineate -source sub-03_ses-test_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped ++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] @@ -600,7 +599,7 @@ volume 0 + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + wsinc5 CUBE(5) mask has 1000 points ++ Output dataset ./anat_w_skull_warped+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.2 +++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.4 ++ ########################################################### foreach run ( 01 ) 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc @@ -619,38 +618,38 @@ foreach run ( 01 ) ++ Authored by: Emperor Zhark ++ Loading dataset pb03.sub_03.r01.blur+tlrc ++ Forming automask - + Fixed clip level = 710.685547 - + Used gradual clip level = 648.283936 .. 804.968506 - + Number voxels above clip level = 30766 + + Fixed clip level = 710.102234 + + Used gradual clip level = 629.363342 .. 793.875061 + + Number voxels above clip level = 28228 + Clustering voxels ... - + Largest cluster has 30766 voxels + + Largest cluster has 28228 voxels + Clustering voxels ... - + Largest cluster has 30698 voxels - + Filled 56 voxels in small holes; now have 30754 voxels + + Largest cluster has 28140 voxels + + Filled 49 voxels in small holes; now have 28189 voxels + Clustering voxels ... - + Largest cluster has 30753 voxels + + Largest cluster has 28189 voxels + Clustering non-brain voxels ... + Clustering voxels ... - + Largest cluster has 78597 voxels - + Mask now has 30753 voxels + + Largest cluster has 81161 voxels + + Mask now has 28189 voxels ++ Dilating automask + Clustering voxels ... - + Largest cluster has 73337 voxels -++ 36013 voxels in the mask [out of 109350: 32.93%] + + Largest cluster has 76139 voxels +++ 33211 voxels in the mask [out of 109350: 30.37%] ++ first 4 x-planes are zero [from L] -++ last 5 x-planes are zero [from R] -++ first 0 y-planes are zero [from P] -++ last 0 y-planes are zero [from A] -++ first 6 z-planes are zero [from I] +++ last 3 x-planes are zero [from R] +++ first 4 y-planes are zero [from P] +++ last 3 y-planes are zero [from A] +++ first 3 z-planes are zero [from I] ++ last 3 z-planes are zero [from S] ++ Output dataset ./rm.mask_r01+tlrc.BRIK -++ CPU time = 0.280000 sec +++ CPU time = 0.290000 sec end 3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 ++ processing 1 input datasets... ++ padding all datasets by 0 (for dilations) ++ frac 0 over 1 volumes gives min count 0 -++ voxel limits: 0 clipped, 36013 survived, 73337 were zero +++ voxel limits: 0 clipped, 33211 survived, 76139 were zero ++ writing result full_mask.sub_03... ++ Output dataset ./full_mask.sub_03+tlrc.BRIK 3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-test_T1w_ns+tlrc -prefix rm.resam.anat @@ -668,10 +667,10 @@ tee out.mask_ae_overlap.txt ++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] #A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK #A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) -36013 30704 40588 26129 9884 4575 27.4456 14.9003 1.0267 0.6317 1.1274 +33211 30704 36000 27915 5296 2789 15.9465 9.0835 0.9461 0.9206 0.9824 3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_dice.txt -0.783279 +0.873504 3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ no -frac option: defaulting to -union @@ -694,18 +693,17 @@ foreach run ( 01 ) end 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D -1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_sub_03 -total number of censored TRs (simple form) = 44 -1deval -a motion_sub_03_censor.1D -b outcount_sub_03_censor.1D -expr a*b -set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 +total number of censored TRs (simple form) = 21 +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D -show_trs_uncensored encoded` -1d_tool.py -infile censor_sub_03_combined_2.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor censor_sub_03_combined_2.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 ++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD -++ STAT automask has 93751 voxels (out of 109350 = 85.7%) +++ STAT automask has 97119 voxels (out of 109350 = 88.8%) ++ Skipping check for initial transients ++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ ++ -stim_times using TR=2.5 s for stimulus timing conversion @@ -719,10 +717,10 @@ set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D ++ ** GUESSED ** -stim_times 5 using LOCAL times ------------------------------------------------------------ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task': - 0 0 0 0 0 0.333 0.333 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control': + 0 0 0 0 0 0.333 0.333 -0.5 0.333 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 -++ Number of time points: 238 (before censor) ; 194 (after) +++ Number of time points: 238 (before censor) ; 217 (after) + Number of parameters: 22 [17 baseline ; 5 signal] ++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) ++ Wrote matrix image to file X.jpg @@ -739,34 +737,34 @@ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task ++ (c) Synthesis of sub-model datasets using 3dSynthesize ++ ========================================================== ++ Wrote matrix values to file X.nocensor.xmat.1D -++ ----- Signal+Baseline matrix condition [X] (194x22): 8.14751 ++ VERY GOOD ++ -++ ----- Signal-only matrix condition [X] (194x5): 1.4614 ++ VERY GOOD ++ -++ ----- Baseline-only matrix condition [X] (194x17): 8.00108 ++ VERY GOOD ++ -++ ----- stim_base-only matrix condition [X] (194x12): 6.40992 ++ VERY GOOD ++ -++ ----- polort-only matrix condition [X] (194x5): 1.11242 ++ VERY GOOD ++ -++ +++++ Matrix inverse average error = 1.22155e-14 ++ VERY GOOD ++ -++ Matrix setup time = 0.60 s -++ Calculations starting; elapsed time=1.217 +++ ----- Signal+Baseline matrix condition [X] (217x22): 7.87414 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (217x5): 1.46311 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (217x17): 7.75168 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (217x12): 6.17475 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (217x5): 1.09587 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 1.12762e-14 ++ VERY GOOD ++ +++ Matrix setup time = 0.72 s +++ Calculations starting; elapsed time=1.442 ++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=13.567 -++ Smallest FDR q [0 Full_Fstat] = 1.14224e-12 -++ Smallest FDR q [2 Correct_Task#0_Tstat] = 3.09596e-09 -++ Smallest FDR q [3 Correct_Task_Fstat] = 3.09588e-09 -*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.312787 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.312288 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.300188 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [9 No_Response_Control_Fstat] = 0.299698 ==> few true single voxel detections -++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 2.9327e-11 -++ Smallest FDR q [12 No_Response_Task_Fstat] = 2.9328e-11 -++ Smallest FDR q [14 Response_Control#0_Tstat] = 1.66531e-07 -++ Smallest FDR q [15 Response_Control_Fstat] = 1.66531e-07 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 2.95886e-08 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 2.95896e-08 +++ Calculations finished; elapsed time=16.076 +++ Smallest FDR q [0 Full_Fstat] = 6.90525e-13 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 1.79484e-09 +++ Smallest FDR q [3 Correct_Task_Fstat] = 1.79495e-09 +*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.33841 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.337718 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.107315 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [9 No_Response_Control_Fstat] = 0.107315 ==> few true single voxel detections +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 4.83707e-12 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 4.83707e-12 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 1.04292e-06 +++ Smallest FDR q [15 Response_Control_Fstat] = 1.04299e-06 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 4.28411e-07 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 4.28347e-07 ++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + created 13 FDR curves in bucket header ++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK ++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK -++ #Flops=3.55203e+10 Average Dot Product=36.8509 +++ #Flops=3.97183e+10 Average Dot Product=37.2229 if ( 0 != 0 ) then 1d_tool.py -show_cormat_warnings -infile X.xmat.1D tee out.cormat_warn.txt @@ -775,16 +773,16 @@ Warnings regarding Correlation Matrix: X.xmat.1D severity correlation cosine regressor pair -------- ----------- ------ ---------------------------------------- - medium: 0.561 0.640 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 + medium: 0.566 0.642 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD ++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 1.1 s -3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237] +++ elapsed time = 1.5 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] ++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.signal.all+tlrc.BRIK -3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237] +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] ++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.noise.all+tlrc.BRIK @@ -798,14 +796,14 @@ Warnings regarding Correlation Matrix: X.xmat.1D ++ Output dataset ./rm.errts.unit+tlrc.BRIK 3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc ++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -+++ 36013 voxels survive the mask ++++ 33211 voxels survive the mask 3dTstat -sos -prefix - gmean.errts.unit.1D' ++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D --- GCOR = 0.140811 +-- GCOR = 0.137338 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP ++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: A cast of thousands @@ -834,16 +832,16 @@ foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237] +if ( 2..50,60,61,68..101,104..160,163..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] ++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 36013 -*+ WARNING: removed 269 voxels from mask because they are constant in time -++ detrending start: 15 baseline funcs, 194 time points - + detrending done (1.90 CPU s thus far) -++ start ACF calculations out to radius = 28.03 mm - + ACF done (56.24 CPU s thus far) +++ Number of voxels in mask = 33211 +*+ WARNING: removed 235 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 217 time points + + detrending done (2.29 CPU s thus far) +++ start ACF calculations out to radius = 27.77 mm + + ACF done (57.21 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: RWC et al. @@ -864,24 +862,24 @@ set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.656416 5.22886 14.4219 13.5135 -average epits ACF blurs: 0.656416 5.22886 14.4219 13.5135 -echo 0.656416 5.22886 14.4219 13.5135 # epits ACF blur estimates +echo average epits ACF blurs: 0.643102 5.25242 13.8038 13.5137 +average epits ACF blurs: 0.643102 5.25242 13.8038 13.5137 +echo 0.643102 5.25242 13.8038 13.5137 # epits ACF blur estimates touch blur.errts.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..47,60,61,69..72,75..94,97..100,104..137,143..160,164..186,191,194..225,228..237] +if ( 2..50,60,61,68..101,104..160,163..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] ++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 36013 -*+ WARNING: removed 269 voxels from mask because they are constant in time -++ detrending start: 15 baseline funcs, 194 time points - + detrending done (1.91 CPU s thus far) -++ start ACF calculations out to radius = 27.62 mm - + ACF done (53.59 CPU s thus far) +++ Number of voxels in mask = 33211 +*+ WARNING: removed 235 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 217 time points + + detrending done (2.32 CPU s thus far) +++ start ACF calculations out to radius = 27.41 mm + + ACF done (57.85 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++ Authored by: RWC et al. @@ -902,15 +900,15 @@ set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.712442 5.22743 14.2881 13.2541 -average errts ACF blurs: 0.712442 5.22743 14.2881 13.2541 -echo 0.712442 5.22743 14.2881 13.2541 # errts ACF blur estimates +echo average errts ACF blurs: 0.694971 5.17822 14.3851 13.2323 +average errts ACF blurs: 0.694971 5.17822 14.3851 13.2323 +echo 0.694971 5.17822 14.3851 13.2323 # errts ACF blur estimates gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD -gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 ++ writing ss review basic: @ss_review_basic ++ writing ss review driver: @ss_review_driver ++ writing ss review drive commands: @ss_review_driver_commands -rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.out.cen.r01.1D rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD tee out.ss_review.sub_03.txt if ( -e @ss_review_basic ) ./@ss_review_basic ./@ss_review_basic @@ -922,40 +920,40 @@ final anatomy dset : anat_final.sub_03+tlrc.HEAD final stats dset : stats.sub_03+tlrc.HEAD final voxel resolution : 4.000000 4.000000 4.000000 -motion limit : 0.3 -num TRs above mot limit : 29 +motion limit : 0.5 +num TRs above mot limit : 13 average motion (per TR) : 0.179191 -average censored motion : 0.111049 +average censored motion : 0.129595 max motion displacement : 5.04394 max censored displacement : 3.96802 -outlier limit : 0.5 +outlier limit : 0.1 average outlier frac (TR) : 0.0152516 -num TRs above out limit : 1 +num TRs above out limit : 8 num runs found : 1 num TRs per run : 238 -num TRs per run (applied) : 194 -num TRs per run (censored): 44 -fraction censored per run : 0.184874 +num TRs per run (applied) : 217 +num TRs per run (censored): 21 +fraction censored per run : 0.0882353 TRs total (uncensored) : 238 -TRs total : 194 +TRs total : 217 degrees of freedom used : 22 -degrees of freedom left : 172 +degrees of freedom left : 195 -TRs censored : 44 -censor fraction : 0.184874 +TRs censored : 21 +censor fraction : 0.088235 num regs of interest : 5 num TRs per stim (orig) : 71 43 64 28 79 -num TRs censored per stim : 5 0 19 9 17 -fraction TRs censored : 0.070 0.000 0.297 0.321 0.215 +num TRs censored per stim : 0 0 13 6 12 +fraction TRs censored : 0.000 0.000 0.203 0.214 0.152 ave mot per sresp (orig) : 0.124806 0.112975 0.230781 0.273948 0.190656 -ave mot per sresp (cens) : 0.113477 0.112975 0.095777 0.114754 0.093013 +ave mot per sresp (cens) : 0.124806 0.112975 0.122112 0.144313 0.107954 -TSNR average : 202.889 -global correlation (GCOR) : 0.140811 -anat/EPI mask Dice coef : 0.783279 -maximum F-stat (masked) : 33.52 -blur estimates (ACF) : 0.712442 5.22743 14.2881 +TSNR average : 196.396 +global correlation (GCOR) : 0.137338 +anat/EPI mask Dice coef : 0.873504 +maximum F-stat (masked) : 39.2089 +blur estimates (ACF) : 0.694971 5.17822 14.3851 blur estimates (FWHM) : 0 0 0 ** TR #0 outliers: possible pre-steady state TRs in run 01 @@ -963,4 +961,4 @@ blur estimates (FWHM) : 0 0 0 cd .. echo execution finished: `date` date -execution finished: Thu Aug 3 20:43:53 EDT 2017 +execution finished: Thu Aug 3 22:20:22 EDT 2017 diff --git a/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 index e3af51b..3c5e106 100755 --- a/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Thu Aug 3 20:35:22 2017" +echo "auto-generated by afni_proc.py, Thu Aug 3 22:13:37 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -79,11 +79,6 @@ foreach run ( $runs ) 3dToutcount -automask -fraction -polort 4 -legendre \ pb00.$subj.r$run.tcat+orig > outcount.r$run.1D - # censor outlier TRs per run, ignoring the first 0 TRs - # - censor when more than 0.5 of automask voxels are outliers - # - step() defines which TRs to remove via censoring - 1deval -a outcount.r$run.1D -expr "1-step(a-0.5)" > rm.out.cen.r$run.1D - # outliers at TR 0 might suggest pre-steady state TRs if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ @@ -94,9 +89,6 @@ end # catenate outlier counts into a single time series cat outcount.r*.1D > outcount_rall.1D -# catenate outlier censor files into a single time series -cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D - # ================================= tshift ================================= # time shift data so all slice timing is the same foreach run ( $runs ) @@ -115,7 +107,6 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ -save_skullstrip -suffix _al_junk \ -epi vr_base+orig -epi_base 0 \ -epi_strip 3dAutomask \ - -cost nmi \ -volreg off -tshift off # ================================== tlrc ================================== @@ -280,20 +271,16 @@ end # create censor file motion_${subj}_censor.1D, for censoring motion 1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ -show_censor_count -censor_prev_TR \ - -censor_motion 0.3 motion_${subj} - -# combine multiple censor files -1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \ - -expr "a*b" > censor_${subj}_combined_2.1D + -censor_motion 0.5 motion_${subj} # note TRs that were not censored -set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -show_trs_uncensored encoded` # ------------------------------ # run the regression analysis 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ - -censor censor_${subj}_combined_2.1D \ + -censor motion_${subj}_censor.1D \ -polort 4 \ -num_stimts 17 \ -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D 'GAM' \ @@ -319,7 +306,7 @@ set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -448,7 +435,7 @@ gen_epi_review.py -script @epi_review.$subj \ # generate scripts to review single subject results # (try with defaults, but do not allow bad exit status) -gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 # ========================== auto block: finalize ========================== @@ -475,9 +462,8 @@ echo "execution finished: `date`" # /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ # -tcat_remove_first_trs 0 -dsets \ # /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ -# -align_opts_aea -cost nmi -tlrc_base MNI_avg152T1+tlrc -volreg_align_to \ -# third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 \ -# -regress_stim_times \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ @@ -485,9 +471,9 @@ echo "execution finished: `date`" # /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ # -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ # No_Response_Task Response_Control -regress_basis GAM \ -# -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ -# -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ -# 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ -# -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 \ -# Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ -# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ +# -regress_opts_3dD -gltsym 'SYM: 0.333*Correct_Task \ +# +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control \ +# -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ +# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err index b506101..0327aca 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err +++ b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err @@ -1,4 +1,4 @@ -*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.312787 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.312288 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.300188 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [9 No_Response_Control_Fstat] = 0.299698 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.33841 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.337718 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.107315 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [9 No_Response_Control_Fstat] = 0.107315 ==> few true single voxel detections diff --git a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd index f78bb04..968b10b 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd +++ b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd @@ -1,4 +1,4 @@ -# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor censor_sub_03_combined_2.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Task' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ From 18be69d15b0af37ba880f884113ec94b3213ce2f Mon Sep 17 00:00:00 2001 From: Monica Li Date: Thu, 3 Aug 2017 22:51:57 -0400 Subject: [PATCH 06/18] add Exp-2 scripts --- Exp-2.sh | 21 + .../subj.sub_03/.orig.cmd.ap.sub_03 | 48 + .../subj.sub_03/.orig.cmd.usubj.sub_03 | 29 + .../subj.sub_03/.orig.proc.sub_03 | 492 +++++++++ .../group.retest/subj.sub_03/cmd.ap.sub_03 | 47 + .../subj.sub_03/output.cmd.ap.sub_03 | 29 + .../subj.sub_03/output.proc.sub_03 | 954 +++++++++++++++++ .../group.retest/subj.sub_03/proc.sub_03 | 480 +++++++++ .../subj.sub_03/sub_03.results/stats.REML_cmd | 5 + .../subj.sub_03/.orig.cmd.ap.sub_03 | 48 + .../subj.sub_03/.orig.cmd.usubj.sub_03 | 29 + .../group.test/subj.sub_03/.orig.proc.sub_03 | 491 +++++++++ .../group.test/subj.sub_03/cmd.ap.sub_03 | 47 + .../subj.sub_03/output.cmd.ap.sub_03 | 29 + .../group.test/subj.sub_03/output.proc.sub_03 | 964 ++++++++++++++++++ .../group.test/subj.sub_03/proc.sub_03 | 479 +++++++++ .../sub_03.results/3dDeconvolve.err | 2 + .../subj.sub_03/sub_03.results/stats.REML_cmd | 5 + 18 files changed, 4199 insertions(+) create mode 100755 Exp-2.sh create mode 100755 Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 create mode 100644 Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 create mode 100755 Exp-2/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 create mode 100755 Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 create mode 100644 Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 create mode 100644 Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 create mode 100755 Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 create mode 100644 Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd create mode 100755 Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 create mode 100644 Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 create mode 100755 Exp-2/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 create mode 100755 Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 create mode 100644 Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 create mode 100644 Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 create mode 100755 Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 create mode 100644 Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err create mode 100644 Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd diff --git a/Exp-2.sh b/Exp-2.sh new file mode 100755 index 0000000..0dafb4e --- /dev/null +++ b/Exp-2.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +# 1. Threshold the stats at p <.05 +3dmerge -1zscore -1thresh 1.96 -1noneg \ +-prefix Exp-2/stats.test.thresh \ +'Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.sub_03+tlrc[17]' + +3dmerge -1zscore -1thresh 1.96 -1noneg \ +-prefix Exp-2/stats.retest.thresh \ +'Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.sub_03+tlrc[17]' + +# 2. Calculate a mask that contains overlapping regions of the brain in both sessions +3dmask_tool -input Exp-2/subject_results/group.*/subj.sub_03/sub_03.results/mask_group+tlrc.HEAD \ +-frac 1.0 -prefix Exp-2/mask + +# 3. Binarize the thresholded images +3dcalc -a Exp-2/stats.test.thresh+tlrc -prefix Exp-2/stats.test.bin -expr 'astep(a,.1)' +3dcalc -a Exp-2/stats.retest.thresh+tlrc -prefix Exp-2/stats.retest.bin -expr 'astep(a,.1)' + +# 4. Calculate the Dice coefficient +3ddot -mask Exp-2/mask+tlrc -dodice Exp-2/stats.test.bin+tlrc Exp-2/stats.retest.bin+tlrc \ No newline at end of file diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 new file mode 100755 index 0000000..4726041 --- /dev/null +++ b/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 @@ -0,0 +1,48 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.40 (March 30, 2017) +# creation date: Thu Aug 3 22:03:06 2017 + +# set data directories +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = $top_dir/sub-03/ses-retest/anat +set epi_dir = $top_dir/sub-03/ses-retest/func + +# set subject and group identifiers +set subj = sub_03 +set group_id = retest + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $anat_dir/sub-03_ses-retest_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ + -tlrc_base MNI_avg152T1+tlrc \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 6.0 \ + -regress_stim_times \ + $top_dir/timing_sub-03_ses-retest_Correct_Task.1D \ + $top_dir/timing_sub-03_ses-retest_Incorrect_Task.1D \ + $top_dir/timing_sub-03_ses-retest_No_Response_Control.1D \ + $top_dir/timing_sub-03_ses-retest_No_Response_Task.1D \ + $top_dir/timing_sub-03_ses-retest_Response_Control.1D \ + -regress_stim_labels \ + Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ + Response_Control \ + -regress_basis 'GAM' \ + -regress_censor_motion 0.3 \ + -regress_censor_outliers 0.5 \ + -regress_apply_mot_types demean deriv \ + -regress_opts_3dD \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control \ + -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts \ + -regress_run_clustsim no + diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 new file mode 100644 index 0000000..e94908e --- /dev/null +++ b/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 @@ -0,0 +1,29 @@ +uber_subject.py \ + -cvar subj_dir subject_results/group.retest/subj.sub_03 \ + -svar anat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ + \ + -svar blur_size 6.0 \ + -svar epi \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ + \ + -svar gid retest \ + -svar gltsym '0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -svar gltsym_label Landmark-Detection \ + -svar outlier_limit 0.5 \ + -svar regress_mot_deriv yes \ + -svar run_clustsim no \ + -svar sid sub_03 \ + -svar stim \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ + \ + -svar stim_basis 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' \ + -svar stim_label Correct_Task Incorrect_Task No_Response_Control \ + No_Response_Task Response_Control \ + -svar stim_type times times times times times \ + -svar tlrc_base MNI_avg152T1+tlrc diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 new file mode 100755 index 0000000..e883f7a --- /dev/null +++ b/Exp-2/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 @@ -0,0 +1,492 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Aug 3 22:03:22 2017" +echo "(version 5.15, April 25, 2017)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + +# =========================== auto block: setup ============================ +# script setup + +# take note of the AFNI version +afni -ver + +# check that the current AFNI version is recent enough +afni_history -check_date 23 Sep 2016 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 23 Sep 2016)" + echo " (consider: @update.afni.binaries -defaults)" + exit +endif + +# the user may specify a single subject to run with +if ( $#argv > 0 ) then + set subj = $argv[1] +else + set subj = sub_03 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ + $output_dir/sub-03_ses-retest_T1w + +# ============================ auto block: tcat ============================ +# apply 3dTcat to copy input dsets to results dir, while +# removing the first 0 TRs +3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 238 ) + +# ------------------------------------------------------- +# enter the results directory (can begin processing data) +cd $output_dir + + +# ========================== auto block: outcount ========================== +# data check: compute outlier fraction for each volume +touch out.pre_ss_warn.txt +foreach run ( $runs ) + 3dToutcount -automask -fraction -polort 4 -legendre \ + pb00.$subj.r$run.tcat+orig > outcount.r$run.1D + + # censor outlier TRs per run, ignoring the first 0 TRs + # - censor when more than 0.5 of automask voxels are outliers + # - step() defines which TRs to remove via censoring + 1deval -a outcount.r$run.1D -expr "1-step(a-0.5)" > rm.out.cen.r$run.1D + + # outliers at TR 0 might suggest pre-steady state TRs + if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then + echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ + >> out.pre_ss_warn.txt + endif +end + +# catenate outlier counts into a single time series +cat outcount.r*.1D > outcount_rall.1D + +# catenate outlier censor files into a single time series +cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D + +# ================================= tshift ================================= +# time shift data so all slice timing is the same +foreach run ( $runs ) + 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + pb00.$subj.r$run.tcat+orig +end + +# -------------------------------- +# extract volreg registration base +3dbucket -prefix vr_base pb01.$subj.r01.tshift+orig"[2]" + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-03_ses-retest_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-retest_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-03_ses-retest_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-03_ses-retest_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base vr_base+orig \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg/epi2anat/tlrc xforms + cat_matvec -ONELINE \ + sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform: volreg/epi2anat/tlrc + 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc mask_epi_extents + +# and apply the extents mask to the EPI data +# (delete any time series with missing data) +foreach run ( $runs ) + 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc \ + -expr 'a*b' -prefix pb02.$subj.r$run.volreg +end + +# warp the volreg base EPI dataset to make a final version +cat_matvec -ONELINE \ + sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I > \ + mat.basewarp.aff12.1D + +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input vr_base+orig \ + -1Dmatrix_apply mat.basewarp.aff12.1D \ + -mast_dxyz 4 \ + -prefix final_epi_vr_base + +# create an anat_final dataset, aligned with stats +3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.$subj + +# record final registration costs +3dAllineate -base final_epi_vr_base+tlrc -allcostX \ + -input anat_final.$subj+tlrc |& tee out.allcostX.txt + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-03_ses-retest_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== blur ================================== +# blur each volume of each run +foreach run ( $runs ) + 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.$subj.r$run.blur \ + pb02.$subj.r$run.volreg+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc +end + +# create union of inputs, output type is byte +3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj + +# ---- create subject anatomy mask, mask_anat.$subj+tlrc ---- +# (resampled from tlrc anat) +3dresample -master full_mask.$subj+tlrc -input sub-03_ses-retest_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute overlaps between anat and EPI masks +3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_overlap.txt + +# note Dice coefficient of masks, as well +3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_dice.txt + +# ---- create group anatomy mask, mask_group+tlrc ---- +# (resampled from tlrc base anat, MNI_avg152T1+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/monicali/abin/MNI_avg152T1+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= scale ================================== +# scale each voxel time series to have a mean of 100 +# (be sure no negatives creep in) +# (subject to a range of [0,200]) +foreach run ( $runs ) + 3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.3 motion_${subj} + +# combine multiple censor files +1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \ + -expr "a*b" > censor_${subj}_combined_2.1D + +# note TRs that were not censored +set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ + -show_trs_uncensored encoded` + +# ------------------------------ +# run the regression analysis +3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ + -censor censor_${subj}_combined_2.1D \ + -polort 4 \ + -num_stimts 17 \ + -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D 'GAM' \ + -stim_label 1 Correct_Task \ + -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D 'GAM' \ + -stim_label 2 Incorrect_Task \ + -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D \ + 'GAM' \ + -stim_label 3 No_Response_Control \ + -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D 'GAM' \ + -stim_label 4 No_Response_Task \ + -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D 'GAM' \ + -stim_label 5 Response_Control \ + -stim_file 6 motion_demean.1D'[0]' -stim_base 6 -stim_label 6 roll_01 \ + -stim_file 7 motion_demean.1D'[1]' -stim_base 7 -stim_label 7 pitch_01 \ + -stim_file 8 motion_demean.1D'[2]' -stim_base 8 -stim_label 8 yaw_01 \ + -stim_file 9 motion_demean.1D'[3]' -stim_base 9 -stim_label 9 dS_01 \ + -stim_file 10 motion_demean.1D'[4]' -stim_base 10 -stim_label 10 dL_01 \ + -stim_file 11 motion_demean.1D'[5]' -stim_base 11 -stim_label 11 dP_01 \ + -stim_file 12 motion_deriv.1D'[0]' -stim_base 12 -stim_label 12 roll_02 \ + -stim_file 13 motion_deriv.1D'[1]' -stim_base 13 -stim_label 13 pitch_02 \ + -stim_file 14 motion_deriv.1D'[2]' -stim_base 14 -stim_label 14 yaw_02 \ + -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ + -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ + -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -glt_label 1 Landmark-Detection \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc"[$ktrs]" +3dcalc -a rm.signal.all+tlrc \ + -b rm.noise.all+tlrc \ + -c full_mask.$subj+tlrc \ + -expr 'c*a/b' -prefix TSNR.$subj + +# --------------------------------------------------- +# compute and store GCOR (global correlation average) +# (sum of squares of global mean of unit errts) +3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[5]' > ideal_Correct_Task.1D +1dcat X.nocensor.xmat.1D'[6]' > ideal_Incorrect_Task.1D +1dcat X.nocensor.xmat.1D'[7]' > ideal_No_Response_Control.1D +1dcat X.nocensor.xmat.1D'[8]' > ideal_No_Response_Task.1D +1dcat X.nocensor.xmat.1D'[9]' > ideal_Response_Control.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]" + +# also, create a stimulus-only X-matrix, for easy review +1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D + +# ============================ blur estimation ============================= +# compute blur estimates +touch blur_est.$subj.1D # start with empty file + +# create directory for ACF curve files +mkdir files_ACF + +# -- estimate blur for each run in epits -- +touch blur.epits.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +echo average epits FWHM blurs: $blurs +echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +echo average epits ACF blurs: $blurs +echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D + +# -- estimate blur for each run in errts -- +touch blur.errts.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +echo average errts FWHM blurs: $blurs +echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +echo average errts ACF blurs: $blurs +echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ +# -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ +# 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ +# -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 \ +# Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ +# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 new file mode 100755 index 0000000..5445cbe --- /dev/null +++ b/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 @@ -0,0 +1,47 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.40 (March 30, 2017) +# creation date: Thu Aug 3 22:03:06 2017 + +# set data directories +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = $top_dir/sub-03/ses-retest/anat +set epi_dir = $top_dir/sub-03/ses-retest/func + +# set subject and group identifiers +set subj = sub_03 +set group_id = retest + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $anat_dir/sub-03_ses-retest_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ + -tlrc_base MNI_avg152T1+tlrc \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 3.0 \ + -regress_stim_times \ + $top_dir/timing_sub-03_ses-retest_Correct_Task.1D \ + $top_dir/timing_sub-03_ses-retest_Incorrect_Task.1D \ + $top_dir/timing_sub-03_ses-retest_No_Response_Control.1D \ + $top_dir/timing_sub-03_ses-retest_No_Response_Task.1D \ + $top_dir/timing_sub-03_ses-retest_Response_Control.1D \ + -regress_stim_labels \ + Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ + Response_Control \ + -regress_basis 'GAM' \ + -regress_censor_motion 0.5 \ + -regress_apply_mot_types demean deriv \ + -regress_opts_3dD \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control \ + -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts \ + -regress_run_clustsim no + diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 new file mode 100644 index 0000000..2e864af --- /dev/null +++ b/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 @@ -0,0 +1,29 @@ +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat +set epi_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func +set subj = sub_03 +set group_id = retest +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control + -0.5*No_Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +-- applying orig view as +orig +-- tcat: reps is now 238 +++ updating polort to 4, from run len 595.0 s +-- volreg: using base dset vr_base+orig +++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 4 mm tlrc voxels +-- applying anat warps to 1 dataset(s): sub-03_ses-retest_T1w +-- masking: group anat = 'MNI_avg152T1+tlrc', exists = 1 +-- have 1 ROI dict entries ... +-- will apply motion types: demean, deriv +-- using default: will not apply EPI Automask + (see 'MASKING NOTE' from the -help for details) + +------------------------------------- +** warning have only 1 run to analyze +------------------------------------- + +--> script is file: proc.sub_03 + consider the script execution command: + + tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 new file mode 100644 index 0000000..c3819f0 --- /dev/null +++ b/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 @@ -0,0 +1,954 @@ +echo auto-generated by afni_proc.py, Thu Aug 3 22:21:58 2017 +auto-generated by afni_proc.py, Thu Aug 3 22:21:58 2017 +echo (version 5.15, April 25, 2017) +(version 5.15, April 25, 2017) +echo execution started: `date` +date +execution started: Thu Aug 3 22:35:55 EDT 2017 +afni -ver +Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) +afni_history -check_date 23 Sep 2016 +-- is current: afni_history as new as: 23 Sep 2016 + most recent entry is: 21 Jul 2017 +if ( 0 ) then +if ( 0 > 0 ) then +set subj = sub_03 +endif +set output_dir = sub_03.results +if ( -d sub_03.results ) then +set runs = ( `count -digits 2 1 1` ) +count -digits 2 1 1 +mkdir sub_03.results +mkdir sub_03.results/stimuli +cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D sub_03.results/stimuli +3dcopy /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz sub_03.results/sub-03_ses-retest_T1w +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] +++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ elapsed time = 1.5 s +set tr_counts = ( 238 ) +cd sub_03.results +touch out.pre_ss_warn.txt +foreach run ( 01 ) +3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig +++ 3dToutcount: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. +++ 18031 voxels passed mask/clip +if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then +1deval -a outcount.r01.1D{0} -expr step(a-0.4) +echo ** TR #0 outliers: possible pre-steady state TRs in run 01 +endif +end +cat outcount.r01.1D +foreach run ( 01 ) +3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig +++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. +*+ WARNING: dataset is already aligned in time! +*+ WARNING: ==>> output dataset is just a copy of input dataset +end +3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] +++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off +#++ align_epi_anat version: 1.57 +#++ turning off volume registration +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./sub-03_ses-retest_T1w+orig +#++ Multi-cost is lpc +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-retest_T1w* +#Script is running (command trimmed): + 3dcopy ./sub-03_ses-retest_T1w+orig ./__tt_sub-03_ses-retest_T1w+orig +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ Removing skull from anat data +#Script is running (command trimmed): + 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-retest_T1w+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-retest_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-retest_T1w+orig.BRIK is 7.491219 degrees from plumb. +#Script is running (command trimmed): + 3dinfo ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' +#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig is ***oblique**** +#Script is running (command trimmed): + 3dAttribute DELTA ./__tt_sub-03_ses-retest_T1w_ns+orig +#++ Spacing for anat to oblique epi alignment is 1.000000 +#++ Matching obliquity of anat to epi +#Script is running (command trimmed): + 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-retest_T1w_ns_obla2e_mat.1D +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Deobliquing original dataset before obliquing +++ Combining oblique transformations +++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.BRIK +#++ using 0th sub-brick because only one found +#Script is running (command trimmed): + 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' +++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ resampling epi to match anat data +#Script is running (command trimmed): + 3dresample -master ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_vr_base_ts+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_vr_base_ts+orig.BRIK is 4.947676 degrees from plumb. +#++ removing skull or area outside brain +#Script is running (command trimmed): + 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig +++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset ./__tt_vr_base_ts_rs+orig +++ Forming automask + + Fixed clip level = 708.019226 + + Used gradual clip level = 621.023193 .. 754.463989 + + Number voxels above clip level = 1151758 + + Clustering voxels ... + + Largest cluster has 1151071 voxels + + Clustering voxels ... + + Largest cluster has 1150607 voxels + + Filled 381 voxels in small holes; now have 1150988 voxels + + Filled 16522 voxels in large holes; now have 1167510 voxels + + Clustering voxels ... + + Largest cluster has 1167476 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 14352028 voxels + + Mask now has 1167476 voxels +++ 1167476 voxels in the mask [out of 15519504: 7.52%] +++ first 64 x-planes are zero [from R] +++ last 68 x-planes are zero [from L] +++ first 30 y-planes are zero [from A] +++ last 22 y-planes are zero [from P] +++ first 107 z-planes are zero [from I] +++ last 48 z-planes are zero [from S] +++ applying mask to original data +++ Writing masked data +++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK +++ CPU time = 3.960000 sec +#++ Computing weight mask +#Script is running (command trimmed): + 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1728.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#Script is running (command trimmed): + 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1728.000000))' +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK +#++ Aligning anat data to epi data +#Script is running (command trimmed): + 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets +++ 1356008 voxels in -source_automask+4 +++ Zero-pad: not needed +++ 1167476 voxels [7.5%] in weight mask +++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal+orig.BRIK +++ Number of points for matching = 1167476 +++ Local correlation: blok type = 'RHDD(6.54321)' +++ shift param auto-range: -84.4..84.4 -70.6..70.6 -85.1..85.1 + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 + + 12 free parameters +++ Normalized convergence radius = 0.001000 +++ OpenMP thread count = 4 +++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= +++ ========== sub-brick #0 ========== [total CPU to here=9.2 s] +++ *** Fine pass begins *** + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - copying weight image + + - using 1167476 points from base image [use_all=0] + + * Exit alignment setup routine + + 1097666 total points stored in 2068 'RHDD(6.54321)' bloks + + - Initial cost = -0.053122 + + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +********************************************************************************************************************************************** + + - Finalish cost = -0.295415 ; 350 funcs +********** + + - Final cost = -0.295420 ; 136 funcs + + Final fine fit Parameters: + x-shift= 0.2981 y-shift=-0.5136 z-shift=-1.2234 + z-angle= 0.4394 x-angle= 1.9668 y-angle=-5.3161 + x-scale= 0.9674 y-scale= 0.9725 z-scale= 1.0191 + y/x-shear= 0.0000 z/x-shear= 0.0099 z/y-shear= 0.0534 + + - Fine net CPU time = 35.3 s +++ Computing output image +++ image warp: parameters = 0.2981 -0.5136 -1.2234 0.4394 1.9668 -5.3161 0.9674 0.9725 1.0191 0.0000 0.0099 0.0534 +++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk+orig.BRIK +++ Wrote -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D +++ 3dAllineate: total CPU time = 47.0 sec Elapsed = 40.4 +++ ########################################################### +++ # Please check results visually for alignment quality # +++ ########################################################### +++ # '-autoweight' is recommended when using -lpc or -lpa # +++ # If your results are not good, please try again. # +++ ########################################################### +#Script is running (command trimmed): + cat_matvec -ONELINE ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D ./__tt_sub-03_ses-retest_T1w_ns_obla2e_mat.1D -I > ./sub-03_ses-retest_T1w_al_junk_mat.aff12.1D +#++ Combining anat to epi and oblique transformations +#Script is running (command trimmed): + 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-retest_T1w_al_junk -input ./__tt_sub-03_ses-retest_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +++ Source dataset: ./__tt_sub-03_ses-retest_T1w_ns+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +++ ========== sub-brick #0 ========== [total CPU to here=0.1 s] + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - no weight image + + - using 11 points from base image [use_all=0] + + * Exit alignment setup routine +++ using -1Dmatrix_apply +++ Computing output image +++ image warp: parameters = 0.9618 0.0448 -0.0985 14.5442 -0.0314 0.9711 -0.0538 -1.5252 0.0911 0.0281 1.0141 -11.6150 +++ Output dataset ./sub-03_ses-retest_T1w_al_junk+orig.BRIK +++ 3dAllineate: total CPU time = 2.2 sec Elapsed = 2.8 +++ ########################################################### +#++ Creating final output: skullstripped anat data +copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig +#Script is running (command trimmed): + 3dcopy ./__tt_sub-03_ses-retest_T1w_ns+orig sub-03_ses-retest_T1w_ns +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ Creating final output: anat data aligned to epi +# copy is not necessary +#++ Saving history +#Script is running (command trimmed): + 3dNotes -h "align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ + -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask -volreg off -tshift off" \ + ./sub-03_ses-retest_T1w_al_junk+orig + +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-retest_T1w* + +# Finished alignment successfully + +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-retest_T1w_ns+orig -no_ss +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +Center distance of 26.068730 mm +Padding ... +++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK +Resampling ... +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__ats_tmp__resamp_step+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 7.491219 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +Clipping -0.000100 1013.000100 ... +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./__ats_tmp___rs_sub-03_ses-retest_T1w_ns+tlrc.BRIK +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-retest_T1w_ns+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Registration (linear final interpolation) ... +++ 3dWarpDrive: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Initial scale factor set to 0.30/247.56=8.3e+02 +RMS[0] = 0.364249 0.163911 ITER = 6/137 +0.364249 + +Warping has converged. + +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. +++ 7.491219 degrees from plumb. +*+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations +Applying brain mask +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.BRIK +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK +Unpadding ... +++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ output dataset: ./__ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig.BRIK +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig +*+ WARNING: Changing the space of an ORIG view dataset may cause confusion! +*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space). +*+ WARNING: Consider changing the view of the dataset to TLRC view also +++ 3drefit processed 1 datasets +Changing view of transformed anatomy +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Setting parent with 3drefit -wset sub-03_ses-retest_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc +++ 3drefit processed 1 datasets +++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Warning: ignoring +tlrc on new_prefix. +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc.HEAD -> sub-03_ses-retest_T1w_ns+tlrc.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc.BRIK -> sub-03_ses-retest_T1w_ns+tlrc.BRIK +Cleanup ... +cat_matvec sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I +if ( ! -f sub-03_ses-retest_T1w_ns+tlrc.HEAD ) then +foreach run ( 01 ) +3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig +++ 3dvolreg: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 4.947676 degrees from plumb. +++ Reading in base dataset ./vr_base+orig.BRIK +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 4.947676 degrees from plumb. +++ Reading input dataset ./pb01.sub_03.r01.tshift+orig.BRIK +++ Edging: x=3 y=3 z=2 +++ Creating mask for -maxdisp + + Automask has 19058 voxels + + 3364 voxels left in -maxdisp mask after erosion +++ Initializing alignment base +++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. +++ CPU time for realignment=7.05 s [=0.0296 s/sub-brick] +++ Min : roll=-0.200 pitch=-0.367 yaw=-0.118 dS=-1.139 dL=-0.157 dP=-0.055 +++ Mean: roll=-0.094 pitch=-0.011 yaw=+0.456 dS=-0.124 dL=+0.184 dP=+0.074 +++ Max : roll=+0.027 pitch=+0.449 yaw=+0.935 dS=+0.523 dL=+0.640 dP=+0.245 +++ Max displacements (mm) for each sub-brick: + 1.41(0.00) 0.17(1.52) 0.00(0.17) 0.33(0.33) 0.34(0.10) 0.45(0.12) 0.41(0.06) 0.20(0.28) 0.21(0.16) 0.22(0.05) 0.31(0.29) 0.37(0.19) 0.50(0.19) 0.61(0.12) 0.87(0.29) 0.94(0.10) 1.05(0.18) 1.12(0.12) 1.07(0.11) 0.82(0.28) 0.67(0.28) 0.69(0.13) 0.57(0.16) 0.70(0.22) 0.67(0.04) 0.75(0.13) 0.63(0.15) 0.68(0.19) 0.59(0.12) 0.66(0.09) 0.67(0.04) 0.78(0.19) 0.61(0.19) 0.59(0.05) 0.51(0.16) 0.62(0.22) 0.63(0.12) 0.66(0.12) 0.70(0.10) 0.69(0.04) 0.70(0.03) 0.77(0.07) 0.70(0.16) 0.65(0.14) 0.72(0.10) 0.74(0.16) 0.71(0.08) 0.68(0.10) 0.74(0.12) 0.70(0.13) 0.74(0.19) 0.60(0.21) 0.54(0.09) 0.50(0.12) 0.46(0.11) 0.45(0.08) 0.44(0.09) 0.50(0.23) 0.46(0.11) 0.50(0.15) 0.49(0.11) 0.56(0.15) 0.52(0.11) 0.57(0.17) 0.63(0.15) 0.56(0.12) 0.69(0.13) 0.64(0.26) 0.67(0.18) 0.62(0.07) 0.68(0.18) 0.76(0.27) 0.58(0.33) 0.80(0.22) 0.67(0.15) 0.65(0.08) 0.70(0.08) 0.77(0.08) 0.70(0.12) 0.70(0.14) 0.66(0.08) 0.68(0.12) 0.83(0.18) 0.74(0.22) 0.64(0.22) 0.72(0.14) 0.74(0.13) 0.81(0.14) 0.75(0.10) 0.72(0.07) 0.73(0.07) 0.69(0.16) 0.69(0.12) 0.69(0.17) 0.70(0.13) 0.64(0.16) 0.68(0.16) 0.65(0.10) 0.73(0.17) 0.74(0.06) 0.69(0.10) 0.67(0.05) 0.65(0.15) 0.72(0.12) 0.63(0.25) 0.70(0.15) 0.68(0.14) 0.70(0.17) 0.63(0.21) 0.60(0.07) 0.64(0.08) 0.76(0.16) 0.72(0.14) 0.69(0.15) 0.57(0.24) 0.58(0.06) 0.59(0.04) 0.63(0.08) 0.58(0.07) 0.60(0.07) 0.67(0.10) 0.67(0.25) 0.81(0.23) 0.79(0.06) 0.72(0.11) 0.74(0.04) 0.68(0.15) 0.71(0.14) 0.69(0.04) 0.69(0.09) 0.70(0.11) 0.68(0.11) 0.75(0.16) 0.70(0.12) 0.81(0.19) 0.73(0.10) 0.85(0.14) 0.78(0.10) 0.85(0.07) 0.84(0.05) 0.84(0.04) 0.77(0.09) 0.78(0.09) 0.80(0.06) 0.81(0.03) 0.77(0.11) 0.86(0.13) 0.80(0.16) 0.91(0.15) 0.86(0.10) 0.90(0.07) 0.98(0.08) 1.10(0.14) 1.13(0.06) 1.03(0.12) 1.14(0.17) 1.06(0.09) 1.18(0.12) 1.10(0.11) 1.13(0.07) 1.08(0.14) 1.18(0.15) 1.23(0.07) 1.07(0.19) 1.17(0.13) 1.14(0.10) 1.18(0.07) 1.20(0.05) 1.22(0.07) 1.20(0.07) 1.14(0.13) 1.22(0.14) 1.14(0.14) 1.29(0.18) 1.19(0.11) 1.32(0.17) 1.27(0.10) 1.34(0.16) 1.38(0.05) 1.28(0.19) 1.31(0.09) 1.33(0.05) 1.37(0.10) 1.36(0.05) 1.42(0.14) 1.39(0.10) 1.40(0.06) 1.36(0.08) 1.36(0.03) 1.49(0.13) 1.42(0.09) 1.48(0.10) 1.30(0.24) 1.20(0.16) 1.24(0.10) 1.23(0.11) 1.25(0.03) 1.24(0.08) 1.19(0.11) 1.25(0.11) 1.18(0.08) 1.19(0.04) 1.21(0.06) 1.40(0.25) 1.31(0.26) 1.36(0.14) 1.47(0.11) 1.51(0.07) 1.53(0.06) 1.58(0.06) 1.60(0.08) 1.58(0.11) 1.65(0.10) 1.64(0.11) 1.65(0.13) 1.72(0.09) 1.79(0.07) 1.76(0.09) 1.80(0.13) 1.96(0.20) 1.94(0.03) 1.82(0.16) 1.72(0.20) 1.55(0.33) 1.60(0.32) 1.57(0.14) 1.37(0.21) 1.38(0.20) 1.14(0.38) 1.18(0.25) 1.21(0.30) 0.70(0.63) 0.81(0.24) 0.91(0.13) 1.00(0.10) 1.12(0.13) 1.02(0.23) 1.19(0.19) +++ Max displacement in automask = 1.96 (mm) at sub-brick 219 +++ Max delta displ in automask = 1.52 (mm) at sub-brick 1 +++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK +3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +*+ WARNING: input 'a' is not used in the expression +++ Output dataset ./rm.epi.all1+orig.BRIK +cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb01.sub_03.r01.tshift+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 4.947676 degrees from plumb. +++ Source dataset: ./pb01.sub_03.r01.tshift+orig.HEAD +++ Base dataset: ./sub-03_ses-retest_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 238 sub-bricks ========== +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 6.2 sec Elapsed = 4.3 +++ ########################################################### +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./rm.epi.all1+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./rm.epi.all1+orig.BRIK is 4.947676 degrees from plumb. +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ Output dataset ./rm.epi.1.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 3.3 +3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.epi.min.r01+tlrc.BRIK +end +cat dfile.r01.1D +3dcopy rm.epi.min.r01+tlrc mask_epi_extents +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +foreach run ( 01 ) +3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK +end +cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 4.947676 degrees from plumb. +++ Source dataset: ./vr_base+orig.HEAD +++ Base dataset: ./sub-03_ses-retest_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.2 +++ ########################################################### +3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.sub_03 +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc +tee out.allcostX.txt +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./anat_final.sub_03+tlrc.HEAD +++ Base dataset: ./final_epi_vr_base+tlrc.HEAD +++ Loading datasets +++ 222503 voxels in source_automask+0 +++ Zero-pad: xbot=1 xtop=2 +++ Zero-pad: ybot=0 ytop=1 +++ Zero-pad: zbot=2 ztop=1 +++ Computing -autobox +++ 113297 voxels [89.4%] in weight mask +++ Number of points for matching = 53249 +++ Local correlation: blok type = 'RHDD(14.76)' +*+ WARNING: No output dataset will be calculated +++ OpenMP thread count = 4 +volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +++ allcost output: init #0 + ls = 0.184126 + sp = 0.307224 + mi = -0.531581 + crM = 0.0790675 + nmi = 0.868615 + je = 3.51437 + hel = -0.106047 + crA = 0.2819 + crU = 0.301908 + lss = 0.815874 + lpc = 0.296009 + lpa = 0.703991 + lpc+ = 0.494411 + ncd = 1 +++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 +++ ########################################################### +3dAllineate -source sub-03_ses-retest_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-retest_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-retest_T1w+orig.BRIK is 7.491219 degrees from plumb. +++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers +++ Source dataset: ./sub-03_ses-retest_T1w+orig.HEAD +++ Base dataset: (not given) +++ Loading datasets +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ð++ wsinc5 interpolation setup: + + taper function = Min sidelobe 3 term + + taper cut point = 0.000 + + window radius = 5 voxels + + window shape = Cubical + + The above can be altered via the AFNI_WSINC5_* environment variables. + + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + + wsinc5 CUBE(5) mask has 1000 points +++ Output dataset ./anat_w_skull_warped+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.7 +++ ########################################################### +foreach run ( 01 ) +3dmerge -1blur_fwhm 3.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc +++ 3dmerge: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ default -1dindex = 0 +++ default -1tindex = 1 +Program 3dmerge +3dmerge: edit and combine 3D datasets, by RW Cox +++ editing input dataset in memory (49.6 MB) +..............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK + +end +foreach run ( 01 ) +3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc +++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset pb03.sub_03.r01.blur+tlrc +++ Forming automask + + Fixed clip level = 705.332397 + + Used gradual clip level = 626.181824 .. 751.003906 + + Number voxels above clip level = 28040 + + Clustering voxels ... + + Largest cluster has 28006 voxels + + Clustering voxels ... + + Largest cluster has 27881 voxels + + Filled 94 voxels in small holes; now have 27975 voxels + + Clustering voxels ... + + Largest cluster has 27975 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 81375 voxels + + Mask now has 27975 voxels +++ Dilating automask + + Clustering voxels ... + + Largest cluster has 76204 voxels +++ 33146 voxels in the mask [out of 109350: 30.31%] +++ first 4 x-planes are zero [from L] +++ last 3 x-planes are zero [from R] +++ first 4 y-planes are zero [from P] +++ last 3 y-planes are zero [from A] +++ first 3 z-planes are zero [from I] +++ last 3 z-planes are zero [from S] +++ Output dataset ./rm.mask_r01+tlrc.BRIK +++ CPU time = 0.280000 sec +end +3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 +++ processing 1 input datasets... +++ padding all datasets by 0 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 33146 survived, 76204 were zero +++ writing result full_mask.sub_03... +++ Output dataset ./full_mask.sub_03+tlrc.BRIK +3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-retest_T1w_ns+tlrc -prefix rm.resam.anat +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30574 survived, 78776 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_anat.sub_03... +++ Output dataset ./mask_anat.sub_03+tlrc.BRIK +3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_overlap.txt +++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK +#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) +33146 30574 35621 28099 5047 2475 15.2266 8.0951 0.9461 0.9329 0.9590 +3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_dice.txt +0.881952 +3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30980 survived, 78370 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_group... +++ Output dataset ./mask_group+tlrc.BRIK +foreach run ( 01 ) +3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.mean_r01+tlrc.BRIK +3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK +end +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 +total number of censored TRs (simple form) = 2 +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D + -show_trs_uncensored encoded` +1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: B. Douglas Ward, et al. +++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD +++ STAT automask has 100184 voxels (out of 109350 = 91.6%) +++ Skipping check for initial transients +++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ +++ -stim_times using TR=2.5 s for stimulus timing conversion +++ -stim_times using TR=2.5 s for any -iresp output datasets +++ [you can alter the -iresp TR via the -TR_times option] +++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise +++ ** GUESSED ** -stim_times 1 using LOCAL times +++ ** GUESSED ** -stim_times 2 using LOCAL times +++ ** GUESSED ** -stim_times 3 using LOCAL times +++ ** GUESSED ** -stim_times 4 using LOCAL times +++ ** GUESSED ** -stim_times 5 using LOCAL times +------------------------------------------------------------ +GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control': + 0 0 0 0 0 0.333 0.333 -0.5 0.333 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 + +++ Number of time points: 238 (before censor) ; 236 (after) + + Number of parameters: 22 [17 baseline ; 5 signal] +++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) +++ Wrote matrix image to file X.jpg +++ Wrote matrix values to file X.xmat.1D +++ ========= Things you can do with the matrix file ========= +++ (a) Linear regression with ARMA(1,1) modeling of serial correlation: + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb + +++ N.B.: 3dREMLfit command above written to file stats.REML_cmd +++ (b) Visualization/analysis of the matrix via ExamineXmat.R +++ (c) Synthesis of sub-model datasets using 3dSynthesize +++ ========================================================== +++ Wrote matrix values to file X.nocensor.xmat.1D +++ ----- Signal+Baseline matrix condition [X] (236x22): 5.23887 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (236x5): 1.40108 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (236x17): 5.1314 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (236x12): 3.87376 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (236x5): 1.05506 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 2.74977e-15 ++ VERY GOOD ++ +++ Matrix setup time = 0.66 s +++ Calculations starting; elapsed time=1.246 +++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. +++ Calculations finished; elapsed time=15.833 +++ Smallest FDR q [0 Full_Fstat] = 4.80713e-13 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 8.98106e-12 +++ Smallest FDR q [3 Correct_Task_Fstat] = 8.98004e-12 +++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 1.82055e-05 +++ Smallest FDR q [6 Incorrect_Task_Fstat] = 1.82049e-05 +++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.002104 +++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.0021038 +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 0.008893 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.00889248 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 1.42207e-12 +++ Smallest FDR q [15 Response_Control_Fstat] = 1.422e-12 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 7.0934e-05 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 7.09247e-05 +++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + + created 13 FDR curves in bucket header +++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK +++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK +++ #Flops=4.31862e+10 Average Dot Product=37.4801 +if ( 0 != 0 ) then +1d_tool.py -show_cormat_warnings -infile X.xmat.1D +tee out.cormat_warn.txt + +Warnings regarding Correlation Matrix: X.xmat.1D + + severity correlation cosine regressor pair + -------- ----------- ------ ---------------------------------------- + medium: 0.447 0.539 ( 5 vs. 6) Correct_Task#0 vs. Incorrect_Task#0 + +3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD +++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ elapsed time = 0.6 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..237] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.signal.all+tlrc.BRIK +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..237] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.noise.all+tlrc.BRIK +3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./TSNR.sub_03+tlrc.BRIK +3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc +++ 3dTnorm: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Output dataset ./rm.errts.unit+tlrc.BRIK +3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc +++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++++ 33146 voxels survive the mask +3dTstat -sos -prefix - gmean.errts.unit.1D' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo -- GCOR = `cat out.gcor.1D` +cat out.gcor.1D +-- GCOR = 0.051467 +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./rm.DP+tlrc.BRIK +3dTstat -sum -prefix corr_brain rm.DP+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./corr_brain+tlrc.BRIK +1dcat X.nocensor.xmat.1D[5] +1dcat X.nocensor.xmat.1D[6] +1dcat X.nocensor.xmat.1D[7] +1dcat X.nocensor.xmat.1D[8] +1dcat X.nocensor.xmat.1D[9] +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +++ Output dataset ./sum_ideal.1D +1dcat X.nocensor.xmat.1D[5..9] +touch blur_est.sub_03.1D +mkdir files_ACF +touch blur.epits.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 2..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..237] +++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 33146 +*+ WARNING: removed 239 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 236 time points + + detrending done (2.53 CPU s thus far) +++ start ACF calculations out to radius = 19.19 mm + + ACF done (35.46 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits FWHM blurs: 0 0 0 0 +average epits FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # epits FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits ACF blurs: 0.824146 3.58345 14.0589 9.17809 +average epits ACF blurs: 0.824146 3.58345 14.0589 9.17809 +echo 0.824146 3.58345 14.0589 9.17809 # epits ACF blur estimates +touch blur.errts.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 2..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..237] +++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 33146 +*+ WARNING: removed 239 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 236 time points + + detrending done (2.45 CPU s thus far) +++ start ACF calculations out to radius = 19.08 mm + + ACF done (36.55 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts FWHM blurs: 0 0 0 0 +average errts FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # errts FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts ACF blurs: 0.863011 3.61001 15.0127 9.12364 +average errts ACF blurs: 0.863011 3.61001 15.0127 9.12364 +echo 0.863011 3.61001 15.0127 9.12364 # errts ACF blur estimates +gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 +++ writing ss review basic: @ss_review_basic +++ writing ss review driver: @ss_review_driver +++ writing ss review drive commands: @ss_review_driver_commands +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +tee out.ss_review.sub_03.txt +if ( -e @ss_review_basic ) ./@ss_review_basic +./@ss_review_basic + +subject ID : sub_03 +TRs removed (per run) : 0 +num stim classes provided : 5 +final anatomy dset : anat_final.sub_03+tlrc.HEAD +final stats dset : stats.sub_03+tlrc.HEAD +final voxel resolution : 4.000000 4.000000 4.000000 + +motion limit : 0.5 +num TRs above mot limit : 1 +average motion (per TR) : 0.0937926 +average censored motion : 0.0889158 +max motion displacement : 1.69106 +max censored displacement : 1.69012 +outlier limit : 0.1 +average outlier frac (TR) : 0.00559353 +num TRs above out limit : 1 + +num runs found : 1 +num TRs per run : 238 +num TRs per run (applied) : 236 +num TRs per run (censored): 2 +fraction censored per run : 0.00840336 +TRs total (uncensored) : 238 +TRs total : 236 +degrees of freedom used : 22 +degrees of freedom left : 214 + +TRs censored : 2 +censor fraction : 0.008403 +num regs of interest : 5 +num TRs per stim (orig) : 78 56 46 19 79 +num TRs censored per stim : 0 0 0 0 0 +fraction TRs censored : 0.000 0.000 0.000 0.000 0.000 +ave mot per sresp (orig) : 0.086607 0.082908 0.080591 0.071212 0.078827 +ave mot per sresp (cens) : 0.086607 0.082908 0.080591 0.071212 0.078827 + +TSNR average : 160.267 +global correlation (GCOR) : 0.051467 +anat/EPI mask Dice coef : 0.881952 +maximum F-stat (masked) : 48.5706 +blur estimates (ACF) : 0.863011 3.61001 15.0127 +blur estimates (FWHM) : 0 0 0 + +** TR #0 outliers: possible pre-steady state TRs in run 01 + +cd .. +echo execution finished: `date` +date +execution finished: Thu Aug 3 22:45:13 EDT 2017 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 new file mode 100755 index 0000000..4ac96ab --- /dev/null +++ b/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 @@ -0,0 +1,480 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Aug 3 22:21:58 2017" +echo "(version 5.15, April 25, 2017)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + +# =========================== auto block: setup ============================ +# script setup + +# take note of the AFNI version +afni -ver + +# check that the current AFNI version is recent enough +afni_history -check_date 23 Sep 2016 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 23 Sep 2016)" + echo " (consider: @update.afni.binaries -defaults)" + exit +endif + +# the user may specify a single subject to run with +if ( $#argv > 0 ) then + set subj = $argv[1] +else + set subj = sub_03 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ + $output_dir/sub-03_ses-retest_T1w + +# ============================ auto block: tcat ============================ +# apply 3dTcat to copy input dsets to results dir, while +# removing the first 0 TRs +3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 238 ) + +# ------------------------------------------------------- +# enter the results directory (can begin processing data) +cd $output_dir + + +# ========================== auto block: outcount ========================== +# data check: compute outlier fraction for each volume +touch out.pre_ss_warn.txt +foreach run ( $runs ) + 3dToutcount -automask -fraction -polort 4 -legendre \ + pb00.$subj.r$run.tcat+orig > outcount.r$run.1D + + # outliers at TR 0 might suggest pre-steady state TRs + if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then + echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ + >> out.pre_ss_warn.txt + endif +end + +# catenate outlier counts into a single time series +cat outcount.r*.1D > outcount_rall.1D + +# ================================= tshift ================================= +# time shift data so all slice timing is the same +foreach run ( $runs ) + 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + pb00.$subj.r$run.tcat+orig +end + +# -------------------------------- +# extract volreg registration base +3dbucket -prefix vr_base pb01.$subj.r01.tshift+orig"[2]" + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-03_ses-retest_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-retest_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-03_ses-retest_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-03_ses-retest_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base vr_base+orig \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg/epi2anat/tlrc xforms + cat_matvec -ONELINE \ + sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform: volreg/epi2anat/tlrc + 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc mask_epi_extents + +# and apply the extents mask to the EPI data +# (delete any time series with missing data) +foreach run ( $runs ) + 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc \ + -expr 'a*b' -prefix pb02.$subj.r$run.volreg +end + +# warp the volreg base EPI dataset to make a final version +cat_matvec -ONELINE \ + sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I > \ + mat.basewarp.aff12.1D + +3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc \ + -input vr_base+orig \ + -1Dmatrix_apply mat.basewarp.aff12.1D \ + -mast_dxyz 4 \ + -prefix final_epi_vr_base + +# create an anat_final dataset, aligned with stats +3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.$subj + +# record final registration costs +3dAllineate -base final_epi_vr_base+tlrc -allcostX \ + -input anat_final.$subj+tlrc |& tee out.allcostX.txt + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-03_ses-retest_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== blur ================================== +# blur each volume of each run +foreach run ( $runs ) + 3dmerge -1blur_fwhm 3.0 -doall -prefix pb03.$subj.r$run.blur \ + pb02.$subj.r$run.volreg+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc +end + +# create union of inputs, output type is byte +3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj + +# ---- create subject anatomy mask, mask_anat.$subj+tlrc ---- +# (resampled from tlrc anat) +3dresample -master full_mask.$subj+tlrc -input sub-03_ses-retest_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute overlaps between anat and EPI masks +3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_overlap.txt + +# note Dice coefficient of masks, as well +3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_dice.txt + +# ---- create group anatomy mask, mask_group+tlrc ---- +# (resampled from tlrc base anat, MNI_avg152T1+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/monicali/abin/MNI_avg152T1+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= scale ================================== +# scale each voxel time series to have a mean of 100 +# (be sure no negatives creep in) +# (subject to a range of [0,200]) +foreach run ( $runs ) + 3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.5 motion_${subj} + +# note TRs that were not censored +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ + -show_trs_uncensored encoded` + +# ------------------------------ +# run the regression analysis +3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ + -censor motion_${subj}_censor.1D \ + -polort 4 \ + -num_stimts 17 \ + -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D 'GAM' \ + -stim_label 1 Correct_Task \ + -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D 'GAM' \ + -stim_label 2 Incorrect_Task \ + -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D \ + 'GAM' \ + -stim_label 3 No_Response_Control \ + -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D 'GAM' \ + -stim_label 4 No_Response_Task \ + -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D 'GAM' \ + -stim_label 5 Response_Control \ + -stim_file 6 motion_demean.1D'[0]' -stim_base 6 -stim_label 6 roll_01 \ + -stim_file 7 motion_demean.1D'[1]' -stim_base 7 -stim_label 7 pitch_01 \ + -stim_file 8 motion_demean.1D'[2]' -stim_base 8 -stim_label 8 yaw_01 \ + -stim_file 9 motion_demean.1D'[3]' -stim_base 9 -stim_label 9 dS_01 \ + -stim_file 10 motion_demean.1D'[4]' -stim_base 10 -stim_label 10 dL_01 \ + -stim_file 11 motion_demean.1D'[5]' -stim_base 11 -stim_label 11 dP_01 \ + -stim_file 12 motion_deriv.1D'[0]' -stim_base 12 -stim_label 12 roll_02 \ + -stim_file 13 motion_deriv.1D'[1]' -stim_base 13 -stim_label 13 pitch_02 \ + -stim_file 14 motion_deriv.1D'[2]' -stim_base 14 -stim_label 14 yaw_02 \ + -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ + -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ + -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -glt_label 1 Landmark-Detection \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc"[$ktrs]" +3dcalc -a rm.signal.all+tlrc \ + -b rm.noise.all+tlrc \ + -c full_mask.$subj+tlrc \ + -expr 'c*a/b' -prefix TSNR.$subj + +# --------------------------------------------------- +# compute and store GCOR (global correlation average) +# (sum of squares of global mean of unit errts) +3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[5]' > ideal_Correct_Task.1D +1dcat X.nocensor.xmat.1D'[6]' > ideal_Incorrect_Task.1D +1dcat X.nocensor.xmat.1D'[7]' > ideal_No_Response_Control.1D +1dcat X.nocensor.xmat.1D'[8]' > ideal_No_Response_Task.1D +1dcat X.nocensor.xmat.1D'[9]' > ideal_Response_Control.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]" + +# also, create a stimulus-only X-matrix, for easy review +1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D + +# ============================ blur estimation ============================= +# compute blur estimates +touch blur_est.$subj.1D # start with empty file + +# create directory for ACF curve files +mkdir files_ACF + +# -- estimate blur for each run in epits -- +touch blur.epits.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +echo average epits FWHM blurs: $blurs +echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +echo average epits ACF blurs: $blurs +echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D + +# -- estimate blur for each run in errts -- +touch blur.errts.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +echo average errts FWHM blurs: $blurs +echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +echo average errts ACF blurs: $blurs +echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ +# -regress_opts_3dD -gltsym 'SYM: 0.333*Correct_Task \ +# +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control \ +# -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ +# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd new file mode 100644 index 0000000..a997d7b --- /dev/null +++ b/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd @@ -0,0 +1,5 @@ +# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb $* diff --git a/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 new file mode 100755 index 0000000..70784fa --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 @@ -0,0 +1,48 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.40 (March 30, 2017) +# creation date: Thu Aug 3 22:01:15 2017 + +# set data directories +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = $top_dir/sub-03/ses-test/anat +set epi_dir = $top_dir/sub-03/ses-test/func + +# set subject and group identifiers +set subj = sub_03 +set group_id = test + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $anat_dir/sub-03_ses-test_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $epi_dir/sub-03_ses-test_task-linebisection_bold.nii.gz \ + -tlrc_base MNI_avg152T1+tlrc \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 6.0 \ + -regress_stim_times \ + $top_dir/timing_sub-03_ses-test_Correct_Task.1D \ + $top_dir/timing_sub-03_ses-test_Incorrect_Task.1D \ + $top_dir/timing_sub-03_ses-test_No_Response_Control.1D \ + $top_dir/timing_sub-03_ses-test_No_Response_Task.1D \ + $top_dir/timing_sub-03_ses-test_Response_Control.1D \ + -regress_stim_labels \ + Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ + Response_Control \ + -regress_basis 'GAM' \ + -regress_censor_motion 0.3 \ + -regress_censor_outliers 0.5 \ + -regress_apply_mot_types demean deriv \ + -regress_opts_3dD \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control \ + -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts \ + -regress_run_clustsim no + diff --git a/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 new file mode 100644 index 0000000..8b80dbd --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 @@ -0,0 +1,29 @@ +uber_subject.py \ + -cvar subj_dir subject_results/group.test/subj.sub_03 \ + -svar anat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ + \ + -svar blur_size 6.0 \ + -svar epi \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ + \ + -svar gid test \ + -svar gltsym '0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -svar gltsym_label Landmark-Detection \ + -svar outlier_limit 0.5 \ + -svar regress_mot_deriv yes \ + -svar run_clustsim no \ + -svar sid sub_03 \ + -svar stim \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ + \ + -svar stim_basis 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' \ + -svar stim_label Correct_Task Incorrect_Task No_Response_Control \ + No_Response_Task Response_Control \ + -svar stim_type times times times times times \ + -svar tlrc_base MNI_avg152T1+tlrc diff --git a/Exp-2/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 new file mode 100755 index 0000000..bb99a95 --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 @@ -0,0 +1,491 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Aug 3 22:01:23 2017" +echo "(version 5.15, April 25, 2017)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + +# =========================== auto block: setup ============================ +# script setup + +# take note of the AFNI version +afni -ver + +# check that the current AFNI version is recent enough +afni_history -check_date 23 Sep 2016 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 23 Sep 2016)" + echo " (consider: @update.afni.binaries -defaults)" + exit +endif + +# the user may specify a single subject to run with +if ( $#argv > 0 ) then + set subj = $argv[1] +else + set subj = sub_03 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ + $output_dir/sub-03_ses-test_T1w + +# ============================ auto block: tcat ============================ +# apply 3dTcat to copy input dsets to results dir, while +# removing the first 0 TRs +3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 238 ) + +# ------------------------------------------------------- +# enter the results directory (can begin processing data) +cd $output_dir + + +# ========================== auto block: outcount ========================== +# data check: compute outlier fraction for each volume +touch out.pre_ss_warn.txt +foreach run ( $runs ) + 3dToutcount -automask -fraction -polort 4 -legendre \ + pb00.$subj.r$run.tcat+orig > outcount.r$run.1D + + # censor outlier TRs per run, ignoring the first 0 TRs + # - censor when more than 0.5 of automask voxels are outliers + # - step() defines which TRs to remove via censoring + 1deval -a outcount.r$run.1D -expr "1-step(a-0.5)" > rm.out.cen.r$run.1D + + # outliers at TR 0 might suggest pre-steady state TRs + if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then + echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ + >> out.pre_ss_warn.txt + endif +end + +# catenate outlier counts into a single time series +cat outcount.r*.1D > outcount_rall.1D + +# catenate outlier censor files into a single time series +cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D + +# ================================= tshift ================================= +# time shift data so all slice timing is the same +foreach run ( $runs ) + 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + pb00.$subj.r$run.tcat+orig +end + +# -------------------------------- +# extract volreg registration base +3dbucket -prefix vr_base pb01.$subj.r01.tshift+orig"[2]" + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-03_ses-test_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-test_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-03_ses-test_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base vr_base+orig \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg/epi2anat/tlrc xforms + cat_matvec -ONELINE \ + sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform: volreg/epi2anat/tlrc + 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc mask_epi_extents + +# and apply the extents mask to the EPI data +# (delete any time series with missing data) +foreach run ( $runs ) + 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc \ + -expr 'a*b' -prefix pb02.$subj.r$run.volreg +end + +# warp the volreg base EPI dataset to make a final version +cat_matvec -ONELINE \ + sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I > \ + mat.basewarp.aff12.1D + +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input vr_base+orig \ + -1Dmatrix_apply mat.basewarp.aff12.1D \ + -mast_dxyz 4 \ + -prefix final_epi_vr_base + +# create an anat_final dataset, aligned with stats +3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.$subj + +# record final registration costs +3dAllineate -base final_epi_vr_base+tlrc -allcostX \ + -input anat_final.$subj+tlrc |& tee out.allcostX.txt + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-03_ses-test_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== blur ================================== +# blur each volume of each run +foreach run ( $runs ) + 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.$subj.r$run.blur \ + pb02.$subj.r$run.volreg+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc +end + +# create union of inputs, output type is byte +3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj + +# ---- create subject anatomy mask, mask_anat.$subj+tlrc ---- +# (resampled from tlrc anat) +3dresample -master full_mask.$subj+tlrc -input sub-03_ses-test_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute overlaps between anat and EPI masks +3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_overlap.txt + +# note Dice coefficient of masks, as well +3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_dice.txt + +# ---- create group anatomy mask, mask_group+tlrc ---- +# (resampled from tlrc base anat, MNI_avg152T1+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/monicali/abin/MNI_avg152T1+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= scale ================================== +# scale each voxel time series to have a mean of 100 +# (be sure no negatives creep in) +# (subject to a range of [0,200]) +foreach run ( $runs ) + 3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.3 motion_${subj} + +# combine multiple censor files +1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \ + -expr "a*b" > censor_${subj}_combined_2.1D + +# note TRs that were not censored +set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \ + -show_trs_uncensored encoded` + +# ------------------------------ +# run the regression analysis +3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ + -censor censor_${subj}_combined_2.1D \ + -polort 4 \ + -num_stimts 17 \ + -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D 'GAM' \ + -stim_label 1 Correct_Task \ + -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D 'GAM' \ + -stim_label 2 Incorrect_Task \ + -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D 'GAM' \ + -stim_label 3 No_Response_Control \ + -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D 'GAM' \ + -stim_label 4 No_Response_Task \ + -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D 'GAM' \ + -stim_label 5 Response_Control \ + -stim_file 6 motion_demean.1D'[0]' -stim_base 6 -stim_label 6 roll_01 \ + -stim_file 7 motion_demean.1D'[1]' -stim_base 7 -stim_label 7 pitch_01 \ + -stim_file 8 motion_demean.1D'[2]' -stim_base 8 -stim_label 8 yaw_01 \ + -stim_file 9 motion_demean.1D'[3]' -stim_base 9 -stim_label 9 dS_01 \ + -stim_file 10 motion_demean.1D'[4]' -stim_base 10 -stim_label 10 dL_01 \ + -stim_file 11 motion_demean.1D'[5]' -stim_base 11 -stim_label 11 dP_01 \ + -stim_file 12 motion_deriv.1D'[0]' -stim_base 12 -stim_label 12 roll_02 \ + -stim_file 13 motion_deriv.1D'[1]' -stim_base 13 -stim_label 13 pitch_02 \ + -stim_file 14 motion_deriv.1D'[2]' -stim_base 14 -stim_label 14 yaw_02 \ + -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ + -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ + -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -glt_label 1 Landmark-Detection \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc"[$ktrs]" +3dcalc -a rm.signal.all+tlrc \ + -b rm.noise.all+tlrc \ + -c full_mask.$subj+tlrc \ + -expr 'c*a/b' -prefix TSNR.$subj + +# --------------------------------------------------- +# compute and store GCOR (global correlation average) +# (sum of squares of global mean of unit errts) +3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[5]' > ideal_Correct_Task.1D +1dcat X.nocensor.xmat.1D'[6]' > ideal_Incorrect_Task.1D +1dcat X.nocensor.xmat.1D'[7]' > ideal_No_Response_Control.1D +1dcat X.nocensor.xmat.1D'[8]' > ideal_No_Response_Task.1D +1dcat X.nocensor.xmat.1D'[9]' > ideal_Response_Control.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]" + +# also, create a stimulus-only X-matrix, for easy review +1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D + +# ============================ blur estimation ============================= +# compute blur estimates +touch blur_est.$subj.1D # start with empty file + +# create directory for ACF curve files +mkdir files_ACF + +# -- estimate blur for each run in epits -- +touch blur.epits.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +echo average epits FWHM blurs: $blurs +echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +echo average epits ACF blurs: $blurs +echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D + +# -- estimate blur for each run in errts -- +touch blur.errts.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +echo average errts FWHM blurs: $blurs +echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +echo average errts ACF blurs: $blurs +echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.5 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.3 -regress_censor_outliers 0.5 \ +# -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym 'SYM: \ +# 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task \ +# -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 \ +# Landmark-Detection -regress_make_ideal_sum sum_ideal.1D \ +# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 new file mode 100755 index 0000000..8c884ef --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 @@ -0,0 +1,47 @@ +#!/usr/bin/env tcsh + +# created by uber_subject.py: version 0.40 (March 30, 2017) +# creation date: Thu Aug 3 22:01:15 2017 + +# set data directories +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = $top_dir/sub-03/ses-test/anat +set epi_dir = $top_dir/sub-03/ses-test/func + +# set subject and group identifiers +set subj = sub_03 +set group_id = test + +# run afni_proc.py to create a single subject processing script +afni_proc.py -subj_id $subj \ + -script proc.$subj -scr_overwrite \ + -blocks tshift align tlrc volreg blur mask scale regress \ + -copy_anat $anat_dir/sub-03_ses-test_T1w.nii.gz \ + -tcat_remove_first_trs 0 \ + -dsets $epi_dir/sub-03_ses-test_task-linebisection_bold.nii.gz \ + -tlrc_base MNI_avg152T1+tlrc \ + -volreg_align_to third \ + -volreg_align_e2a \ + -volreg_tlrc_warp \ + -blur_size 3.0 \ + -regress_stim_times \ + $top_dir/timing_sub-03_ses-test_Correct_Task.1D \ + $top_dir/timing_sub-03_ses-test_Incorrect_Task.1D \ + $top_dir/timing_sub-03_ses-test_No_Response_Control.1D \ + $top_dir/timing_sub-03_ses-test_No_Response_Task.1D \ + $top_dir/timing_sub-03_ses-test_Response_Control.1D \ + -regress_stim_labels \ + Correct_Task Incorrect_Task No_Response_Control No_Response_Task \ + Response_Control \ + -regress_basis 'GAM' \ + -regress_censor_motion 0.5 \ + -regress_apply_mot_types demean deriv \ + -regress_opts_3dD \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control \ + -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ + -regress_make_ideal_sum sum_ideal.1D \ + -regress_est_blur_epits \ + -regress_est_blur_errts \ + -regress_run_clustsim no + diff --git a/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 new file mode 100644 index 0000000..242a016 --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 @@ -0,0 +1,29 @@ +set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set anat_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat +set epi_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func +set subj = sub_03 +set group_id = test +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control + -0.5*No_Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +-- applying orig view as +orig +-- tcat: reps is now 238 +++ updating polort to 4, from run len 595.0 s +-- volreg: using base dset vr_base+orig +++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 4 mm tlrc voxels +-- applying anat warps to 1 dataset(s): sub-03_ses-test_T1w +-- masking: group anat = 'MNI_avg152T1+tlrc', exists = 1 +-- have 1 ROI dict entries ... +-- will apply motion types: demean, deriv +-- using default: will not apply EPI Automask + (see 'MASKING NOTE' from the -help for details) + +------------------------------------- +** warning have only 1 run to analyze +------------------------------------- + +--> script is file: proc.sub_03 + consider the script execution command: + + tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + diff --git a/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 new file mode 100644 index 0000000..a36666b --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 @@ -0,0 +1,964 @@ +echo auto-generated by afni_proc.py, Thu Aug 3 22:21:48 2017 +auto-generated by afni_proc.py, Thu Aug 3 22:21:48 2017 +echo (version 5.15, April 25, 2017) +(version 5.15, April 25, 2017) +echo execution started: `date` +date +execution started: Thu Aug 3 22:30:59 EDT 2017 +afni -ver +Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) +afni_history -check_date 23 Sep 2016 +-- is current: afni_history as new as: 23 Sep 2016 + most recent entry is: 21 Jul 2017 +if ( 0 ) then +if ( 0 > 0 ) then +set subj = sub_03 +endif +set output_dir = sub_03.results +if ( -d sub_03.results ) then +set runs = ( `count -digits 2 1 1` ) +count -digits 2 1 1 +mkdir sub_03.results +mkdir sub_03.results/stimuli +cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D sub_03.results/stimuli +3dcopy /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz sub_03.results/sub-03_ses-test_T1w +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[0..$] +++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ elapsed time = 2.1 s +set tr_counts = ( 238 ) +cd sub_03.results +touch out.pre_ss_warn.txt +foreach run ( 01 ) +3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig +++ 3dToutcount: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. +++ 17837 voxels passed mask/clip +if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then +1deval -a outcount.r01.1D{0} -expr step(a-0.4) +echo ** TR #0 outliers: possible pre-steady state TRs in run 01 +endif +end +cat outcount.r01.1D +foreach run ( 01 ) +3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig +++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. +*+ WARNING: dataset is already aligned in time! +*+ WARNING: ==>> output dataset is just a copy of input dataset +end +3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] +++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off +#++ align_epi_anat version: 1.57 +#++ turning off volume registration +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./sub-03_ses-test_T1w+orig +#++ Multi-cost is lpc +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-test_T1w* +#Script is running (command trimmed): + 3dcopy ./sub-03_ses-test_T1w+orig ./__tt_sub-03_ses-test_T1w+orig +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ Removing skull from anat data +#Script is running (command trimmed): + 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-test_T1w+orig -prefix ./__tt_sub-03_ses-test_T1w_ns +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-test_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. +#Script is running (command trimmed): + 3dinfo ./__tt_sub-03_ses-test_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' +#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig is ***oblique**** +#Script is running (command trimmed): + 3dAttribute DELTA ./__tt_sub-03_ses-test_T1w_ns+orig +#++ Spacing for anat to oblique epi alignment is 1.000000 +#++ Matching obliquity of anat to epi +#Script is running (command trimmed): + 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-test_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Deobliquing original dataset before obliquing +++ Combining oblique transformations +++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob+orig.BRIK +#++ using 0th sub-brick because only one found +#Script is running (command trimmed): + 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' +++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ resampling epi to match anat data +#Script is running (command trimmed): + 3dresample -master ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_vr_base_ts+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_vr_base_ts+orig.BRIK is 6.153038 degrees from plumb. +#++ removing skull or area outside brain +#Script is running (command trimmed): + 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig +++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset ./__tt_vr_base_ts_rs+orig +++ Forming automask + + Fixed clip level = 722.140930 + + Used gradual clip level = 624.995605 .. 827.664490 + + Number voxels above clip level = 1139938 + + Clustering voxels ... + + Largest cluster has 1138291 voxels + + Clustering voxels ... + + Largest cluster has 1137874 voxels + + Filled 374 voxels in small holes; now have 1138248 voxels + + Filled 17631 voxels in large holes; now have 1155879 voxels + + Clustering voxels ... + + Largest cluster has 1155874 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 15251279 voxels + + Mask now has 1155874 voxels +++ 1155874 voxels in the mask [out of 16407153: 7.04%] +++ first 71 x-planes are zero [from R] +++ last 75 x-planes are zero [from L] +++ first 33 y-planes are zero [from A] +++ last 17 y-planes are zero [from P] +++ first 123 z-planes are zero [from I] +++ last 36 z-planes are zero [from S] +++ applying mask to original data +++ Writing masked data +++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK +++ CPU time = 3.570000 sec +#++ Computing weight mask +#Script is running (command trimmed): + 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1890.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#Script is running (command trimmed): + 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1890.000000))' +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK +#++ Aligning anat data to epi data +#Script is running (command trimmed): + 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns_ob+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets +++ 1350442 voxels in -source_automask+4 +++ Zero-pad: not needed +++ 1155874 voxels [7.0%] in weight mask +++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal+orig.BRIK +++ Number of points for matching = 1155874 +++ Local correlation: blok type = 'RHDD(6.54321)' +++ shift param auto-range: -89.2..89.2 -69.3..69.3 -86.7..86.7 + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 + + 12 free parameters +++ Normalized convergence radius = 0.001000 +++ OpenMP thread count = 4 +++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= +++ ========== sub-brick #0 ========== [total CPU to here=9.8 s] +++ *** Fine pass begins *** + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - copying weight image + + - using 1155874 points from base image [use_all=0] + + * Exit alignment setup routine + + 1095215 total points stored in 2075 'RHDD(6.54321)' bloks + + - Initial cost = -0.096907 + + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +*************************************************************************************************************************************************************************************************************************************************************************************************** + + - Finalish cost = -0.235911 ; 645 funcs +** + + - Final cost = -0.235912 ; 97 funcs + + Final fine fit Parameters: + x-shift= 0.2099 y-shift=-0.6560 z-shift=-1.7075 + z-angle=-0.6314 x-angle= 4.7459 y-angle=-1.0126 + x-scale= 0.9677 y-scale= 0.9751 z-scale= 1.0200 + y/x-shear=-0.0038 z/x-shear= 0.0093 z/y-shear= 0.0929 + + - Fine net CPU time = 51.8 s +++ Computing output image +++ image warp: parameters = 0.2099 -0.6560 -1.7075 -0.6314 4.7459 -1.0126 0.9677 0.9751 1.0200 -0.0038 0.0093 0.0929 +++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk+orig.BRIK +++ Wrote -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D +++ 3dAllineate: total CPU time = 64.0 sec Elapsed = 38.0 +++ ########################################################### +++ # Please check results visually for alignment quality # +++ ########################################################### +++ # '-autoweight' is recommended when using -lpc or -lpa # +++ # If your results are not good, please try again. # +++ ########################################################### +#Script is running (command trimmed): + cat_matvec -ONELINE ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D -I > ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D +#++ Combining anat to epi and oblique transformations +#Script is running (command trimmed): + 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-test_T1w_al_junk -input ./__tt_sub-03_ses-test_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +++ ========== sub-brick #0 ========== [total CPU to here=0.1 s] + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - no weight image + + - using 11 points from base image [use_all=0] + + * Exit alignment setup routine +++ using -1Dmatrix_apply +++ Computing output image +++ image warp: parameters = 0.9643 -0.0770 -0.0643 8.3030 0.0414 0.9701 -0.0701 -8.0767 0.0578 0.0003 1.0212 -4.7196 +++ Output dataset ./sub-03_ses-test_T1w_al_junk+orig.BRIK +++ 3dAllineate: total CPU time = 2.4 sec Elapsed = 5.6 +++ ########################################################### +#++ Creating final output: skullstripped anat data +copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig +#Script is running (command trimmed): + 3dcopy ./__tt_sub-03_ses-test_T1w_ns+orig sub-03_ses-test_T1w_ns +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#++ Creating final output: anat data aligned to epi +# copy is not necessary +#++ Saving history +#Script is running (command trimmed): + 3dNotes -h "align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ + -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask -volreg off -tshift off" \ + ./sub-03_ses-test_T1w_al_junk+orig + +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-test_T1w* + +# Finished alignment successfully + +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-test_T1w_ns+orig -no_ss +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. + +*********** Warning ************* +Dataset centers are 52.843487 mm +apart. If registration fails, or if +parts of the original anatomy gets +cropped, try adding option + -init_xform AUTO_CENTER +to your @auto_tlrc command. + +********************************* + +Padding ... +++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK +Resampling ... +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__ats_tmp__resamp_step+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 6.455733 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +Clipping -0.000100 1158.000100 ... +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./__ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.BRIK +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Registration (linear final interpolation) ... +++ 3dWarpDrive: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Initial scale factor set to 0.30/273.95=9.2e+02 +RMS[0] = 0.384861 0.16449 ITER = 6/137 +0.384861 + +Warping has converged. + +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ 6.455733 degrees from plumb. +*+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations +Applying brain mask +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK +++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.BRIK +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ././__ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK +Unpadding ... +++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ output dataset: ./__ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.BRIK +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig +*+ WARNING: Changing the space of an ORIG view dataset may cause confusion! +*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space). +*+ WARNING: Consider changing the view of the dataset to TLRC view also +++ 3drefit processed 1 datasets +Changing view of transformed anatomy +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Setting parent with 3drefit -wset sub-03_ses-test_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc +++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc +++ 3drefit processed 1 datasets +++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Warning: ignoring +tlrc on new_prefix. +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.HEAD -> sub-03_ses-test_T1w_ns+tlrc.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.BRIK -> sub-03_ses-test_T1w_ns+tlrc.BRIK +Cleanup ... +cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I +if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then +foreach run ( 01 ) +3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig +++ 3dvolreg: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 6.153038 degrees from plumb. +++ Reading in base dataset ./vr_base+orig.BRIK +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 6.153038 degrees from plumb. +++ Reading input dataset ./pb01.sub_03.r01.tshift+orig.BRIK +++ Edging: x=3 y=3 z=2 +++ Creating mask for -maxdisp + + Automask has 18932 voxels + + 3319 voxels left in -maxdisp mask after erosion +++ Initializing alignment base +++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. +++ CPU time for realignment=9.58 s [=0.0403 s/sub-brick] +++ Min : roll=-0.125 pitch=-0.838 yaw=-0.100 dS=-1.314 dL=-0.122 dP=-0.602 +++ Mean: roll=+0.244 pitch=-0.353 yaw=+1.492 dS=+1.594 dL=+0.625 dP=-0.273 +++ Max : roll=+0.752 pitch=+0.977 yaw=+2.780 dS=+2.627 dL=+1.582 dP=+0.307 +++ Max displacements (mm) for each sub-brick: + 1.52(0.00) 0.25(1.43) 0.00(0.25) 0.40(0.40) 0.85(0.46) 0.73(0.21) 0.34(0.44) 0.80(0.50) 0.82(0.05) 0.97(0.22) 0.87(0.11) 1.14(0.27) 1.23(0.16) 1.37(0.28) 1.26(0.16) 1.40(0.16) 1.34(0.10) 1.53(0.22) 1.37(0.18) 1.47(0.12) 1.43(0.07) 1.39(0.23) 1.43(0.08) 1.54(0.12) 1.51(0.07) 1.54(0.05) 1.54(0.05) 1.63(0.10) 1.61(0.10) 1.65(0.10) 1.58(0.17) 1.71(0.19) 1.62(0.17) 1.77(0.19) 1.79(0.08) 1.95(0.18) 1.92(0.03) 2.10(0.19) 2.00(0.14) 2.23(0.27) 2.03(0.25) 2.26(0.23) 2.09(0.31) 2.37(0.33) 2.12(0.35) 2.37(0.41) 2.24(0.24) 2.31(0.12) 2.16(0.21) 1.75(0.92) 1.69(0.29) 1.26(0.56) 0.82(1.06) 1.02(0.77) 1.77(1.06) 2.02(2.37) 2.06(0.37) 3.95(3.75) 3.32(0.64) 3.59(1.18) 3.39(0.23) 3.42(0.10) 3.04(0.50) 2.05(1.20) 2.22(0.39) 3.63(1.92) 1.23(3.45) 1.76(1.27) 2.43(0.95) 2.71(0.28) 2.77(0.09) 3.03(0.29) 2.84(0.35) 2.83(0.31) 2.96(0.54) 2.87(0.19) 2.94(0.08) 2.89(0.08) 2.81(0.17) 2.77(0.22) 2.81(0.14) 2.95(0.14) 2.95(0.08) 3.06(0.14) 3.10(0.07) 3.01(0.16) 3.28(0.30) 3.28(0.02) 3.43(0.18) 3.45(0.06) 3.56(0.13) 3.57(0.06) 3.65(0.08) 3.70(0.08) 3.59(0.15) 3.66(0.17) 3.19(0.76) 3.37(0.22) 3.17(0.24) 3.47(0.52) 3.40(0.19) 3.40(0.24) 3.00(0.74) 3.66(1.10) 3.60(0.37) 3.73(0.37) 3.84(0.14) 3.89(0.14) 3.87(0.11) 3.89(0.14) 3.80(0.15) 3.73(0.12) 3.58(0.20) 3.69(0.13) 3.73(0.21) 3.94(0.25) 3.97(0.12) 4.13(0.21) 4.09(0.08) 4.18(0.13) 4.31(0.20) 4.11(0.27) 4.31(0.31) 4.13(0.23) 3.87(0.38) 3.82(0.12) 3.71(0.29) 3.74(0.07) 3.87(0.25) 3.89(0.04) 4.03(0.17) 4.19(0.19) 4.11(0.13) 4.27(0.21) 4.04(0.40) 4.27(0.29) 4.15(0.16) 4.26(0.14) 4.45(0.22) 4.07(0.63) 4.50(0.54) 4.38(0.16) 4.90(0.59) 4.74(0.24) 4.66(0.13) 4.65(0.20) 4.60(0.17) 4.66(0.26) 4.53(0.16) 4.73(0.26) 4.77(0.11) 4.69(0.13) 4.51(0.35) 4.52(0.15) 4.72(0.22) 4.55(0.21) 4.72(0.18) 4.65(0.12) 4.70(0.06) 4.79(0.14) 5.04(0.26) 4.95(0.48) 5.70(1.30) 5.19(0.83) 5.18(0.35) 5.42(0.26) 5.61(0.36) 5.74(0.24) 5.78(0.09) 5.89(0.15) 5.83(0.13) 5.83(0.10) 5.80(0.06) 5.73(0.25) 5.59(0.28) 5.50(0.39) 5.51(0.31) 5.49(0.23) 5.37(0.20) 5.45(0.10) 5.55(0.10) 5.64(0.17) 5.69(0.08) 5.62(0.12) 5.73(0.14) 5.69(0.09) 5.45(0.51) 5.28(0.22) 5.59(0.71) 5.03(0.73) 4.43(0.85) 4.81(0.47) 5.08(0.37) 5.55(0.73) 5.80(0.42) 5.82(0.13) 5.79(0.07) 6.03(0.40) 5.85(0.36) 5.89(0.09) 5.76(0.31) 5.95(0.23) 6.06(0.14) 5.97(0.17) 6.01(0.08) 6.11(0.29) 6.11(0.07) 6.21(0.16) 6.12(0.24) 6.18(0.07) 6.15(0.16) 6.15(0.10) 6.11(0.10) 6.23(0.23) 6.11(0.23) 6.18(0.10) 6.13(0.07) 6.12(0.08) 6.14(0.15) 6.04(0.16) 6.16(0.16) 6.15(0.11) 5.93(0.28) 6.00(0.08) 5.90(0.20) 5.86(0.40) 5.77(0.25) 6.07(0.68) 6.04(0.20) 5.99(0.20) 6.28(0.40) 6.31(0.10) 6.35(0.22) 6.33(0.19) 6.10(0.42) 6.01(0.25) 6.16(0.24) 6.13(0.07) +++ Max displacement in automask = 6.35 (mm) at sub-brick 232 +++ Max delta displ in automask = 3.75 (mm) at sub-brick 57 +++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK +3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +*+ WARNING: input 'a' is not used in the expression +++ Output dataset ./rm.epi.all1+orig.BRIK +cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb01.sub_03.r01.tshift+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 6.153038 degrees from plumb. +++ Source dataset: ./pb01.sub_03.r01.tshift+orig.HEAD +++ Base dataset: ./sub-03_ses-test_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 238 sub-bricks ========== +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 6.0 sec Elapsed = 4.9 +++ ########################################################### +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./rm.epi.all1+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./rm.epi.all1+orig.BRIK is 6.153038 degrees from plumb. +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ Output dataset ./rm.epi.1.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 4.1 +3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.epi.min.r01+tlrc.BRIK +end +cat dfile.r01.1D +3dcopy rm.epi.min.r01+tlrc mask_epi_extents +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +foreach run ( 01 ) +3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK +end +cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 6.153038 degrees from plumb. +++ Source dataset: ./vr_base+orig.HEAD +++ Base dataset: ./sub-03_ses-test_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.2 +++ ########################################################### +3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.sub_03 +++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc +tee out.allcostX.txt +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./anat_final.sub_03+tlrc.HEAD +++ Base dataset: ./final_epi_vr_base+tlrc.HEAD +++ Loading datasets +++ 223015 voxels in source_automask+0 +++ Zero-pad: xbot=2 xtop=2 +++ Zero-pad: ybot=0 ytop=1 +++ Zero-pad: zbot=1 ztop=1 +++ Computing -autobox +++ 113223 voxels [89.4%] in weight mask +++ Number of points for matching = 53214 +++ Local correlation: blok type = 'RHDD(14.76)' +*+ WARNING: No output dataset will be calculated +++ OpenMP thread count = 4 +volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +++ allcost output: init #0 + ls = 0.183754 + sp = 0.30567 + mi = -0.534639 + crM = 0.0839806 + nmi = 0.868199 + je = 3.52175 + hel = -0.107071 + crA = 0.290078 + crU = 0.302909 + lss = 0.816246 + lpc = 0.339594 + lpa = 0.660406 + lpc+ = 0.540057 + ncd = 0.974675 +++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.5 +++ ########################################################### +3dAllineate -source sub-03_ses-test_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped +++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. +++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers +++ Source dataset: ./sub-03_ses-test_T1w+orig.HEAD +++ Base dataset: (not given) +++ Loading datasets +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ð++ wsinc5 interpolation setup: + + taper function = Min sidelobe 3 term + + taper cut point = 0.000 + + window radius = 5 voxels + + window shape = Cubical + + The above can be altered via the AFNI_WSINC5_* environment variables. + + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + + wsinc5 CUBE(5) mask has 1000 points +++ Output dataset ./anat_w_skull_warped+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.1 sec Elapsed = 2.0 +++ ########################################################### +foreach run ( 01 ) +3dmerge -1blur_fwhm 3.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc +++ 3dmerge: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ default -1dindex = 0 +++ default -1tindex = 1 +Program 3dmerge +3dmerge: edit and combine 3D datasets, by RW Cox +++ editing input dataset in memory (49.6 MB) +..............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK + +end +foreach run ( 01 ) +3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc +++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset pb03.sub_03.r01.blur+tlrc +++ Forming automask + + Fixed clip level = 721.097839 + + Used gradual clip level = 636.466919 .. 805.468140 + + Number voxels above clip level = 27995 + + Clustering voxels ... + + Largest cluster has 27978 voxels + + Clustering voxels ... + + Largest cluster has 27818 voxels + + Filled 108 voxels in small holes; now have 27926 voxels + + Clustering voxels ... + + Largest cluster has 27926 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 81416 voxels + + Mask now has 27934 voxels +++ Dilating automask + + Clustering voxels ... + + Largest cluster has 76286 voxels +++ 33064 voxels in the mask [out of 109350: 30.24%] +++ first 4 x-planes are zero [from L] +++ last 3 x-planes are zero [from R] +++ first 4 y-planes are zero [from P] +++ last 3 y-planes are zero [from A] +++ first 3 z-planes are zero [from I] +++ last 3 z-planes are zero [from S] +++ Output dataset ./rm.mask_r01+tlrc.BRIK +++ CPU time = 0.280000 sec +end +3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 +++ processing 1 input datasets... +++ padding all datasets by 0 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 33064 survived, 76286 were zero +++ writing result full_mask.sub_03... +++ Output dataset ./full_mask.sub_03+tlrc.BRIK +3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-test_T1w_ns+tlrc -prefix rm.resam.anat +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30704 survived, 78646 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_anat.sub_03... +++ Output dataset ./mask_anat.sub_03+tlrc.BRIK +3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_overlap.txt +++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +#A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK +#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) +33064 30704 35830 27938 5126 2766 15.5033 9.0086 0.9518 0.9265 0.9782 +3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_dice.txt +0.876239 +3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30980 survived, 78370 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_group... +++ Output dataset ./mask_group+tlrc.BRIK +foreach run ( 01 ) +3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.mean_r01+tlrc.BRIK +3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK +end +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 +total number of censored TRs (simple form) = 21 +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D + -show_trs_uncensored encoded` +1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: B. Douglas Ward, et al. +++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD +++ STAT automask has 97119 voxels (out of 109350 = 88.8%) +++ Skipping check for initial transients +++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ +++ -stim_times using TR=2.5 s for stimulus timing conversion +++ -stim_times using TR=2.5 s for any -iresp output datasets +++ [you can alter the -iresp TR via the -TR_times option] +++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise +++ ** GUESSED ** -stim_times 1 using LOCAL times +++ ** GUESSED ** -stim_times 2 using LOCAL times +++ ** GUESSED ** -stim_times 3 using LOCAL times +++ ** GUESSED ** -stim_times 4 using LOCAL times +++ ** GUESSED ** -stim_times 5 using LOCAL times +------------------------------------------------------------ +GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control': + 0 0 0 0 0 0.333 0.333 -0.5 0.333 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 + +++ Number of time points: 238 (before censor) ; 217 (after) + + Number of parameters: 22 [17 baseline ; 5 signal] +++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) +++ Wrote matrix image to file X.jpg +++ Wrote matrix values to file X.xmat.1D +++ ========= Things you can do with the matrix file ========= +++ (a) Linear regression with ARMA(1,1) modeling of serial correlation: + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb + +++ N.B.: 3dREMLfit command above written to file stats.REML_cmd +++ (b) Visualization/analysis of the matrix via ExamineXmat.R +++ (c) Synthesis of sub-model datasets using 3dSynthesize +++ ========================================================== +++ Wrote matrix values to file X.nocensor.xmat.1D +++ ----- Signal+Baseline matrix condition [X] (217x22): 7.87414 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (217x5): 1.46311 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (217x17): 7.75168 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (217x12): 6.17475 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (217x5): 1.09587 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 1.12762e-14 ++ VERY GOOD ++ +++ Matrix setup time = 0.77 s +++ Calculations starting; elapsed time=1.314 +++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. +++ Calculations finished; elapsed time=14.889 +++ Smallest FDR q [0 Full_Fstat] = 1.54028e-12 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 7.9356e-11 +++ Smallest FDR q [3 Correct_Task_Fstat] = 7.9356e-11 +*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.123923 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.123702 ==> few true single voxel detections +++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.054463 +++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.0543708 +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 1.38372e-11 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 1.38372e-11 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 4.43676e-05 +++ Smallest FDR q [15 Response_Control_Fstat] = 4.43706e-05 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.000204818 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.000204822 +++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + + created 13 FDR curves in bucket header +++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK +++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK +++ #Flops=3.97183e+10 Average Dot Product=37.2229 +if ( 0 != 0 ) then +1d_tool.py -show_cormat_warnings -infile X.xmat.1D +tee out.cormat_warn.txt + +Warnings regarding Correlation Matrix: X.xmat.1D + + severity correlation cosine regressor pair + -------- ----------- ------ ---------------------------------------- + medium: 0.566 0.642 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 + +3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD +++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ elapsed time = 0.9 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.signal.all+tlrc.BRIK +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.noise.all+tlrc.BRIK +3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./TSNR.sub_03+tlrc.BRIK +3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc +++ 3dTnorm: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RW Cox +++ Output dataset ./rm.errts.unit+tlrc.BRIK +3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc +++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] ++++ 33064 voxels survive the mask +3dTstat -sos -prefix - gmean.errts.unit.1D' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo -- GCOR = `cat out.gcor.1D` +cat out.gcor.1D +-- GCOR = 0.0653973 +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP +++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./rm.DP+tlrc.BRIK +3dTstat -sum -prefix corr_brain rm.DP+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./corr_brain+tlrc.BRIK +1dcat X.nocensor.xmat.1D[5] +1dcat X.nocensor.xmat.1D[6] +1dcat X.nocensor.xmat.1D[7] +1dcat X.nocensor.xmat.1D[8] +1dcat X.nocensor.xmat.1D[9] +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +++ Output dataset ./sum_ideal.1D +1dcat X.nocensor.xmat.1D[5..9] +touch blur_est.sub_03.1D +mkdir files_ACF +touch blur.epits.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 2..50,60,61,68..101,104..160,163..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] +++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 33064 +*+ WARNING: removed 254 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 217 time points + + detrending done (2.33 CPU s thus far) +++ start ACF calculations out to radius = 18.97 mm + + ACF done (32.36 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits FWHM blurs: 0 0 0 0 +average epits FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # epits FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits ACF blurs: 0.834334 3.52471 15.2586 9.03233 +average epits ACF blurs: 0.834334 3.52471 15.2586 9.03233 +echo 0.834334 3.52471 15.2586 9.03233 # epits ACF blur estimates +touch blur.errts.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 2..50,60,61,68..101,104..160,163..237 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] +++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 33064 +*+ WARNING: removed 254 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 217 time points + + detrending done (2.27 CPU s thus far) +++ start ACF calculations out to radius = 18.90 mm + + ACF done (32.31 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts FWHM blurs: 0 0 0 0 +average errts FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # errts FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts ACF blurs: 0.86343 3.55309 16.3317 9.01111 +average errts ACF blurs: 0.86343 3.55309 16.3317 9.01111 +echo 0.86343 3.55309 16.3317 9.01111 # errts ACF blur estimates +gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 +++ writing ss review basic: @ss_review_basic +++ writing ss review driver: @ss_review_driver +++ writing ss review drive commands: @ss_review_driver_commands +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +tee out.ss_review.sub_03.txt +if ( -e @ss_review_basic ) ./@ss_review_basic +./@ss_review_basic + +subject ID : sub_03 +TRs removed (per run) : 0 +num stim classes provided : 5 +final anatomy dset : anat_final.sub_03+tlrc.HEAD +final stats dset : stats.sub_03+tlrc.HEAD +final voxel resolution : 4.000000 4.000000 4.000000 + +motion limit : 0.5 +num TRs above mot limit : 13 +average motion (per TR) : 0.179191 +average censored motion : 0.129595 +max motion displacement : 5.04394 +max censored displacement : 3.96802 +outlier limit : 0.1 +average outlier frac (TR) : 0.0152516 +num TRs above out limit : 8 + +num runs found : 1 +num TRs per run : 238 +num TRs per run (applied) : 217 +num TRs per run (censored): 21 +fraction censored per run : 0.0882353 +TRs total (uncensored) : 238 +TRs total : 217 +degrees of freedom used : 22 +degrees of freedom left : 195 + +TRs censored : 21 +censor fraction : 0.088235 +num regs of interest : 5 +num TRs per stim (orig) : 71 43 64 28 79 +num TRs censored per stim : 0 0 13 6 12 +fraction TRs censored : 0.000 0.000 0.203 0.214 0.152 +ave mot per sresp (orig) : 0.124806 0.112975 0.230781 0.273948 0.190656 +ave mot per sresp (cens) : 0.124806 0.112975 0.122112 0.144313 0.107954 + +TSNR average : 135.813 +global correlation (GCOR) : 0.0653973 +anat/EPI mask Dice coef : 0.876239 +maximum F-stat (masked) : 42.6934 +blur estimates (ACF) : 0.86343 3.55309 16.3317 +blur estimates (FWHM) : 0 0 0 + +** TR #0 outliers: possible pre-steady state TRs in run 01 + +cd .. +echo execution finished: `date` +date +execution finished: Thu Aug 3 22:35:55 EDT 2017 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 new file mode 100755 index 0000000..7e92ab6 --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 @@ -0,0 +1,479 @@ +#!/bin/tcsh -xef + +echo "auto-generated by afni_proc.py, Thu Aug 3 22:21:48 2017" +echo "(version 5.15, April 25, 2017)" +echo "execution started: `date`" + +# execute via : +# tcsh -xef proc.sub_03 |& tee output.proc.sub_03 + +# =========================== auto block: setup ============================ +# script setup + +# take note of the AFNI version +afni -ver + +# check that the current AFNI version is recent enough +afni_history -check_date 23 Sep 2016 +if ( $status ) then + echo "** this script requires newer AFNI binaries (than 23 Sep 2016)" + echo " (consider: @update.afni.binaries -defaults)" + exit +endif + +# the user may specify a single subject to run with +if ( $#argv > 0 ) then + set subj = $argv[1] +else + set subj = sub_03 +endif + +# assign output directory name +set output_dir = $subj.results + +# verify that the results directory does not yet exist +if ( -d $output_dir ) then + echo output dir "$subj.results" already exists + exit +endif + +# set list of runs +set runs = (`count -digits 2 1 1`) + +# create results and stimuli directories +mkdir $output_dir +mkdir $output_dir/stimuli + +# copy stim files into stimulus directory +cp \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ + /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ + $output_dir/stimuli + +# copy anatomy to results dir +3dcopy \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ + $output_dir/sub-03_ses-test_T1w + +# ============================ auto block: tcat ============================ +# apply 3dTcat to copy input dsets to results dir, while +# removing the first 0 TRs +3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ + /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' + +# and make note of repetitions (TRs) per run +set tr_counts = ( 238 ) + +# ------------------------------------------------------- +# enter the results directory (can begin processing data) +cd $output_dir + + +# ========================== auto block: outcount ========================== +# data check: compute outlier fraction for each volume +touch out.pre_ss_warn.txt +foreach run ( $runs ) + 3dToutcount -automask -fraction -polort 4 -legendre \ + pb00.$subj.r$run.tcat+orig > outcount.r$run.1D + + # outliers at TR 0 might suggest pre-steady state TRs + if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then + echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \ + >> out.pre_ss_warn.txt + endif +end + +# catenate outlier counts into a single time series +cat outcount.r*.1D > outcount_rall.1D + +# ================================= tshift ================================= +# time shift data so all slice timing is the same +foreach run ( $runs ) + 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + pb00.$subj.r$run.tcat+orig +end + +# -------------------------------- +# extract volreg registration base +3dbucket -prefix vr_base pb01.$subj.r01.tshift+orig"[2]" + +# ================================= align ================================== +# for e2a: compute anat alignment transformation to EPI registration base +# (new anat will be intermediate, stripped, sub-03_ses-test_T1w_ns+orig) +align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ + -save_skullstrip -suffix _al_junk \ + -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask \ + -volreg off -tshift off + +# ================================== tlrc ================================== +# warp anatomy to standard space +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-test_T1w_ns+orig -no_ss + +# store forward transformation matrix in a text file +cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D + +# ================================= volreg ================================= +# align each dset to base volume, align to anat, warp to tlrc space + +# verify that we have a +tlrc warp dataset +if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then + echo "** missing +tlrc warp dataset: sub-03_ses-test_T1w_ns+tlrc.HEAD" + exit +endif + +# register and warp +foreach run ( $runs ) + # register each volume to the base + 3dvolreg -verbose -zpad 1 -base vr_base+orig \ + -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \ + -cubic \ + -1Dmatrix_save mat.r$run.vr.aff12.1D \ + pb01.$subj.r$run.tshift+orig + + # create an all-1 dataset to mask the extents of the warp + 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 \ + -prefix rm.epi.all1 + + # catenate volreg/epi2anat/tlrc xforms + cat_matvec -ONELINE \ + sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I \ + mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D + + # apply catenated xform: volreg/epi2anat/tlrc + 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input pb01.$subj.r$run.tshift+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 \ + -prefix rm.epi.nomask.r$run + + # warp the all-1 dataset for extents masking + 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input rm.epi.all1+orig \ + -1Dmatrix_apply mat.r$run.warp.aff12.1D \ + -mast_dxyz 4 -final NN -quiet \ + -prefix rm.epi.1.r$run + + # make an extents intersection mask of this run + 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc +end + +# make a single file of registration params +cat dfile.r*.1D > dfile_rall.1D + +# ---------------------------------------- +# create the extents mask: mask_epi_extents+tlrc +# (this is a mask of voxels that have valid data at every TR) +# (only 1 run, so just use 3dcopy to keep naming straight) +3dcopy rm.epi.min.r01+tlrc mask_epi_extents + +# and apply the extents mask to the EPI data +# (delete any time series with missing data) +foreach run ( $runs ) + 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc \ + -expr 'a*b' -prefix pb02.$subj.r$run.volreg +end + +# warp the volreg base EPI dataset to make a final version +cat_matvec -ONELINE \ + sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I \ + sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I > \ + mat.basewarp.aff12.1D + +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc \ + -input vr_base+orig \ + -1Dmatrix_apply mat.basewarp.aff12.1D \ + -mast_dxyz 4 \ + -prefix final_epi_vr_base + +# create an anat_final dataset, aligned with stats +3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.$subj + +# record final registration costs +3dAllineate -base final_epi_vr_base+tlrc -allcostX \ + -input anat_final.$subj+tlrc |& tee out.allcostX.txt + +# ----------------------------------------- +# warp anat follower datasets (affine) +3dAllineate -source sub-03_ses-test_T1w+orig \ + -master anat_final.$subj+tlrc \ + -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D \ + -prefix anat_w_skull_warped + +# ================================== blur ================================== +# blur each volume of each run +foreach run ( $runs ) + 3dmerge -1blur_fwhm 3.0 -doall -prefix pb03.$subj.r$run.blur \ + pb02.$subj.r$run.volreg+tlrc +end + +# ================================== mask ================================== +# create 'full_mask' dataset (union mask) +foreach run ( $runs ) + 3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc +end + +# create union of inputs, output type is byte +3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj + +# ---- create subject anatomy mask, mask_anat.$subj+tlrc ---- +# (resampled from tlrc anat) +3dresample -master full_mask.$subj+tlrc -input sub-03_ses-test_T1w_ns+tlrc \ + -prefix rm.resam.anat + +# convert to binary anat mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc \ + -prefix mask_anat.$subj + +# compute overlaps between anat and EPI masks +3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_overlap.txt + +# note Dice coefficient of masks, as well +3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc \ + |& tee out.mask_ae_dice.txt + +# ---- create group anatomy mask, mask_group+tlrc ---- +# (resampled from tlrc base anat, MNI_avg152T1+tlrc) +3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ + -input /Users/monicali/abin/MNI_avg152T1+tlrc + +# convert to binary group mask; fill gaps and holes +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ + -prefix mask_group + +# ================================= scale ================================== +# scale each voxel time series to have a mean of 100 +# (be sure no negatives creep in) +# (subject to a range of [0,200]) +foreach run ( $runs ) + 3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc + 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \ + -c mask_epi_extents+tlrc \ + -expr 'c * min(200, a/b*100)*step(a)*step(b)' \ + -prefix pb04.$subj.r$run.scale +end + +# ================================ regress ================================= + +# compute de-meaned motion parameters (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -demean -write motion_demean.1D + +# compute motion parameter derivatives (for use in regression) +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -derivative -demean -write motion_deriv.1D + +# create censor file motion_${subj}_censor.1D, for censoring motion +1d_tool.py -infile dfile_rall.1D -set_nruns 1 \ + -show_censor_count -censor_prev_TR \ + -censor_motion 0.5 motion_${subj} + +# note TRs that were not censored +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ + -show_trs_uncensored encoded` + +# ------------------------------ +# run the regression analysis +3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \ + -censor motion_${subj}_censor.1D \ + -polort 4 \ + -num_stimts 17 \ + -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D 'GAM' \ + -stim_label 1 Correct_Task \ + -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D 'GAM' \ + -stim_label 2 Incorrect_Task \ + -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D 'GAM' \ + -stim_label 3 No_Response_Control \ + -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D 'GAM' \ + -stim_label 4 No_Response_Task \ + -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D 'GAM' \ + -stim_label 5 Response_Control \ + -stim_file 6 motion_demean.1D'[0]' -stim_base 6 -stim_label 6 roll_01 \ + -stim_file 7 motion_demean.1D'[1]' -stim_base 7 -stim_label 7 pitch_01 \ + -stim_file 8 motion_demean.1D'[2]' -stim_base 8 -stim_label 8 yaw_01 \ + -stim_file 9 motion_demean.1D'[3]' -stim_base 9 -stim_label 9 dS_01 \ + -stim_file 10 motion_demean.1D'[4]' -stim_base 10 -stim_label 10 dL_01 \ + -stim_file 11 motion_demean.1D'[5]' -stim_base 11 -stim_label 11 dP_01 \ + -stim_file 12 motion_deriv.1D'[0]' -stim_base 12 -stim_label 12 roll_02 \ + -stim_file 13 motion_deriv.1D'[1]' -stim_base 13 -stim_label 13 pitch_02 \ + -stim_file 14 motion_deriv.1D'[2]' -stim_base 14 -stim_label 14 yaw_02 \ + -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ + -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ + -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ + -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ + +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -glt_label 1 Landmark-Detection \ + -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ + -x1D_uncensored X.nocensor.xmat.1D \ + -fitts fitts.$subj \ + -errts errts.${subj} \ + -bucket stats.$subj + + +# if 3dDeconvolve fails, terminate the script +if ( $status != 0 ) then + echo '---------------------------------------' + echo '** 3dDeconvolve error, failing...' + echo ' (consider the file 3dDeconvolve.err)' + exit +endif + + +# display any large pairwise correlations from the X-matrix +1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt + +# create an all_runs dataset to match the fitts, errts, etc. +3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD + +# -------------------------------------------------- +# create a temporal signal to noise ratio dataset +# signal: if 'scale' block, mean should be 100 +# noise : compute standard deviation of errts +3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]" +3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc"[$ktrs]" +3dcalc -a rm.signal.all+tlrc \ + -b rm.noise.all+tlrc \ + -c full_mask.$subj+tlrc \ + -expr 'c*a/b' -prefix TSNR.$subj + +# --------------------------------------------------- +# compute and store GCOR (global correlation average) +# (sum of squares of global mean of unit errts) +3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc +3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc \ + > gmean.errts.unit.1D +3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D +echo "-- GCOR = `cat out.gcor.1D`" + +# --------------------------------------------------- +# compute correlation volume +# (per voxel: average correlation across masked brain) +# (now just dot product with average unit time series) +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP +3dTstat -sum -prefix corr_brain rm.DP+tlrc + +# create ideal files for fixed response stim types +1dcat X.nocensor.xmat.1D'[5]' > ideal_Correct_Task.1D +1dcat X.nocensor.xmat.1D'[6]' > ideal_Incorrect_Task.1D +1dcat X.nocensor.xmat.1D'[7]' > ideal_No_Response_Control.1D +1dcat X.nocensor.xmat.1D'[8]' > ideal_No_Response_Task.1D +1dcat X.nocensor.xmat.1D'[9]' > ideal_Response_Control.1D + +# -------------------------------------------------------- +# compute sum of non-baseline regressors from the X-matrix +# (use 1d_tool.py to get list of regressor colums) +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]" + +# also, create a stimulus-only X-matrix, for easy review +1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D + +# ============================ blur estimation ============================= +# compute blur estimates +touch blur_est.$subj.1D # start with empty file + +# create directory for ACF curve files +mkdir files_ACF + +# -- estimate blur for each run in epits -- +touch blur.epits.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \ + all_runs.$subj+tlrc"[$trs]" >> blur.epits.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +echo average epits FWHM blurs: $blurs +echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +echo average epits ACF blurs: $blurs +echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D + +# -- estimate blur for each run in errts -- +touch blur.errts.1D + +# restrict to uncensored TRs, per run +foreach run ( $runs ) + set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ + -show_trs_run $run` + if ( $trs == "" ) continue + 3dFWHMx -detrend -mask full_mask.$subj+tlrc \ + -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \ + errts.${subj}+tlrc"[$trs]" >> blur.errts.1D +end + +# compute average FWHM blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +echo average errts FWHM blurs: $blurs +echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D + +# compute average ACF blur (from every other row) and append +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +echo average errts ACF blurs: $blurs +echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D + + +# ================== auto block: generate review scripts =================== + +# generate a review script for the unprocessed EPI data +gen_epi_review.py -script @epi_review.$subj \ + -dsets pb00.$subj.r*.tcat+orig.HEAD + +# generate scripts to review single subject results +# (try with defaults, but do not allow bad exit status) +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 + +# ========================== auto block: finalize ========================== + +# remove temporary files +\rm -f rm.* + +# if the basic subject review script is here, run it +# (want this to be the last text output) +if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt + +# return to parent directory +cd .. + +echo "execution finished: `date`" + + + + +# ========================================================================== +# script generated by the command: +# +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ +# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ +# -regress_opts_3dD -gltsym 'SYM: 0.333*Correct_Task \ +# +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control \ +# -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ +# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err b/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err new file mode 100644 index 0000000..6aceed6 --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err @@ -0,0 +1,2 @@ +*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.123923 ==> few true single voxel detections +*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.123702 ==> few true single voxel detections diff --git a/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd new file mode 100644 index 0000000..968b10b --- /dev/null +++ b/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd @@ -0,0 +1,5 @@ +# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb $* From 8efdaa958d2d19d3ad852da0b06f126cc07278f9 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Thu, 3 Aug 2017 23:01:52 -0400 Subject: [PATCH 07/18] rm tmp file --- ...3_ses-test_task-linebisection_events.tsv.swp | Bin 16384 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 sub-03/ses-test/func/.sub-03_ses-test_task-linebisection_events.tsv.swp diff --git a/sub-03/ses-test/func/.sub-03_ses-test_task-linebisection_events.tsv.swp b/sub-03/ses-test/func/.sub-03_ses-test_task-linebisection_events.tsv.swp deleted file mode 100644 index 9b9f05f6f36c5dd41cf0befdb97f128159547847..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16384 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z9)!Cfz>V;4^84rESMYuKGJGBaycb@h&wqh=-+wXhfBxhM;yfc-lg#?owp)|>QfCb;+~Rcz@xMHZe)PIaxMTtoSK z@dRz5Cmo}>U3OM{Y$+*j_vj?LUM9Wu78IwcyLI1!O(mzxSj%Z|f=vaVPH9XKN(I!n z`*cZhJL#>ru Date: Fri, 4 Aug 2017 13:12:58 -0400 Subject: [PATCH 08/18] fix regression contrast also delete redundant output files --- .../group.retest/subj.sub_03/cmd.ap.sub_03 | 7 +- .../subj.sub_03/output.cmd.ap.sub_03 | 11 +- .../subj.sub_03/output.proc.sub_03 | 256 +++-- .../group.retest/subj.sub_03/proc.sub_03 | 61 +- .../subj.sub_03/sub_03.results/stats.REML_cmd | 5 - .../group.test/subj.sub_03/cmd.ap.sub_03 | 7 +- .../subj.sub_03/output.cmd.ap.sub_03 | 11 +- .../group.test/subj.sub_03/output.proc.sub_03 | 959 +----------------- .../group.test/subj.sub_03/proc.sub_03 | 61 +- .../sub_03.results/3dDeconvolve.err | 4 - .../subj.sub_03/sub_03.results/stats.REML_cmd | 5 - .../group.retest/subj.sub_03/cmd.ap.sub_03 | 7 +- .../subj.sub_03/output.cmd.ap.sub_03 | 11 +- .../subj.sub_03/output.proc.sub_03 | 256 +++-- .../group.retest/subj.sub_03/proc.sub_03 | 61 +- .../subj.sub_03/sub_03.results/stats.REML_cmd | 5 - .../group.test/subj.sub_03/cmd.ap.sub_03 | 7 +- .../subj.sub_03/output.cmd.ap.sub_03 | 11 +- .../group.test/subj.sub_03/output.proc.sub_03 | 258 +++-- .../group.test/subj.sub_03/proc.sub_03 | 61 +- .../sub_03.results/3dDeconvolve.err | 2 - .../subj.sub_03/sub_03.results/stats.REML_cmd | 5 - 22 files changed, 514 insertions(+), 1557 deletions(-) mode change 100755 => 100644 Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 mode change 100755 => 100644 Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 delete mode 100644 Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd mode change 100755 => 100644 Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 mode change 100755 => 100644 Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 delete mode 100644 Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err delete mode 100644 Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd mode change 100755 => 100644 Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 mode change 100755 => 100644 Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 delete mode 100644 Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd mode change 100755 => 100644 Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 mode change 100755 => 100644 Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 delete mode 100644 Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err delete mode 100644 Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 old mode 100755 new mode 100644 index 05ecd7d..876ffcd --- a/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 @@ -4,7 +4,7 @@ # creation date: Thu Aug 3 22:03:06 2017 # set data directories -set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set top_dir = /Users/mli/Desktop/playground set anat_dir = $top_dir/sub-03/ses-retest/anat set epi_dir = $top_dir/sub-03/ses-retest/func @@ -37,9 +37,8 @@ afni_proc.py -subj_id $subj \ -regress_censor_motion 0.5 \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ - -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control \ - -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ + -*Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 index 26e0d70..725babe 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 @@ -1,11 +1,10 @@ -set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground -set anat_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat -set epi_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func +set top_dir = /Users/mli/Desktop/playground +set anat_dir = /Users/mli/Desktop/playground/sub-03/ses-retest/anat +set epi_dir = /Users/mli/Desktop/playground/sub-03/ses-retest/func set subj = sub_03 set group_id = retest -afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control - -0.5*No_Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task + -*Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig -- tcat: reps is now 238 ++ updating polort to 4, from run len 595.0 s diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 index 8498c74..363e30f 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 @@ -1,15 +1,15 @@ -echo auto-generated by afni_proc.py, Thu Aug 3 22:21:05 2017 -auto-generated by afni_proc.py, Thu Aug 3 22:21:05 2017 +echo auto-generated by afni_proc.py, Fri Aug 4 12:45:31 2017 +auto-generated by afni_proc.py, Fri Aug 4 12:45:31 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Thu Aug 3 22:24:53 EDT 2017 +execution started: Fri Aug 4 12:45:35 EDT 2017 afni -ver -Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) +Precompiled binary macosx_10.7_local: Jul 27 2017 (Version AFNI_17.2.05) afni_history -check_date 23 Sep 2016 -- is current: afni_history as new as: 23 Sep 2016 - most recent entry is: 21 Jul 2017 + most recent entry is: 27 Jul 2017 if ( 0 ) then if ( 0 > 0 ) then set subj = sub_03 @@ -20,18 +20,18 @@ set runs = ( `count -digits 2 1 1` ) count -digits 2 1 1 mkdir sub_03.results mkdir sub_03.results/stimuli -cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D sub_03.results/stimuli -3dcopy /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz sub_03.results/sub-03_ses-retest_T1w -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] -++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 1.5 s +cp /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D sub_03.results/stimuli +3dcopy /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz sub_03.results/sub-03_ses-retest_T1w +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] +++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ elapsed time = 0.8 s set tr_counts = ( 238 ) cd sub_03.results touch out.pre_ss_warn.txt foreach run ( 01 ) 3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig -++ 3dToutcount: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dToutcount: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -49,7 +49,7 @@ end cat outcount.r01.1D foreach run ( 01 ) 3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig -++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTshift: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -62,7 +62,7 @@ foreach run ( 01 ) *+ WARNING: ==>> output dataset is just a copy of input dataset end 3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] -++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off #++ align_epi_anat version: 1.57 #++ turning off volume registration @@ -80,7 +80,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s \rm -f ./__tt_sub-03_ses-retest_T1w* #Script is running (command trimmed): 3dcopy ./sub-03_ses-retest_T1w+orig ./__tt_sub-03_ses-retest_T1w+orig -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ Removing skull from anat data #Script is running (command trimmed): 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-retest_T1w+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns @@ -94,22 +94,21 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Oblique dataset:./__tt_sub-03_ses-retest_T1w+orig.BRIK is 7.491219 degrees from plumb. #Script is running (command trimmed): 3dinfo ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' -#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig is ***oblique**** +#++ Dataset /Users/mli/Desktop/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig is ***oblique**** #Script is running (command trimmed): 3dAttribute DELTA ./__tt_sub-03_ses-retest_T1w_ns+orig #++ Spacing for anat to oblique epi alignment is 1.000000 #++ Matching obliquity of anat to epi #Script is running (command trimmed): 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-retest_T1w_ns_obla2e_mat.1D -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Deobliquing original dataset before obliquing ++ Combining oblique transformations -++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.BRIK #++ using 0th sub-brick because only one found #Script is running (command trimmed): 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' -++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ resampling epi to match anat data #Script is running (command trimmed): 3dresample -master ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu @@ -124,7 +123,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s #++ removing skull or area outside brain #Script is running (command trimmed): 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig -++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAutomask: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset ./__tt_vr_base_ts_rs+orig ++ Forming automask @@ -152,21 +151,19 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ last 48 z-planes are zero [from S] ++ applying mask to original data ++ Writing masked data -++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK -++ CPU time = 4.220000 sec +++ CPU time = 3.660000 sec #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1728.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1728.000000 on /Users/mli/Desktop/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig #Script is running (command trimmed): 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1728.000000))' -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK #++ Aligning anat data to epi data #Script is running (command trimmed): 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.HEAD ++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD @@ -174,7 +171,6 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ 1356008 voxels in -source_automask+4 ++ Zero-pad: not needed ++ 1167476 voxels [7.5%] in weight mask -++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal+orig.BRIK ++ Number of points for matching = 1167476 ++ Local correlation: blok type = 'RHDD(6.54321)' ++ shift param auto-range: -84.4..84.4 -70.6..70.6 -85.1..85.1 @@ -188,7 +184,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Normalized convergence radius = 0.001000 ++ OpenMP thread count = 4 ++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= -++ ========== sub-brick #0 ========== [total CPU to here=9.4 s] +++ ========== sub-brick #0 ========== [total CPU to here=8.5 s] ++ *** Fine pass begins *** + * Enter alignment setup routine + - copying base image @@ -208,12 +204,11 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s z-angle= 0.4394 x-angle= 1.9668 y-angle=-5.3161 x-scale= 0.9674 y-scale= 0.9725 z-scale= 1.0191 y/x-shear= 0.0000 z/x-shear= 0.0099 z/y-shear= 0.0534 - + - Fine net CPU time = 34.7 s + + - Fine net CPU time = 33.9 s ++ Computing output image ++ image warp: parameters = 0.2981 -0.5136 -1.2234 0.4394 1.9668 -5.3161 0.9674 0.9725 1.0191 0.0000 0.0099 0.0534 -++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk+orig.BRIK ++ Wrote -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 46.5 sec Elapsed = 34.1 +++ 3dAllineate: total CPU time = 44.8 sec Elapsed = 27.6 ++ ########################################################### ++ # Please check results visually for alignment quality # ++ ########################################################### @@ -225,7 +220,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s #++ Combining anat to epi and oblique transformations #Script is running (command trimmed): 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-retest_T1w_al_junk -input ./__tt_sub-03_ses-retest_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__tt_sub-03_ses-retest_T1w_ns+orig.BRIK, @@ -256,14 +251,13 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ using -1Dmatrix_apply ++ Computing output image ++ image warp: parameters = 0.9618 0.0448 -0.0985 14.5442 -0.0314 0.9711 -0.0538 -1.5252 0.0911 0.0281 1.0141 -11.6150 -++ Output dataset ./sub-03_ses-retest_T1w_al_junk+orig.BRIK -++ 3dAllineate: total CPU time = 2.1 sec Elapsed = 5.2 +++ 3dAllineate: total CPU time = 2.2 sec Elapsed = 1.7 ++ ########################################################### #++ Creating final output: skullstripped anat data -copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig +copying from dataset /Users/mli/Desktop/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/mli/Desktop/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig #Script is running (command trimmed): 3dcopy ./__tt_sub-03_ses-retest_T1w_ns+orig sub-03_ses-retest_T1w_ns -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ Creating final output: anat data aligned to epi # copy is not necessary #++ Saving history @@ -300,7 +294,7 @@ copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subjec ++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. Center distance of 26.068730 mm Padding ... -++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dZeropad: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK Resampling ... *+ WARNING: If you are performing spatial transformations on an oblique dset, @@ -311,9 +305,8 @@ Resampling ... on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__ats_tmp__resamp_step+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -322,9 +315,8 @@ Resampling ... on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 7.491219 degrees from plumb. -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -334,26 +326,25 @@ Resampling ... See 3dWarp -help for details. ++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. Clipping -0.000100 1013.000100 ... -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ./__ats_tmp___rs_sub-03_ses-retest_T1w_ns+tlrc.BRIK -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-retest_T1w_ns+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets Registration (linear final interpolation) ... -++ 3dWarpDrive: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarpDrive: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Initial scale factor set to 0.30/247.56=8.3e+02 RMS[0] = 0.364249 0.163911 ITER = 6/137 @@ -361,8 +352,8 @@ RMS[0] = 0.364249 0.163911 ITER = 6/137 Warping has converged. -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, @@ -375,21 +366,19 @@ Warping has converged. ++ 7.491219 degrees from plumb. *+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations Applying brain mask -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox -++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drename: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.HEAD -++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.BRIK -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK.gz -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.BRIK.gz +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK Unpadding ... -++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dZeropad: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ output dataset: ./__ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig.BRIK -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig *+ WARNING: Changing the space of an ORIG view dataset may cause confusion! @@ -397,17 +386,17 @@ Unpadding ... *+ WARNING: Consider changing the view of the dataset to TLRC view also ++ 3drefit processed 1 datasets Changing view of transformed anatomy -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets Setting parent with 3drefit -wset sub-03_ses-retest_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc ++ 3drefit processed 1 datasets -++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drename: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Warning: ignoring +tlrc on new_prefix. ++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc.HEAD -> sub-03_ses-retest_T1w_ns+tlrc.HEAD ++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc.BRIK -> sub-03_ses-retest_T1w_ns+tlrc.BRIK @@ -416,7 +405,7 @@ cat_matvec sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I if ( ! -f sub-03_ses-retest_T1w_ns+tlrc.HEAD ) then foreach run ( 01 ) 3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig -++ 3dvolreg: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dvolreg: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base+orig.BRIK, @@ -435,7 +424,7 @@ foreach run ( 01 ) + 3364 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=7.04 s [=0.0296 s/sub-brick] +++ CPU time for realignment=6.37 s [=0.0268 s/sub-brick] ++ Min : roll=-0.200 pitch=-0.367 yaw=-0.118 dS=-1.139 dL=-0.157 dP=-0.055 ++ Mean: roll=-0.094 pitch=-0.011 yaw=+0.456 dS=-0.124 dL=+0.184 dP=+0.074 ++ Max : roll=+0.027 pitch=+0.449 yaw=+0.935 dS=+0.523 dL=+0.640 dP=+0.245 @@ -445,13 +434,12 @@ foreach run ( 01 ) ++ Max delta displ in automask = 1.52 (mm) at sub-brick 1 ++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK 3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression -++ Output dataset ./rm.epi.all1+orig.BRIK cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.sub_03.r01.tshift+orig.BRIK, @@ -470,11 +458,11 @@ cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retes ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 ++ ========== Applying transformation to 238 sub-bricks ========== -volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 6.2 sec Elapsed = 5.3 +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 6.1 sec Elapsed = 3.8 ++ ########################################################### 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./rm.epi.all1+orig.BRIK, @@ -486,25 +474,23 @@ volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20. ++ Oblique dataset:./rm.epi.all1+orig.BRIK is 4.947676 degrees from plumb. ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ Output dataset ./rm.epi.1.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.4 sec Elapsed = 3.7 +++ 3dAllineate: total CPU time = 3.6 sec Elapsed = 3.1 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox -++ Output dataset ./rm.epi.min.r01+tlrc.BRIK end cat dfile.r01.1D 3dcopy rm.epi.min.r01+tlrc mask_epi_extents -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] foreach run ( 01 ) 3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK end cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base+orig.BRIK, @@ -523,14 +509,14 @@ cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retes ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 ++ ========== Applying transformation to 1 sub-bricks ========== -volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK -++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.3 +volume 0Ø++ Output dataset ./final_epi_vr_base+tlrc.BRIK +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.1 ++ ########################################################### 3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.sub_03 -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] 3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc tee out.allcostX.txt -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./anat_final.sub_03+tlrc.HEAD ++ Base dataset: ./final_epi_vr_base+tlrc.HEAD @@ -545,7 +531,7 @@ tee out.allcostX.txt ++ Local correlation: blok type = 'RHDD(14.76)' *+ WARNING: No output dataset will be calculated ++ OpenMP thread count = 4 -volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +volume 0Ø + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 ++ allcost output: init #0 ls = 0.184126 sp = 0.307224 @@ -564,7 +550,7 @@ volume 0 ++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 ++ ########################################################### 3dAllineate -source sub-03_ses-retest_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-retest_T1w+orig.BRIK, @@ -580,7 +566,7 @@ volume 0 ++ Loading datasets ++ OpenMP thread count = 4 ++ ========== Applying transformation to 1 sub-bricks ========== -volume 0Ð++ wsinc5 interpolation setup: +volume 0Ø++ wsinc5 interpolation setup: + taper function = Min sidelobe 3 term + taper cut point = 0.000 + window radius = 5 voxels @@ -589,11 +575,11 @@ volume 0 + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + wsinc5 CUBE(5) mask has 1000 points ++ Output dataset ./anat_w_skull_warped+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 2.1 +++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.3 ++ ########################################################### foreach run ( 01 ) 3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc -++ 3dmerge: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dmerge: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ default -1dindex = 0 ++ default -1tindex = 1 Program 3dmerge @@ -604,7 +590,7 @@ Program 3dmerge end foreach run ( 01 ) 3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc -++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAutomask: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset pb03.sub_03.r01.blur+tlrc ++ Forming automask @@ -632,8 +618,7 @@ foreach run ( 01 ) ++ last 2 y-planes are zero [from A] ++ first 3 z-planes are zero [from I] ++ last 3 z-planes are zero [from S] -++ Output dataset ./rm.mask_r01+tlrc.BRIK -++ CPU time = 0.280000 sec +++ CPU time = 0.270000 sec end 3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 ++ processing 1 input datasets... @@ -641,7 +626,6 @@ end ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 33241 survived, 76109 were zero ++ writing result full_mask.sub_03... -++ Output dataset ./full_mask.sub_03+tlrc.BRIK 3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-retest_T1w_ns+tlrc -prefix rm.resam.anat 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 ++ no -frac option: defaulting to -union @@ -651,17 +635,16 @@ end ++ voxel limits: 0 clipped, 30574 survived, 78776 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_anat.sub_03... -++ Output dataset ./mask_anat.sub_03+tlrc.BRIK 3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_overlap.txt -++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dOverlap: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK #A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) 33241 30574 35745 28070 5171 2504 15.5561 8.1900 0.9405 0.9263 0.9667 3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_dice.txt 0.87973 -3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc +3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/mli/abin/MNI_avg152T1+tlrc 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ no -frac option: defaulting to -union ++ processing 1 input datasets... @@ -670,14 +653,13 @@ tee out.mask_ae_dice.txt ++ voxel limits: 0 clipped, 30980 survived, 78370 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_group... -++ Output dataset ./mask_group+tlrc.BRIK foreach run ( 01 ) 3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.mean_r01+tlrc.BRIK 3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK end @@ -688,9 +670,8 @@ total number of censored TRs (simple form) = 2 set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D -show_trs_uncensored encoded` 1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 -++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +++ 3dDeconvolve: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD ++ STAT automask has 100184 voxels (out of 109350 = 91.6%) @@ -705,10 +686,11 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D ++ ** GUESSED ** -stim_times 3 using LOCAL times ++ ** GUESSED ** -stim_times 4 using LOCAL times ++ ** GUESSED ** -stim_times 5 using LOCAL times +*+ WARNING: -gltsym: Can't interpret '*' scale factor in '-*Response_Control' -- replaced by 1 +*+ WARNING: -gltsym: '*' scale factor in '-*Response_Control' not at start of string? ------------------------------------------------------------ -GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control': - 0 0 0 0 0 0.333 0.333 -0.5 0.333 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 +GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': + 0 0 0 0 0 0.5 0.5 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 ++ Number of time points: 238 (before censor) ; 236 (after) + Number of parameters: 22 [17 baseline ; 5 signal] @@ -734,9 +716,9 @@ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task ++ ----- polort-only matrix condition [X] (236x5): 1.05506 ++ VERY GOOD ++ ++ +++++ Matrix inverse average error = 2.74977e-15 ++ VERY GOOD ++ ++ Matrix setup time = 0.64 s -++ Calculations starting; elapsed time=1.296 +++ Calculations starting; elapsed time=1.346 ++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=15.878 +++ Calculations finished; elapsed time=15.873 ++ Smallest FDR q [0 Full_Fstat] = 2.20611e-13 ++ Smallest FDR q [2 Correct_Task#0_Tstat] = 4.23368e-12 ++ Smallest FDR q [3 Correct_Task_Fstat] = 4.23389e-12 @@ -748,8 +730,8 @@ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task ++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.0018156 ++ Smallest FDR q [14 Response_Control#0_Tstat] = 7.47239e-13 ++ Smallest FDR q [15 Response_Control_Fstat] = 7.47258e-13 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.000154149 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.000154153 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 3.58106e-13 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 3.58045e-13 ++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + created 13 FDR curves in bucket header ++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK @@ -766,40 +748,40 @@ Warnings regarding Correlation Matrix: X.xmat.1D medium: 0.447 0.539 ( 5 vs. 6) Correct_Task#0 vs. Incorrect_Task#0 3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD -++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 1.2 s +++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ elapsed time = 0.4 s 3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..237] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.signal.all+tlrc.BRIK 3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..237] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.noise.all+tlrc.BRIK 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./TSNR.sub_03+tlrc.BRIK 3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc -++ 3dTnorm: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTnorm: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Output dataset ./rm.errts.unit+tlrc.BRIK 3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc -++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dmaskave: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ 33241 voxels survive the mask 3dTstat -sos -prefix - gmean.errts.unit.1D' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D -- GCOR = 0.109705 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./rm.DP+tlrc.BRIK 3dTstat -sum -prefix corr_brain rm.DP+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./corr_brain+tlrc.BRIK 1dcat X.nocensor.xmat.1D[5] @@ -810,7 +792,7 @@ cat out.gcor.1D set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` 1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 ++ Output dataset ./sum_ideal.1D @@ -824,22 +806,22 @@ set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 if ( 2..237 == ) continue 3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..237] -++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob ++ Number of voxels in mask = 33241 *+ WARNING: removed 220 voxels from mask because they are constant in time ++ detrending start: 17 baseline funcs, 236 time points - + detrending done (2.52 CPU s thus far) + + detrending done (2.92 CPU s thus far) ++ start ACF calculations out to radius = 27.83 mm - + ACF done (64.84 CPU s thus far) + + ACF done (63.36 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D -++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png end set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) 3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 @@ -848,13 +830,13 @@ average epits FWHM blurs: 0 0 0 0 echo 0 0 0 0 # epits FWHM blur estimates set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) 3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.63099 5.37461 12.731 13.5951 -average epits ACF blurs: 0.63099 5.37461 12.731 13.5951 -echo 0.63099 5.37461 12.731 13.5951 # epits ACF blur estimates +echo average epits ACF blurs: 0.631007 5.37466 12.7311 13.5952 +average epits ACF blurs: 0.631007 5.37466 12.7311 13.5952 +echo 0.631007 5.37466 12.7311 13.5952 # epits ACF blur estimates touch blur.errts.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded @@ -862,22 +844,22 @@ set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 if ( 2..237 == ) continue 3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..237] -++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob ++ Number of voxels in mask = 33241 *+ WARNING: removed 220 voxels from mask because they are constant in time ++ detrending start: 17 baseline funcs, 236 time points - + detrending done (2.49 CPU s thus far) + + detrending done (3.01 CPU s thus far) ++ start ACF calculations out to radius = 27.36 mm - + ACF done (64.46 CPU s thus far) + + ACF done (63.19 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D -++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png end set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) 3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 @@ -886,19 +868,19 @@ average errts FWHM blurs: 0 0 0 0 echo 0 0 0 0 # errts FWHM blur estimates set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) 3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.694841 5.25415 13.1837 13.2188 -average errts ACF blurs: 0.694841 5.25415 13.1837 13.2188 -echo 0.694841 5.25415 13.1837 13.2188 # errts ACF blur estimates +echo average errts ACF blurs: 0.694842 5.25419 13.1836 13.2188 +average errts ACF blurs: 0.694842 5.25419 13.1836 13.2188 +echo 0.694842 5.25419 13.1836 13.2188 # errts ACF blur estimates gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD gen_ss_review_scripts.py -mot_limit 0.5 -exit0 ++ writing ss review basic: @ss_review_basic ++ writing ss review driver: @ss_review_driver ++ writing ss review drive commands: @ss_review_driver_commands -rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK.gz rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK.gz rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK.gz rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK.gz rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD tee out.ss_review.sub_03.txt if ( -e @ss_review_basic ) ./@ss_review_basic ./@ss_review_basic @@ -943,7 +925,7 @@ TSNR average : 234.187 global correlation (GCOR) : 0.109705 anat/EPI mask Dice coef : 0.87973 maximum F-stat (masked) : 48.3344 -blur estimates (ACF) : 0.694841 5.25415 13.1837 +blur estimates (ACF) : 0.694842 5.25419 13.1836 blur estimates (FWHM) : 0 0 0 ** TR #0 outliers: possible pre-steady state TRs in run 01 @@ -951,4 +933,4 @@ blur estimates (FWHM) : 0 0 0 cd .. echo execution finished: `date` date -execution finished: Thu Aug 3 22:30:59 EDT 2017 +execution finished: Fri Aug 4 12:49:48 EDT 2017 diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 old mode 100755 new mode 100644 index 2004341..dc0c6f0 --- a/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Thu Aug 3 22:21:05 2017" +echo "auto-generated by afni_proc.py, Fri Aug 4 12:45:31 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -45,24 +45,23 @@ mkdir $output_dir mkdir $output_dir/stimuli # copy stim files into stimulus directory -cp \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ +cp /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D \ $output_dir/stimuli # copy anatomy to results dir -3dcopy \ - /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ +3dcopy \ + /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ $output_dir/sub-03_ses-retest_T1w # ============================ auto block: tcat ============================ # apply 3dTcat to copy input dsets to results dir, while # removing the first 0 TRs 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ - /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' + /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' # and make note of repetitions (TRs) per run set tr_counts = ( 238 ) @@ -240,7 +239,7 @@ end # ---- create group anatomy mask, mask_group+tlrc ---- # (resampled from tlrc base anat, MNI_avg152T1+tlrc) 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ - -input /Users/monicali/abin/MNI_avg152T1+tlrc + -input /Users/mli/abin/MNI_avg152T1+tlrc # convert to binary group mask; fill gaps and holes 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ @@ -306,8 +305,7 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ - -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -458,23 +456,22 @@ echo "execution finished: `date`" # ========================================================================== # script generated by the command: # -# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ -# tshift align tlrc volreg blur mask scale regress -copy_anat \ -# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ -# -tcat_remove_first_trs 0 -dsets \ -# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ -# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ -# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ -# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ -# No_Response_Task Response_Control -regress_basis GAM \ -# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ -# -regress_opts_3dD -gltsym 'SYM: 0.333*Correct_Task \ -# +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control \ -# -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ -# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ +# -regress_opts_3dD -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ +# -*Response_Control' -glt_label 1 Landmark-Detection \ +# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ # -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd deleted file mode 100644 index a997d7b..0000000 --- a/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd +++ /dev/null @@ -1,5 +0,0 @@ -# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 - -3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ - -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ - -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb $* diff --git a/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 old mode 100755 new mode 100644 index 50f5fd0..98608cd --- a/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 @@ -4,7 +4,7 @@ # creation date: Thu Aug 3 22:01:15 2017 # set data directories -set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set top_dir = /Users/mli/Desktop/playground set anat_dir = $top_dir/sub-03/ses-test/anat set epi_dir = $top_dir/sub-03/ses-test/func @@ -37,9 +37,8 @@ afni_proc.py -subj_id $subj \ -regress_censor_motion 0.5 \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ - -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control \ - -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ + -*Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 index 7e616bd..930c067 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 @@ -1,11 +1,10 @@ -set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground -set anat_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat -set epi_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func +set top_dir = /Users/mli/Desktop/playground +set anat_dir = /Users/mli/Desktop/playground/sub-03/ses-test/anat +set epi_dir = /Users/mli/Desktop/playground/sub-03/ses-test/func set subj = sub_03 set group_id = test -afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control - -0.5*No_Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task + -*Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig -- tcat: reps is now 238 ++ updating polort to 4, from run len 595.0 s diff --git a/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 index e668689..45b7b68 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 @@ -1,964 +1,21 @@ -echo auto-generated by afni_proc.py, Thu Aug 3 22:13:37 2017 -auto-generated by afni_proc.py, Thu Aug 3 22:13:37 2017 +echo auto-generated by afni_proc.py, Fri Aug 4 12:43:15 2017 +auto-generated by afni_proc.py, Fri Aug 4 12:43:15 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Thu Aug 3 22:14:07 EDT 2017 +execution started: Fri Aug 4 12:43:28 EDT 2017 afni -ver -Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) +Precompiled binary macosx_10.7_local: Jul 27 2017 (Version AFNI_17.2.05) afni_history -check_date 23 Sep 2016 -- is current: afni_history as new as: 23 Sep 2016 - most recent entry is: 21 Jul 2017 + most recent entry is: 27 Jul 2017 if ( 0 ) then if ( 0 > 0 ) then set subj = sub_03 endif set output_dir = sub_03.results if ( -d sub_03.results ) then -set runs = ( `count -digits 2 1 1` ) -count -digits 2 1 1 -mkdir sub_03.results -mkdir sub_03.results/stimuli -cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D sub_03.results/stimuli -3dcopy /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz sub_03.results/sub-03_ses-test_T1w -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[0..$] -++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 1.5 s -set tr_counts = ( 238 ) -cd sub_03.results -touch out.pre_ss_warn.txt -foreach run ( 01 ) -3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig -++ 3dToutcount: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./pb00.sub_03.r01.tcat+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. -++ 17837 voxels passed mask/clip -if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then -1deval -a outcount.r01.1D{0} -expr step(a-0.4) -echo ** TR #0 outliers: possible pre-steady state TRs in run 01 -endif -end -cat outcount.r01.1D -foreach run ( 01 ) -3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig -++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./pb00.sub_03.r01.tcat+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. -*+ WARNING: dataset is already aligned in time! -*+ WARNING: ==>> output dataset is just a copy of input dataset -end -3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] -++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off -#++ align_epi_anat version: 1.57 -#++ turning off volume registration -#Script is running (command trimmed): - 3dAttribute DELTA ./vr_base+orig -#Script is running (command trimmed): - 3dAttribute DELTA ./vr_base+orig -#Script is running (command trimmed): - 3dAttribute DELTA ./sub-03_ses-test_T1w+orig -#++ Multi-cost is lpc -#++ Removing all the temporary files -#Script is running: - \rm -f ./__tt_vr_base* -#Script is running: - \rm -f ./__tt_sub-03_ses-test_T1w* -#Script is running (command trimmed): - 3dcopy ./sub-03_ses-test_T1w+orig ./__tt_sub-03_ses-test_T1w+orig -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -#++ Removing skull from anat data -#Script is running (command trimmed): - 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-test_T1w+orig -prefix ./__tt_sub-03_ses-test_T1w_ns -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./__tt_sub-03_ses-test_T1w+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./__tt_sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. -#Script is running (command trimmed): - 3dinfo ./__tt_sub-03_ses-test_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' -#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig is ***oblique**** -#Script is running (command trimmed): - 3dAttribute DELTA ./__tt_sub-03_ses-test_T1w_ns+orig -#++ Spacing for anat to oblique epi alignment is 1.000000 -#++ Matching obliquity of anat to epi -#Script is running (command trimmed): - 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-test_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Deobliquing original dataset before obliquing -++ Combining oblique transformations -++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob+orig.BRIK -#++ using 0th sub-brick because only one found -#Script is running (command trimmed): - 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' -++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -#++ resampling epi to match anat data -#Script is running (command trimmed): - 3dresample -master ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./__tt_vr_base_ts+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./__tt_vr_base_ts+orig.BRIK is 6.153038 degrees from plumb. -#++ removing skull or area outside brain -#Script is running (command trimmed): - 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig -++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Emperor Zhark -++ Loading dataset ./__tt_vr_base_ts_rs+orig -++ Forming automask - + Fixed clip level = 722.140930 - + Used gradual clip level = 624.995605 .. 827.664490 - + Number voxels above clip level = 1139938 - + Clustering voxels ... - + Largest cluster has 1138291 voxels - + Clustering voxels ... - + Largest cluster has 1137874 voxels - + Filled 374 voxels in small holes; now have 1138248 voxels - + Filled 17631 voxels in large holes; now have 1155879 voxels - + Clustering voxels ... - + Largest cluster has 1155874 voxels - + Clustering non-brain voxels ... - + Clustering voxels ... - + Largest cluster has 15251279 voxels - + Mask now has 1155874 voxels -++ 1155874 voxels in the mask [out of 16407153: 7.04%] -++ first 71 x-planes are zero [from R] -++ last 75 x-planes are zero [from L] -++ first 33 y-planes are zero [from A] -++ last 17 y-planes are zero [from P] -++ first 123 z-planes are zero [from I] -++ last 36 z-planes are zero [from S] -++ applying mask to original data -++ Writing masked data -++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK -++ CPU time = 3.580000 sec -#++ Computing weight mask -#Script is running (command trimmed): - 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1890.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig -#Script is running (command trimmed): - 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1890.000000))' -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK -#++ Aligning anat data to epi data -#Script is running (command trimmed): - 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Zhark the Registrator -++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns_ob+orig.HEAD -++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD -++ Loading datasets -++ 1350442 voxels in -source_automask+4 -++ Zero-pad: not needed -++ 1155874 voxels [7.0%] in weight mask -++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal+orig.BRIK -++ Number of points for matching = 1155874 -++ Local correlation: blok type = 'RHDD(6.54321)' -++ shift param auto-range: -89.2..89.2 -69.3..69.3 -86.7..86.7 - + Range param#4 [z-angle] = -6.000000 .. 6.000000 - + Range param#5 [x-angle] = -6.000000 .. 6.000000 - + Range param#6 [y-angle] = -6.000000 .. 6.000000 - + Range param#1 [x-shift] = -10.000000 .. 10.000000 - + Range param#2 [y-shift] = -10.000000 .. 10.000000 - + Range param#3 [z-shift] = -10.000000 .. 10.000000 - + 12 free parameters -++ Normalized convergence radius = 0.001000 -++ OpenMP thread count = 4 -++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= -++ ========== sub-brick #0 ========== [total CPU to here=9.7 s] -++ *** Fine pass begins *** - + * Enter alignment setup routine - + - copying base image - + - copying source image - + - copying weight image - + - using 1155874 points from base image [use_all=0] - + * Exit alignment setup routine - + 1095215 total points stored in 2075 'RHDD(6.54321)' bloks - + - Initial cost = -0.096907 - + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 -*************************************************************************************************************************************************************************************************************************************************************************************************** - + - Finalish cost = -0.235911 ; 645 funcs -** - + - Final cost = -0.235912 ; 97 funcs - + Final fine fit Parameters: - x-shift= 0.2099 y-shift=-0.6560 z-shift=-1.7075 - z-angle=-0.6314 x-angle= 4.7459 y-angle=-1.0126 - x-scale= 0.9677 y-scale= 0.9751 z-scale= 1.0200 - y/x-shear=-0.0038 z/x-shear= 0.0093 z/y-shear= 0.0929 - + - Fine net CPU time = 50.4 s -++ Computing output image -++ image warp: parameters = 0.2099 -0.6560 -1.7075 -0.6314 4.7459 -1.0126 0.9677 0.9751 1.0200 -0.0038 0.0093 0.0929 -++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk+orig.BRIK -++ Wrote -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 62.5 sec Elapsed = 39.9 -++ ########################################################### -++ # Please check results visually for alignment quality # -++ ########################################################### -++ # '-autoweight' is recommended when using -lpc or -lpa # -++ # If your results are not good, please try again. # -++ ########################################################### -#Script is running (command trimmed): - cat_matvec -ONELINE ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D -I > ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D -#++ Combining anat to epi and oblique transformations -#Script is running (command trimmed): - 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-test_T1w_al_junk -input ./__tt_sub-03_ses-test_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Zhark the Registrator -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./__tt_sub-03_ses-test_T1w_ns+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./__tt_sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. -++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns+orig.HEAD -++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD -++ Loading datasets - + Range param#4 [z-angle] = -6.000000 .. 6.000000 - + Range param#5 [x-angle] = -6.000000 .. 6.000000 - + Range param#6 [y-angle] = -6.000000 .. 6.000000 - + Range param#1 [x-shift] = -10.000000 .. 10.000000 - + Range param#2 [y-shift] = -10.000000 .. 10.000000 - + Range param#3 [z-shift] = -10.000000 .. 10.000000 -++ OpenMP thread count = 4 -++ ========== Applying transformation to 1 sub-bricks ========== -++ ========== sub-brick #0 ========== [total CPU to here=0.1 s] - + * Enter alignment setup routine - + - copying base image - + - copying source image - + - no weight image - + - using 11 points from base image [use_all=0] - + * Exit alignment setup routine -++ using -1Dmatrix_apply -++ Computing output image -++ image warp: parameters = 0.9643 -0.0770 -0.0643 8.3030 0.0414 0.9701 -0.0701 -8.0767 0.0578 0.0003 1.0212 -4.7196 -++ Output dataset ./sub-03_ses-test_T1w_al_junk+orig.BRIK -++ 3dAllineate: total CPU time = 2.4 sec Elapsed = 4.6 -++ ########################################################### -#++ Creating final output: skullstripped anat data -copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig -#Script is running (command trimmed): - 3dcopy ./__tt_sub-03_ses-test_T1w_ns+orig sub-03_ses-test_T1w_ns -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -#++ Creating final output: anat data aligned to epi -# copy is not necessary -#++ Saving history -#Script is running (command trimmed): - 3dNotes -h "align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ - -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 \ - -epi_strip 3dAutomask -volreg off -tshift off" \ - ./sub-03_ses-test_T1w_al_junk+orig - -#++ Removing all the temporary files -#Script is running: - \rm -f ./__tt_vr_base* -#Script is running: - \rm -f ./__tt_sub-03_ses-test_T1w* - -# Finished alignment successfully - -@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-test_T1w_ns+orig -no_ss -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./sub-03_ses-test_T1w_ns+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./sub-03_ses-test_T1w_ns+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. - -*********** Warning ************* -Dataset centers are 52.843487 mm -apart. If registration fails, or if -parts of the original anatomy gets -cropped, try adding option - -init_xform AUTO_CENTER -to your @auto_tlrc command. - -********************************* - -Padding ... -++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK -Resampling ... -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./sub-03_ses-test_T1w_ns+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./__ats_tmp__resamp_step+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 6.455733 degrees from plumb. -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./sub-03_ses-test_T1w_ns+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. -Clipping -0.000100 1158.000100 ... -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ./__ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.BRIK -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.HEAD - + Changed dataset view type and filenames. -++ 3drefit processed 1 datasets -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD - + Changed dataset view type and filenames. -++ 3drefit processed 1 datasets -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD - + Changed dataset view type and filenames. -++ 3drefit processed 1 datasets -Registration (linear final interpolation) ... -++ 3dWarpDrive: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Initial scale factor set to 0.30/273.95=9.2e+02 -RMS[0] = 0.384861 0.16449 ITER = 6/137 -0.384861 - -Warping has converged. - -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./sub-03_ses-test_T1w_ns+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. -++ 6.455733 degrees from plumb. -*+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations -Applying brain mask -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.HEAD -++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.BRIK -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK -Unpadding ... -++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ output dataset: ./__ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.BRIK -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig -*+ WARNING: Changing the space of an ORIG view dataset may cause confusion! -*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space). -*+ WARNING: Consider changing the view of the dataset to TLRC view also -++ 3drefit processed 1 datasets -Changing view of transformed anatomy -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.HEAD - + Changed dataset view type and filenames. -++ 3drefit processed 1 datasets -Setting parent with 3drefit -wset sub-03_ses-test_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc -++ 3drefit processed 1 datasets -++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Warning: ignoring +tlrc on new_prefix. -++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.HEAD -> sub-03_ses-test_T1w_ns+tlrc.HEAD -++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.BRIK -> sub-03_ses-test_T1w_ns+tlrc.BRIK -Cleanup ... -cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I -if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then -foreach run ( 01 ) -3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig -++ 3dvolreg: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./vr_base+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./vr_base+orig.BRIK is 6.153038 degrees from plumb. -++ Reading in base dataset ./vr_base+orig.BRIK -++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 6.153038 degrees from plumb. -++ Reading input dataset ./pb01.sub_03.r01.tshift+orig.BRIK -++ Edging: x=3 y=3 z=2 -++ Creating mask for -maxdisp - + Automask has 18932 voxels - + 3319 voxels left in -maxdisp mask after erosion -++ Initializing alignment base -++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=10 s [=0.0421 s/sub-brick] -++ Min : roll=-0.125 pitch=-0.838 yaw=-0.100 dS=-1.314 dL=-0.122 dP=-0.602 -++ Mean: roll=+0.244 pitch=-0.353 yaw=+1.492 dS=+1.594 dL=+0.625 dP=-0.273 -++ Max : roll=+0.752 pitch=+0.977 yaw=+2.780 dS=+2.627 dL=+1.582 dP=+0.307 -++ Max displacements (mm) for each sub-brick: - 1.52(0.00) 0.25(1.43) 0.00(0.25) 0.40(0.40) 0.85(0.46) 0.73(0.21) 0.34(0.44) 0.80(0.50) 0.82(0.05) 0.97(0.22) 0.87(0.11) 1.14(0.27) 1.23(0.16) 1.37(0.28) 1.26(0.16) 1.40(0.16) 1.34(0.10) 1.53(0.22) 1.37(0.18) 1.47(0.12) 1.43(0.07) 1.39(0.23) 1.43(0.08) 1.54(0.12) 1.51(0.07) 1.54(0.05) 1.54(0.05) 1.63(0.10) 1.61(0.10) 1.65(0.10) 1.58(0.17) 1.71(0.19) 1.62(0.17) 1.77(0.19) 1.79(0.08) 1.95(0.18) 1.92(0.03) 2.10(0.19) 2.00(0.14) 2.23(0.27) 2.03(0.25) 2.26(0.23) 2.09(0.31) 2.37(0.33) 2.12(0.35) 2.37(0.41) 2.24(0.24) 2.31(0.12) 2.16(0.21) 1.75(0.92) 1.69(0.29) 1.26(0.56) 0.82(1.06) 1.02(0.77) 1.77(1.06) 2.02(2.37) 2.06(0.37) 3.95(3.75) 3.32(0.64) 3.59(1.18) 3.39(0.23) 3.42(0.10) 3.04(0.50) 2.05(1.20) 2.22(0.39) 3.63(1.92) 1.23(3.45) 1.76(1.27) 2.43(0.95) 2.71(0.28) 2.77(0.09) 3.03(0.29) 2.84(0.35) 2.83(0.31) 2.96(0.54) 2.87(0.19) 2.94(0.08) 2.89(0.08) 2.81(0.17) 2.77(0.22) 2.81(0.14) 2.95(0.14) 2.95(0.08) 3.06(0.14) 3.10(0.07) 3.01(0.16) 3.28(0.30) 3.28(0.02) 3.43(0.18) 3.45(0.06) 3.56(0.13) 3.57(0.06) 3.65(0.08) 3.70(0.08) 3.59(0.15) 3.66(0.17) 3.19(0.76) 3.37(0.22) 3.17(0.24) 3.47(0.52) 3.40(0.19) 3.40(0.24) 3.00(0.74) 3.66(1.10) 3.60(0.37) 3.73(0.37) 3.84(0.14) 3.89(0.14) 3.87(0.11) 3.89(0.14) 3.80(0.15) 3.73(0.12) 3.58(0.20) 3.69(0.13) 3.73(0.21) 3.94(0.25) 3.97(0.12) 4.13(0.21) 4.09(0.08) 4.18(0.13) 4.31(0.20) 4.11(0.27) 4.31(0.31) 4.13(0.23) 3.87(0.38) 3.82(0.12) 3.71(0.29) 3.74(0.07) 3.87(0.25) 3.89(0.04) 4.03(0.17) 4.19(0.19) 4.11(0.13) 4.27(0.21) 4.04(0.40) 4.27(0.29) 4.15(0.16) 4.26(0.14) 4.45(0.22) 4.07(0.63) 4.50(0.54) 4.38(0.16) 4.90(0.59) 4.74(0.24) 4.66(0.13) 4.65(0.20) 4.60(0.17) 4.66(0.26) 4.53(0.16) 4.73(0.26) 4.77(0.11) 4.69(0.13) 4.51(0.35) 4.52(0.15) 4.72(0.22) 4.55(0.21) 4.72(0.18) 4.65(0.12) 4.70(0.06) 4.79(0.14) 5.04(0.26) 4.95(0.48) 5.70(1.30) 5.19(0.83) 5.18(0.35) 5.42(0.26) 5.61(0.36) 5.74(0.24) 5.78(0.09) 5.89(0.15) 5.83(0.13) 5.83(0.10) 5.80(0.06) 5.73(0.25) 5.59(0.28) 5.50(0.39) 5.51(0.31) 5.49(0.23) 5.37(0.20) 5.45(0.10) 5.55(0.10) 5.64(0.17) 5.69(0.08) 5.62(0.12) 5.73(0.14) 5.69(0.09) 5.45(0.51) 5.28(0.22) 5.59(0.71) 5.03(0.73) 4.43(0.85) 4.81(0.47) 5.08(0.37) 5.55(0.73) 5.80(0.42) 5.82(0.13) 5.79(0.07) 6.03(0.40) 5.85(0.36) 5.89(0.09) 5.76(0.31) 5.95(0.23) 6.06(0.14) 5.97(0.17) 6.01(0.08) 6.11(0.29) 6.11(0.07) 6.21(0.16) 6.12(0.24) 6.18(0.07) 6.15(0.16) 6.15(0.10) 6.11(0.10) 6.23(0.23) 6.11(0.23) 6.18(0.10) 6.13(0.07) 6.12(0.08) 6.14(0.15) 6.04(0.16) 6.16(0.16) 6.15(0.11) 5.93(0.28) 6.00(0.08) 5.90(0.20) 5.86(0.40) 5.77(0.25) 6.07(0.68) 6.04(0.20) 5.99(0.20) 6.28(0.40) 6.31(0.10) 6.35(0.22) 6.33(0.19) 6.10(0.42) 6.01(0.25) 6.16(0.24) 6.13(0.07) -++ Max displacement in automask = 6.35 (mm) at sub-brick 232 -++ Max delta displ in automask = 3.75 (mm) at sub-brick 57 -++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK -3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -*+ WARNING: input 'a' is not used in the expression -++ Output dataset ./rm.epi.all1+orig.BRIK -cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D -3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Zhark the Registrator -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./pb01.sub_03.r01.tshift+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 6.153038 degrees from plumb. -++ Source dataset: ./pb01.sub_03.r01.tshift+orig.HEAD -++ Base dataset: ./sub-03_ses-test_T1w_ns+tlrc.HEAD -++ Loading datasets -++ NOTE: base and source coordinate systems have different handedness - + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ master dataset for output = base -++ changing output grid spacing to 4.0000 mm -++ OpenMP thread count = 4 -++ ========== Applying transformation to 238 sub-bricks ========== -volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 6.4 sec Elapsed = 16.3 -++ ########################################################### -3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Zhark the Registrator -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./rm.epi.all1+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./rm.epi.all1+orig.BRIK is 6.153038 degrees from plumb. -++ NOTE: base and source coordinate systems have different handedness - + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ Output dataset ./rm.epi.1.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 4.3 -3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -++ Output dataset ./rm.epi.min.r01+tlrc.BRIK -end -cat dfile.r01.1D -3dcopy rm.epi.min.r01+tlrc mask_epi_extents -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -foreach run ( 01 ) -3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK -end -cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I -3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Zhark the Registrator -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./vr_base+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./vr_base+orig.BRIK is 6.153038 degrees from plumb. -++ Source dataset: ./vr_base+orig.HEAD -++ Base dataset: ./sub-03_ses-test_T1w_ns+tlrc.HEAD -++ Loading datasets -++ NOTE: base and source coordinate systems have different handedness - + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ master dataset for output = base -++ changing output grid spacing to 4.0000 mm -++ OpenMP thread count = 4 -++ ========== Applying transformation to 1 sub-bricks ========== -volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK -++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.2 -++ ########################################################### -3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.sub_03 -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc -tee out.allcostX.txt -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Zhark the Registrator -++ Source dataset: ./anat_final.sub_03+tlrc.HEAD -++ Base dataset: ./final_epi_vr_base+tlrc.HEAD -++ Loading datasets -++ 223015 voxels in source_automask+0 -++ Zero-pad: xbot=2 xtop=2 -++ Zero-pad: ybot=0 ytop=1 -++ Zero-pad: zbot=1 ztop=1 -++ Computing -autobox -++ 113223 voxels [89.4%] in weight mask -++ Number of points for matching = 53214 -++ Local correlation: blok type = 'RHDD(14.76)' -*+ WARNING: No output dataset will be calculated -++ OpenMP thread count = 4 -volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 -++ allcost output: init #0 - ls = 0.183754 - sp = 0.30567 - mi = -0.534639 - crM = 0.0839806 - nmi = 0.868199 - je = 3.52175 - hel = -0.107071 - crA = 0.290078 - crU = 0.302909 - lss = 0.816246 - lpc = 0.339594 - lpa = 0.660406 - lpc+ = 0.540057 - ncd = 0.974675 -++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.5 -++ ########################################################### -3dAllineate -source sub-03_ses-test_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Zhark the Registrator -*+ WARNING: If you are performing spatial transformations on an oblique dset, - such as ./sub-03_ses-test_T1w+orig.BRIK, - or viewing/combining it with volumes of differing obliquity, - you should consider running: - 3dWarp -deoblique - on this and other oblique datasets in the same session. - See 3dWarp -help for details. -++ Oblique dataset:./sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. -++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers -++ Source dataset: ./sub-03_ses-test_T1w+orig.HEAD -++ Base dataset: (not given) -++ Loading datasets -++ OpenMP thread count = 4 -++ ========== Applying transformation to 1 sub-bricks ========== -volume 0Ð++ wsinc5 interpolation setup: - + taper function = Min sidelobe 3 term - + taper cut point = 0.000 - + window radius = 5 voxels - + window shape = Cubical - + The above can be altered via the AFNI_WSINC5_* environment variables. - + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) - + wsinc5 CUBE(5) mask has 1000 points -++ Output dataset ./anat_w_skull_warped+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.4 -++ ########################################################### -foreach run ( 01 ) -3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc -++ 3dmerge: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ default -1dindex = 0 -++ default -1tindex = 1 -Program 3dmerge -3dmerge: edit and combine 3D datasets, by RW Cox -++ editing input dataset in memory (49.6 MB) -..............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK - -end -foreach run ( 01 ) -3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc -++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: Emperor Zhark -++ Loading dataset pb03.sub_03.r01.blur+tlrc -++ Forming automask - + Fixed clip level = 710.102234 - + Used gradual clip level = 629.363342 .. 793.875061 - + Number voxels above clip level = 28228 - + Clustering voxels ... - + Largest cluster has 28228 voxels - + Clustering voxels ... - + Largest cluster has 28140 voxels - + Filled 49 voxels in small holes; now have 28189 voxels - + Clustering voxels ... - + Largest cluster has 28189 voxels - + Clustering non-brain voxels ... - + Clustering voxels ... - + Largest cluster has 81161 voxels - + Mask now has 28189 voxels -++ Dilating automask - + Clustering voxels ... - + Largest cluster has 76139 voxels -++ 33211 voxels in the mask [out of 109350: 30.37%] -++ first 4 x-planes are zero [from L] -++ last 3 x-planes are zero [from R] -++ first 4 y-planes are zero [from P] -++ last 3 y-planes are zero [from A] -++ first 3 z-planes are zero [from I] -++ last 3 z-planes are zero [from S] -++ Output dataset ./rm.mask_r01+tlrc.BRIK -++ CPU time = 0.290000 sec -end -3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 -++ processing 1 input datasets... -++ padding all datasets by 0 (for dilations) -++ frac 0 over 1 volumes gives min count 0 -++ voxel limits: 0 clipped, 33211 survived, 76139 were zero -++ writing result full_mask.sub_03... -++ Output dataset ./full_mask.sub_03+tlrc.BRIK -3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-test_T1w_ns+tlrc -prefix rm.resam.anat -3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 -++ no -frac option: defaulting to -union -++ processing 1 input datasets... -++ padding all datasets by 5 (for dilations) -++ frac 0 over 1 volumes gives min count 0 -++ voxel limits: 0 clipped, 30704 survived, 78646 were zero -++ filled 0 holes (0 voxels) -++ writing result mask_anat.sub_03... -++ Output dataset ./mask_anat.sub_03+tlrc.BRIK -3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc -tee out.mask_ae_overlap.txt -++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -#A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK -#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) -33211 30704 36000 27915 5296 2789 15.9465 9.0835 0.9461 0.9206 0.9824 -3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc -tee out.mask_ae_dice.txt -0.873504 -3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc -3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group -++ no -frac option: defaulting to -union -++ processing 1 input datasets... -++ padding all datasets by 5 (for dilations) -++ frac 0 over 1 volumes gives min count 0 -++ voxel limits: 0 clipped, 30980 survived, 78370 were zero -++ filled 0 holes (0 voxels) -++ writing result mask_group... -++ Output dataset ./mask_group+tlrc.BRIK -foreach run ( 01 ) -3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -++ Output dataset ./rm.mean_r01+tlrc.BRIK -3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK -end -1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D -1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D -1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 -total number of censored TRs (simple form) = 21 -set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D - -show_trs_uncensored encoded` -1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 -++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: B. Douglas Ward, et al. -++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD -++ STAT automask has 97119 voxels (out of 109350 = 88.8%) -++ Skipping check for initial transients -++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ -++ -stim_times using TR=2.5 s for stimulus timing conversion -++ -stim_times using TR=2.5 s for any -iresp output datasets -++ [you can alter the -iresp TR via the -TR_times option] -++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise -++ ** GUESSED ** -stim_times 1 using LOCAL times -++ ** GUESSED ** -stim_times 2 using LOCAL times -++ ** GUESSED ** -stim_times 3 using LOCAL times -++ ** GUESSED ** -stim_times 4 using LOCAL times -++ ** GUESSED ** -stim_times 5 using LOCAL times ------------------------------------------------------------- -GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control': - 0 0 0 0 0 0.333 0.333 -0.5 0.333 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 - -++ Number of time points: 238 (before censor) ; 217 (after) - + Number of parameters: 22 [17 baseline ; 5 signal] -++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) -++ Wrote matrix image to file X.jpg -++ Wrote matrix values to file X.xmat.1D -++ ========= Things you can do with the matrix file ========= -++ (a) Linear regression with ARMA(1,1) modeling of serial correlation: - -3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ - -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ - -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb - -++ N.B.: 3dREMLfit command above written to file stats.REML_cmd -++ (b) Visualization/analysis of the matrix via ExamineXmat.R -++ (c) Synthesis of sub-model datasets using 3dSynthesize -++ ========================================================== -++ Wrote matrix values to file X.nocensor.xmat.1D -++ ----- Signal+Baseline matrix condition [X] (217x22): 7.87414 ++ VERY GOOD ++ -++ ----- Signal-only matrix condition [X] (217x5): 1.46311 ++ VERY GOOD ++ -++ ----- Baseline-only matrix condition [X] (217x17): 7.75168 ++ VERY GOOD ++ -++ ----- stim_base-only matrix condition [X] (217x12): 6.17475 ++ VERY GOOD ++ -++ ----- polort-only matrix condition [X] (217x5): 1.09587 ++ VERY GOOD ++ -++ +++++ Matrix inverse average error = 1.12762e-14 ++ VERY GOOD ++ -++ Matrix setup time = 0.72 s -++ Calculations starting; elapsed time=1.442 -++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=16.076 -++ Smallest FDR q [0 Full_Fstat] = 6.90525e-13 -++ Smallest FDR q [2 Correct_Task#0_Tstat] = 1.79484e-09 -++ Smallest FDR q [3 Correct_Task_Fstat] = 1.79495e-09 -*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.33841 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.337718 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.107315 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [9 No_Response_Control_Fstat] = 0.107315 ==> few true single voxel detections -++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 4.83707e-12 -++ Smallest FDR q [12 No_Response_Task_Fstat] = 4.83707e-12 -++ Smallest FDR q [14 Response_Control#0_Tstat] = 1.04292e-06 -++ Smallest FDR q [15 Response_Control_Fstat] = 1.04299e-06 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 4.28411e-07 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 4.28347e-07 -++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK - + created 13 FDR curves in bucket header -++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK -++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK -++ #Flops=3.97183e+10 Average Dot Product=37.2229 -if ( 0 != 0 ) then -1d_tool.py -show_cormat_warnings -infile X.xmat.1D -tee out.cormat_warn.txt - -Warnings regarding Correlation Matrix: X.xmat.1D - - severity correlation cosine regressor pair - -------- ----------- ------ ---------------------------------------- - medium: 0.566 0.642 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 - -3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD -++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 1.5 s -3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -++ Output dataset ./rm.signal.all+tlrc.BRIK -3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -++ Output dataset ./rm.noise.all+tlrc.BRIK -3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ./TSNR.sub_03+tlrc.BRIK -3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc -++ 3dTnorm: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RW Cox -++ Output dataset ./rm.errts.unit+tlrc.BRIK -3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc -++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -+++ 33211 voxels survive the mask -3dTstat -sos -prefix - gmean.errts.unit.1D' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo -- GCOR = `cat out.gcor.1D` -cat out.gcor.1D --- GCOR = 0.137338 -3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: A cast of thousands -++ Output dataset ./rm.DP+tlrc.BRIK -3dTstat -sum -prefix corr_brain rm.DP+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -++ Output dataset ./corr_brain+tlrc.BRIK -1dcat X.nocensor.xmat.1D[5] -1dcat X.nocensor.xmat.1D[6] -1dcat X.nocensor.xmat.1D[7] -1dcat X.nocensor.xmat.1D[8] -1dcat X.nocensor.xmat.1D[9] -set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` -1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest -3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -++ Output dataset ./sum_ideal.1D -1dcat X.nocensor.xmat.1D[5..9] -touch blur_est.sub_03.1D -mkdir files_ACF -touch blur.epits.1D -foreach run ( 01 ) -set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded - -show_trs_run $run` -1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..50,60,61,68..101,104..160,163..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] -++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: The Bob -++ Number of voxels in mask = 33211 -*+ WARNING: removed 235 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 217 time points - + detrending done (2.29 CPU s thus far) -++ start ACF calculations out to radius = 27.77 mm - + ACF done (57.21 CPU s thus far) -++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D -++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RWC et al. - + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png -end -set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) -3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off -*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits FWHM blurs: 0 0 0 0 -average epits FWHM blurs: 0 0 0 0 -echo 0 0 0 0 # epits FWHM blur estimates -set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) -3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off -*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.643102 5.25242 13.8038 13.5137 -average epits ACF blurs: 0.643102 5.25242 13.8038 13.5137 -echo 0.643102 5.25242 13.8038 13.5137 # epits ACF blur estimates -touch blur.errts.1D -foreach run ( 01 ) -set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded - -show_trs_run $run` -1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..50,60,61,68..101,104..160,163..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] -++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: The Bob -++ Number of voxels in mask = 33211 -*+ WARNING: removed 235 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 217 time points - + detrending done (2.32 CPU s thus far) -++ start ACF calculations out to radius = 27.41 mm - + ACF done (57.85 CPU s thus far) -++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D -++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: RWC et al. - + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png -end -set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) -3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off -*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts FWHM blurs: 0 0 0 0 -average errts FWHM blurs: 0 0 0 0 -echo 0 0 0 0 # errts FWHM blur estimates -set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) -3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ Authored by: KR Hammett & RW Cox -*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off -*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.694971 5.17822 14.3851 13.2323 -average errts ACF blurs: 0.694971 5.17822 14.3851 13.2323 -echo 0.694971 5.17822 14.3851 13.2323 # errts ACF blur estimates -gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD -gen_ss_review_scripts.py -mot_limit 0.5 -exit0 -++ writing ss review basic: @ss_review_basic -++ writing ss review driver: @ss_review_driver -++ writing ss review drive commands: @ss_review_driver_commands -rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD -tee out.ss_review.sub_03.txt -if ( -e @ss_review_basic ) ./@ss_review_basic -./@ss_review_basic - -subject ID : sub_03 -TRs removed (per run) : 0 -num stim classes provided : 5 -final anatomy dset : anat_final.sub_03+tlrc.HEAD -final stats dset : stats.sub_03+tlrc.HEAD -final voxel resolution : 4.000000 4.000000 4.000000 - -motion limit : 0.5 -num TRs above mot limit : 13 -average motion (per TR) : 0.179191 -average censored motion : 0.129595 -max motion displacement : 5.04394 -max censored displacement : 3.96802 -outlier limit : 0.1 -average outlier frac (TR) : 0.0152516 -num TRs above out limit : 8 - -num runs found : 1 -num TRs per run : 238 -num TRs per run (applied) : 217 -num TRs per run (censored): 21 -fraction censored per run : 0.0882353 -TRs total (uncensored) : 238 -TRs total : 217 -degrees of freedom used : 22 -degrees of freedom left : 195 - -TRs censored : 21 -censor fraction : 0.088235 -num regs of interest : 5 -num TRs per stim (orig) : 71 43 64 28 79 -num TRs censored per stim : 0 0 13 6 12 -fraction TRs censored : 0.000 0.000 0.203 0.214 0.152 -ave mot per sresp (orig) : 0.124806 0.112975 0.230781 0.273948 0.190656 -ave mot per sresp (cens) : 0.124806 0.112975 0.122112 0.144313 0.107954 - -TSNR average : 196.396 -global correlation (GCOR) : 0.137338 -anat/EPI mask Dice coef : 0.873504 -maximum F-stat (masked) : 39.2089 -blur estimates (ACF) : 0.694971 5.17822 14.3851 -blur estimates (FWHM) : 0 0 0 - -** TR #0 outliers: possible pre-steady state TRs in run 01 - -cd .. -echo execution finished: `date` -date -execution finished: Thu Aug 3 22:20:22 EDT 2017 +echo output dir sub_03.results already exists +output dir sub_03.results already exists +exit diff --git a/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 old mode 100755 new mode 100644 index 3c5e106..f3cc349 --- a/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Thu Aug 3 22:13:37 2017" +echo "auto-generated by afni_proc.py, Fri Aug 4 12:43:15 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -45,24 +45,23 @@ mkdir $output_dir mkdir $output_dir/stimuli # copy stim files into stimulus directory -cp \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ +cp /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D \ $output_dir/stimuli # copy anatomy to results dir -3dcopy \ - /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ +3dcopy \ + /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ $output_dir/sub-03_ses-test_T1w # ============================ auto block: tcat ============================ # apply 3dTcat to copy input dsets to results dir, while # removing the first 0 TRs 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ - /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' + /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' # and make note of repetitions (TRs) per run set tr_counts = ( 238 ) @@ -240,7 +239,7 @@ end # ---- create group anatomy mask, mask_group+tlrc ---- # (resampled from tlrc base anat, MNI_avg152T1+tlrc) 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ - -input /Users/monicali/abin/MNI_avg152T1+tlrc + -input /Users/mli/abin/MNI_avg152T1+tlrc # convert to binary group mask; fill gaps and holes 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ @@ -305,8 +304,7 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ - -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -457,23 +455,22 @@ echo "execution finished: `date`" # ========================================================================== # script generated by the command: # -# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ -# tshift align tlrc volreg blur mask scale regress -copy_anat \ -# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ -# -tcat_remove_first_trs 0 -dsets \ -# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ -# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ -# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ -# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ -# No_Response_Task Response_Control -regress_basis GAM \ -# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ -# -regress_opts_3dD -gltsym 'SYM: 0.333*Correct_Task \ -# +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control \ -# -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ -# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ +# -regress_opts_3dD -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ +# -*Response_Control' -glt_label 1 Landmark-Detection \ +# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ # -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err deleted file mode 100644 index 0327aca..0000000 --- a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err +++ /dev/null @@ -1,4 +0,0 @@ -*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.33841 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.337718 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.107315 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [9 No_Response_Control_Fstat] = 0.107315 ==> few true single voxel detections diff --git a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd deleted file mode 100644 index 968b10b..0000000 --- a/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd +++ /dev/null @@ -1,5 +0,0 @@ -# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 - -3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ - -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ - -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb $* diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 old mode 100755 new mode 100644 index 5445cbe..9b568a9 --- a/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 @@ -4,7 +4,7 @@ # creation date: Thu Aug 3 22:03:06 2017 # set data directories -set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set top_dir = /Users/mli/Desktop/playground set anat_dir = $top_dir/sub-03/ses-retest/anat set epi_dir = $top_dir/sub-03/ses-retest/func @@ -37,9 +37,8 @@ afni_proc.py -subj_id $subj \ -regress_censor_motion 0.5 \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ - -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control \ - -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ + -*Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 index 2e864af..06b29a0 100644 --- a/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 @@ -1,11 +1,10 @@ -set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground -set anat_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat -set epi_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func +set top_dir = /Users/mli/Desktop/playground +set anat_dir = /Users/mli/Desktop/playground/sub-03/ses-retest/anat +set epi_dir = /Users/mli/Desktop/playground/sub-03/ses-retest/func set subj = sub_03 set group_id = retest -afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control - -0.5*No_Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task + -*Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig -- tcat: reps is now 238 ++ updating polort to 4, from run len 595.0 s diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 index c3819f0..64e976f 100644 --- a/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 +++ b/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 @@ -1,15 +1,15 @@ -echo auto-generated by afni_proc.py, Thu Aug 3 22:21:58 2017 -auto-generated by afni_proc.py, Thu Aug 3 22:21:58 2017 +echo auto-generated by afni_proc.py, Fri Aug 4 12:55:45 2017 +auto-generated by afni_proc.py, Fri Aug 4 12:55:45 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Thu Aug 3 22:35:55 EDT 2017 +execution started: Fri Aug 4 12:55:48 EDT 2017 afni -ver -Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) +Precompiled binary macosx_10.7_local: Jul 27 2017 (Version AFNI_17.2.05) afni_history -check_date 23 Sep 2016 -- is current: afni_history as new as: 23 Sep 2016 - most recent entry is: 21 Jul 2017 + most recent entry is: 27 Jul 2017 if ( 0 ) then if ( 0 > 0 ) then set subj = sub_03 @@ -20,18 +20,18 @@ set runs = ( `count -digits 2 1 1` ) count -digits 2 1 1 mkdir sub_03.results mkdir sub_03.results/stimuli -cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D sub_03.results/stimuli -3dcopy /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz sub_03.results/sub-03_ses-retest_T1w -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] -++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 1.5 s +cp /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D sub_03.results/stimuli +3dcopy /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz sub_03.results/sub-03_ses-retest_T1w +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] +++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ elapsed time = 0.9 s set tr_counts = ( 238 ) cd sub_03.results touch out.pre_ss_warn.txt foreach run ( 01 ) 3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig -++ 3dToutcount: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dToutcount: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -49,7 +49,7 @@ end cat outcount.r01.1D foreach run ( 01 ) 3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig -++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTshift: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -62,7 +62,7 @@ foreach run ( 01 ) *+ WARNING: ==>> output dataset is just a copy of input dataset end 3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] -++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off #++ align_epi_anat version: 1.57 #++ turning off volume registration @@ -80,7 +80,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s \rm -f ./__tt_sub-03_ses-retest_T1w* #Script is running (command trimmed): 3dcopy ./sub-03_ses-retest_T1w+orig ./__tt_sub-03_ses-retest_T1w+orig -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ Removing skull from anat data #Script is running (command trimmed): 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-retest_T1w+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns @@ -94,22 +94,21 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Oblique dataset:./__tt_sub-03_ses-retest_T1w+orig.BRIK is 7.491219 degrees from plumb. #Script is running (command trimmed): 3dinfo ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' -#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig is ***oblique**** +#++ Dataset /Users/mli/Desktop/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig is ***oblique**** #Script is running (command trimmed): 3dAttribute DELTA ./__tt_sub-03_ses-retest_T1w_ns+orig #++ Spacing for anat to oblique epi alignment is 1.000000 #++ Matching obliquity of anat to epi #Script is running (command trimmed): 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-retest_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-retest_T1w_ns_obla2e_mat.1D -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Deobliquing original dataset before obliquing ++ Combining oblique transformations -++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.BRIK #++ using 0th sub-brick because only one found #Script is running (command trimmed): 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' -++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ resampling epi to match anat data #Script is running (command trimmed): 3dresample -master ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu @@ -124,7 +123,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s #++ removing skull or area outside brain #Script is running (command trimmed): 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig -++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAutomask: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset ./__tt_vr_base_ts_rs+orig ++ Forming automask @@ -152,21 +151,19 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ last 48 z-planes are zero [from S] ++ applying mask to original data ++ Writing masked data -++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK -++ CPU time = 3.960000 sec +++ CPU time = 3.970000 sec #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1728.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1728.000000 on /Users/mli/Desktop/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig #Script is running (command trimmed): 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1728.000000))' -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK #++ Aligning anat data to epi data #Script is running (command trimmed): 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-retest_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./__tt_sub-03_ses-retest_T1w_ns_ob+orig.HEAD ++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD @@ -174,7 +171,6 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ 1356008 voxels in -source_automask+4 ++ Zero-pad: not needed ++ 1167476 voxels [7.5%] in weight mask -++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_al_junk_wtal+orig.BRIK ++ Number of points for matching = 1167476 ++ Local correlation: blok type = 'RHDD(6.54321)' ++ shift param auto-range: -84.4..84.4 -70.6..70.6 -85.1..85.1 @@ -188,7 +184,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Normalized convergence radius = 0.001000 ++ OpenMP thread count = 4 ++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= -++ ========== sub-brick #0 ========== [total CPU to here=9.2 s] +++ ========== sub-brick #0 ========== [total CPU to here=10.3 s] ++ *** Fine pass begins *** + * Enter alignment setup routine + - copying base image @@ -208,12 +204,11 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s z-angle= 0.4394 x-angle= 1.9668 y-angle=-5.3161 x-scale= 0.9674 y-scale= 0.9725 z-scale= 1.0191 y/x-shear= 0.0000 z/x-shear= 0.0099 z/y-shear= 0.0534 - + - Fine net CPU time = 35.3 s + + - Fine net CPU time = 36.5 s ++ Computing output image ++ image warp: parameters = 0.2981 -0.5136 -1.2234 0.4394 1.9668 -5.3161 0.9674 0.9725 1.0191 0.0000 0.0099 0.0534 -++ Output dataset ./__tt_sub-03_ses-retest_T1w_ns_ob_temp_al_junk+orig.BRIK ++ Wrote -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 47.0 sec Elapsed = 40.4 +++ 3dAllineate: total CPU time = 49.5 sec Elapsed = 36.2 ++ ########################################################### ++ # Please check results visually for alignment quality # ++ ########################################################### @@ -225,7 +220,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s #++ Combining anat to epi and oblique transformations #Script is running (command trimmed): 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-retest_T1w_al_junk -input ./__tt_sub-03_ses-retest_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__tt_sub-03_ses-retest_T1w_ns+orig.BRIK, @@ -256,14 +251,13 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ using -1Dmatrix_apply ++ Computing output image ++ image warp: parameters = 0.9618 0.0448 -0.0985 14.5442 -0.0314 0.9711 -0.0538 -1.5252 0.0911 0.0281 1.0141 -11.6150 -++ Output dataset ./sub-03_ses-retest_T1w_al_junk+orig.BRIK -++ 3dAllineate: total CPU time = 2.2 sec Elapsed = 2.8 +++ 3dAllineate: total CPU time = 2.2 sec Elapsed = 1.9 ++ ########################################################### #++ Creating final output: skullstripped anat data -copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig +copying from dataset /Users/mli/Desktop/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/mli/Desktop/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig #Script is running (command trimmed): 3dcopy ./__tt_sub-03_ses-retest_T1w_ns+orig sub-03_ses-retest_T1w_ns -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ Creating final output: anat data aligned to epi # copy is not necessary #++ Saving history @@ -300,7 +294,7 @@ copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subjec ++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. Center distance of 26.068730 mm Padding ... -++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dZeropad: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK Resampling ... *+ WARNING: If you are performing spatial transformations on an oblique dset, @@ -311,9 +305,8 @@ Resampling ... on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__ats_tmp__resamp_step+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -322,9 +315,8 @@ Resampling ... on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 7.491219 degrees from plumb. -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -334,26 +326,25 @@ Resampling ... See 3dWarp -help for details. ++ Oblique dataset:./sub-03_ses-retest_T1w_ns+orig.BRIK is 7.491219 degrees from plumb. Clipping -0.000100 1013.000100 ... -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ./__ats_tmp___rs_sub-03_ses-retest_T1w_ns+tlrc.BRIK -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-retest_T1w_ns+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets Registration (linear final interpolation) ... -++ 3dWarpDrive: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarpDrive: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Initial scale factor set to 0.30/247.56=8.3e+02 RMS[0] = 0.364249 0.163911 ITER = 6/137 @@ -361,8 +352,8 @@ RMS[0] = 0.364249 0.163911 ITER = 6/137 Warping has converged. -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-retest_T1w_ns+orig.BRIK, @@ -375,21 +366,19 @@ Warping has converged. ++ 7.491219 degrees from plumb. *+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations Applying brain mask -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox -++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drename: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.HEAD -++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.BRIK -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK.gz -> __ats_tmp___pad40_sub-03_ses-retest_T1w_ns.skl+orig.BRIK.gz +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp___pad40_sub-03_ses-retest_T1w_ns+orig.BRIK Unpadding ... -++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dZeropad: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ output dataset: ./__ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig.BRIK -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig *+ WARNING: Changing the space of an ORIG view dataset may cause confusion! @@ -397,17 +386,17 @@ Unpadding ... *+ WARNING: Consider changing the view of the dataset to TLRC view also ++ 3drefit processed 1 datasets Changing view of transformed anatomy -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+orig.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets Setting parent with 3drefit -wset sub-03_ses-retest_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc ++ 3drefit processed 1 datasets -++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drename: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Warning: ignoring +tlrc on new_prefix. ++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc.HEAD -> sub-03_ses-retest_T1w_ns+tlrc.HEAD ++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-retest_T1w_ns+tlrc.BRIK -> sub-03_ses-retest_T1w_ns+tlrc.BRIK @@ -416,7 +405,7 @@ cat_matvec sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I if ( ! -f sub-03_ses-retest_T1w_ns+tlrc.HEAD ) then foreach run ( 01 ) 3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig -++ 3dvolreg: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dvolreg: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base+orig.BRIK, @@ -435,7 +424,7 @@ foreach run ( 01 ) + 3364 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=7.05 s [=0.0296 s/sub-brick] +++ CPU time for realignment=6.75 s [=0.0284 s/sub-brick] ++ Min : roll=-0.200 pitch=-0.367 yaw=-0.118 dS=-1.139 dL=-0.157 dP=-0.055 ++ Mean: roll=-0.094 pitch=-0.011 yaw=+0.456 dS=-0.124 dL=+0.184 dP=+0.074 ++ Max : roll=+0.027 pitch=+0.449 yaw=+0.935 dS=+0.523 dL=+0.640 dP=+0.245 @@ -445,13 +434,12 @@ foreach run ( 01 ) ++ Max delta displ in automask = 1.52 (mm) at sub-brick 1 ++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK 3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression -++ Output dataset ./rm.epi.all1+orig.BRIK cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.sub_03.r01.tshift+orig.BRIK, @@ -470,11 +458,11 @@ cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retes ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 ++ ========== Applying transformation to 238 sub-bricks ========== -volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 6.2 sec Elapsed = 4.3 +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 6.2 sec Elapsed = 3.8 ++ ########################################################### 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./rm.epi.all1+orig.BRIK, @@ -486,25 +474,23 @@ volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20. ++ Oblique dataset:./rm.epi.all1+orig.BRIK is 4.947676 degrees from plumb. ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ Output dataset ./rm.epi.1.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 3.3 +++ 3dAllineate: total CPU time = 3.6 sec Elapsed = 3.1 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox -++ Output dataset ./rm.epi.min.r01+tlrc.BRIK end cat dfile.r01.1D 3dcopy rm.epi.min.r01+tlrc mask_epi_extents -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] foreach run ( 01 ) 3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK end cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retest_T1w_al_junk_mat.aff12.1D -I 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base+orig.BRIK, @@ -523,14 +509,14 @@ cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retes ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 ++ ========== Applying transformation to 1 sub-bricks ========== -volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK -++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.2 +volume 0Ø++ Output dataset ./final_epi_vr_base+tlrc.BRIK +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.1 ++ ########################################################### 3dcopy sub-03_ses-retest_T1w_ns+tlrc anat_final.sub_03 -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] 3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc tee out.allcostX.txt -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./anat_final.sub_03+tlrc.HEAD ++ Base dataset: ./final_epi_vr_base+tlrc.HEAD @@ -545,7 +531,7 @@ tee out.allcostX.txt ++ Local correlation: blok type = 'RHDD(14.76)' *+ WARNING: No output dataset will be calculated ++ OpenMP thread count = 4 -volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +volume 0Ø + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 ++ allcost output: init #0 ls = 0.184126 sp = 0.307224 @@ -564,7 +550,7 @@ volume 0 ++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 ++ ########################################################### 3dAllineate -source sub-03_ses-retest_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-retest_T1w+orig.BRIK, @@ -580,7 +566,7 @@ volume 0 ++ Loading datasets ++ OpenMP thread count = 4 ++ ========== Applying transformation to 1 sub-bricks ========== -volume 0Ð++ wsinc5 interpolation setup: +volume 0Ø++ wsinc5 interpolation setup: + taper function = Min sidelobe 3 term + taper cut point = 0.000 + window radius = 5 voxels @@ -589,11 +575,11 @@ volume 0 + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + wsinc5 CUBE(5) mask has 1000 points ++ Output dataset ./anat_w_skull_warped+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.7 +++ 3dAllineate: total CPU time = 3.1 sec Elapsed = 1.6 ++ ########################################################### foreach run ( 01 ) 3dmerge -1blur_fwhm 3.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc -++ 3dmerge: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dmerge: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ default -1dindex = 0 ++ default -1tindex = 1 Program 3dmerge @@ -604,7 +590,7 @@ Program 3dmerge end foreach run ( 01 ) 3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc -++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAutomask: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset pb03.sub_03.r01.blur+tlrc ++ Forming automask @@ -632,8 +618,7 @@ foreach run ( 01 ) ++ last 3 y-planes are zero [from A] ++ first 3 z-planes are zero [from I] ++ last 3 z-planes are zero [from S] -++ Output dataset ./rm.mask_r01+tlrc.BRIK -++ CPU time = 0.280000 sec +++ CPU time = 0.290000 sec end 3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 ++ processing 1 input datasets... @@ -641,7 +626,6 @@ end ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 33146 survived, 76204 were zero ++ writing result full_mask.sub_03... -++ Output dataset ./full_mask.sub_03+tlrc.BRIK 3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-retest_T1w_ns+tlrc -prefix rm.resam.anat 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 ++ no -frac option: defaulting to -union @@ -651,17 +635,16 @@ end ++ voxel limits: 0 clipped, 30574 survived, 78776 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_anat.sub_03... -++ Output dataset ./mask_anat.sub_03+tlrc.BRIK 3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_overlap.txt -++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dOverlap: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK #A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) 33146 30574 35621 28099 5047 2475 15.2266 8.0951 0.9461 0.9329 0.9590 3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_dice.txt 0.881952 -3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc +3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/mli/abin/MNI_avg152T1+tlrc 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ no -frac option: defaulting to -union ++ processing 1 input datasets... @@ -670,14 +653,13 @@ tee out.mask_ae_dice.txt ++ voxel limits: 0 clipped, 30980 survived, 78370 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_group... -++ Output dataset ./mask_group+tlrc.BRIK foreach run ( 01 ) 3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.mean_r01+tlrc.BRIK 3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK end @@ -688,9 +670,8 @@ total number of censored TRs (simple form) = 2 set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D -show_trs_uncensored encoded` 1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 -++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +++ 3dDeconvolve: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD ++ STAT automask has 100184 voxels (out of 109350 = 91.6%) @@ -705,10 +686,11 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D ++ ** GUESSED ** -stim_times 3 using LOCAL times ++ ** GUESSED ** -stim_times 4 using LOCAL times ++ ** GUESSED ** -stim_times 5 using LOCAL times +*+ WARNING: -gltsym: Can't interpret '*' scale factor in '-*Response_Control' -- replaced by 1 +*+ WARNING: -gltsym: '*' scale factor in '-*Response_Control' not at start of string? ------------------------------------------------------------ -GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control': - 0 0 0 0 0 0.333 0.333 -0.5 0.333 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 +GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': + 0 0 0 0 0 0.5 0.5 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 ++ Number of time points: 238 (before censor) ; 236 (after) + Number of parameters: 22 [17 baseline ; 5 signal] @@ -734,9 +716,9 @@ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task ++ ----- polort-only matrix condition [X] (236x5): 1.05506 ++ VERY GOOD ++ ++ +++++ Matrix inverse average error = 2.74977e-15 ++ VERY GOOD ++ ++ Matrix setup time = 0.66 s -++ Calculations starting; elapsed time=1.246 +++ Calculations starting; elapsed time=1.556 ++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=15.833 +++ Calculations finished; elapsed time=20.792 ++ Smallest FDR q [0 Full_Fstat] = 4.80713e-13 ++ Smallest FDR q [2 Correct_Task#0_Tstat] = 8.98106e-12 ++ Smallest FDR q [3 Correct_Task_Fstat] = 8.98004e-12 @@ -748,8 +730,8 @@ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task ++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.00889248 ++ Smallest FDR q [14 Response_Control#0_Tstat] = 1.42207e-12 ++ Smallest FDR q [15 Response_Control_Fstat] = 1.422e-12 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 7.0934e-05 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 7.09247e-05 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 7.67542e-13 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 7.67601e-13 ++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + created 13 FDR curves in bucket header ++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK @@ -766,40 +748,40 @@ Warnings regarding Correlation Matrix: X.xmat.1D medium: 0.447 0.539 ( 5 vs. 6) Correct_Task#0 vs. Incorrect_Task#0 3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD -++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 0.6 s +++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ elapsed time = 0.5 s 3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..237] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.signal.all+tlrc.BRIK 3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..237] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.noise.all+tlrc.BRIK 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./TSNR.sub_03+tlrc.BRIK 3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc -++ 3dTnorm: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTnorm: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Output dataset ./rm.errts.unit+tlrc.BRIK 3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc -++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dmaskave: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ 33146 voxels survive the mask 3dTstat -sos -prefix - gmean.errts.unit.1D' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D -- GCOR = 0.051467 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./rm.DP+tlrc.BRIK 3dTstat -sum -prefix corr_brain rm.DP+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./corr_brain+tlrc.BRIK 1dcat X.nocensor.xmat.1D[5] @@ -810,7 +792,7 @@ cat out.gcor.1D set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` 1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 ++ Output dataset ./sum_ideal.1D @@ -824,22 +806,22 @@ set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 if ( 2..237 == ) continue 3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..237] -++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob ++ Number of voxels in mask = 33146 *+ WARNING: removed 239 voxels from mask because they are constant in time ++ detrending start: 17 baseline funcs, 236 time points - + detrending done (2.53 CPU s thus far) + + detrending done (3.15 CPU s thus far) ++ start ACF calculations out to radius = 19.19 mm - + ACF done (35.46 CPU s thus far) + + ACF done (39.49 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D -++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png end set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) 3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 @@ -848,13 +830,13 @@ average epits FWHM blurs: 0 0 0 0 echo 0 0 0 0 # epits FWHM blur estimates set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) 3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.824146 3.58345 14.0589 9.17809 -average epits ACF blurs: 0.824146 3.58345 14.0589 9.17809 -echo 0.824146 3.58345 14.0589 9.17809 # epits ACF blur estimates +echo average epits ACF blurs: 0.824135 3.58341 14.0583 9.17803 +average epits ACF blurs: 0.824135 3.58341 14.0583 9.17803 +echo 0.824135 3.58341 14.0583 9.17803 # epits ACF blur estimates touch blur.errts.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded @@ -862,22 +844,22 @@ set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 if ( 2..237 == ) continue 3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..237] -++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob ++ Number of voxels in mask = 33146 *+ WARNING: removed 239 voxels from mask because they are constant in time ++ detrending start: 17 baseline funcs, 236 time points - + detrending done (2.45 CPU s thus far) + + detrending done (2.94 CPU s thus far) ++ start ACF calculations out to radius = 19.08 mm - + ACF done (36.55 CPU s thus far) + + ACF done (38.80 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D -++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png end set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) 3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 @@ -886,19 +868,19 @@ average errts FWHM blurs: 0 0 0 0 echo 0 0 0 0 # errts FWHM blur estimates set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) 3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.863011 3.61001 15.0127 9.12364 -average errts ACF blurs: 0.863011 3.61001 15.0127 9.12364 -echo 0.863011 3.61001 15.0127 9.12364 # errts ACF blur estimates +echo average errts ACF blurs: 0.863014 3.61002 15.013 9.12366 +average errts ACF blurs: 0.863014 3.61002 15.013 9.12366 +echo 0.863014 3.61002 15.013 9.12366 # errts ACF blur estimates gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD gen_ss_review_scripts.py -mot_limit 0.5 -exit0 ++ writing ss review basic: @ss_review_basic ++ writing ss review driver: @ss_review_driver ++ writing ss review drive commands: @ss_review_driver_commands -rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK.gz rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK.gz rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK.gz rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK.gz rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD tee out.ss_review.sub_03.txt if ( -e @ss_review_basic ) ./@ss_review_basic ./@ss_review_basic @@ -943,7 +925,7 @@ TSNR average : 160.267 global correlation (GCOR) : 0.051467 anat/EPI mask Dice coef : 0.881952 maximum F-stat (masked) : 48.5706 -blur estimates (ACF) : 0.863011 3.61001 15.0127 +blur estimates (ACF) : 0.863014 3.61002 15.013 blur estimates (FWHM) : 0 0 0 ** TR #0 outliers: possible pre-steady state TRs in run 01 @@ -951,4 +933,4 @@ blur estimates (FWHM) : 0 0 0 cd .. echo execution finished: `date` date -execution finished: Thu Aug 3 22:45:13 EDT 2017 +execution finished: Fri Aug 4 13:00:11 EDT 2017 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 old mode 100755 new mode 100644 index 4ac96ab..04780a2 --- a/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 +++ b/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Thu Aug 3 22:21:58 2017" +echo "auto-generated by afni_proc.py, Fri Aug 4 12:55:45 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -45,24 +45,23 @@ mkdir $output_dir mkdir $output_dir/stimuli # copy stim files into stimulus directory -cp \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ +cp /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D \ $output_dir/stimuli # copy anatomy to results dir -3dcopy \ - /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ +3dcopy \ + /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ $output_dir/sub-03_ses-retest_T1w # ============================ auto block: tcat ============================ # apply 3dTcat to copy input dsets to results dir, while # removing the first 0 TRs 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ - /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' + /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' # and make note of repetitions (TRs) per run set tr_counts = ( 238 ) @@ -240,7 +239,7 @@ end # ---- create group anatomy mask, mask_group+tlrc ---- # (resampled from tlrc base anat, MNI_avg152T1+tlrc) 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ - -input /Users/monicali/abin/MNI_avg152T1+tlrc + -input /Users/mli/abin/MNI_avg152T1+tlrc # convert to binary group mask; fill gaps and holes 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ @@ -306,8 +305,7 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ - -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -458,23 +456,22 @@ echo "execution finished: `date`" # ========================================================================== # script generated by the command: # -# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ -# tshift align tlrc volreg blur mask scale regress -copy_anat \ -# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ -# -tcat_remove_first_trs 0 -dsets \ -# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ -# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ -# -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Correct_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-retest_Response_Control.1D \ -# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ -# No_Response_Task Response_Control -regress_basis GAM \ -# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ -# -regress_opts_3dD -gltsym 'SYM: 0.333*Correct_Task \ -# +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control \ -# -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ -# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ +# -regress_opts_3dD -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ +# -*Response_Control' -glt_label 1 Landmark-Detection \ +# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ # -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd deleted file mode 100644 index a997d7b..0000000 --- a/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/stats.REML_cmd +++ /dev/null @@ -1,5 +0,0 @@ -# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 - -3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ - -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ - -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb $* diff --git a/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 old mode 100755 new mode 100644 index 8c884ef..aea25a4 --- a/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 @@ -4,7 +4,7 @@ # creation date: Thu Aug 3 22:01:15 2017 # set data directories -set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground +set top_dir = /Users/mli/Desktop/playground set anat_dir = $top_dir/sub-03/ses-test/anat set epi_dir = $top_dir/sub-03/ses-test/func @@ -37,9 +37,8 @@ afni_proc.py -subj_id $subj \ -regress_censor_motion 0.5 \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ - -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control \ - -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ + -*Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 index 242a016..647e95b 100644 --- a/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 @@ -1,11 +1,10 @@ -set top_dir = /Users/monicali/Google-Drive/IBRAIN/playground -set anat_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat -set epi_dir = /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func +set top_dir = /Users/mli/Desktop/playground +set anat_dir = /Users/mli/Desktop/playground/sub-03/ses-test/anat +set epi_dir = /Users/mli/Desktop/playground/sub-03/ses-test/func set subj = sub_03 set group_id = test -afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control - -0.5*No_Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task + -*Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig -- tcat: reps is now 238 ++ updating polort to 4, from run len 595.0 s diff --git a/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 index a36666b..59d69f8 100644 --- a/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 +++ b/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 @@ -1,15 +1,15 @@ -echo auto-generated by afni_proc.py, Thu Aug 3 22:21:48 2017 -auto-generated by afni_proc.py, Thu Aug 3 22:21:48 2017 +echo auto-generated by afni_proc.py, Fri Aug 4 12:51:09 2017 +auto-generated by afni_proc.py, Fri Aug 4 12:51:09 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Thu Aug 3 22:30:59 EDT 2017 +execution started: Fri Aug 4 12:51:13 EDT 2017 afni -ver -Precompiled binary macosx_10.7_Intel_64: Jul 21 2017 (Version AFNI_17.2.04) +Precompiled binary macosx_10.7_local: Jul 27 2017 (Version AFNI_17.2.05) afni_history -check_date 23 Sep 2016 -- is current: afni_history as new as: 23 Sep 2016 - most recent entry is: 21 Jul 2017 + most recent entry is: 27 Jul 2017 if ( 0 ) then if ( 0 > 0 ) then set subj = sub_03 @@ -20,18 +20,18 @@ set runs = ( `count -digits 2 1 1` ) count -digits 2 1 1 mkdir sub_03.results mkdir sub_03.results/stimuli -cp /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D sub_03.results/stimuli -3dcopy /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz sub_03.results/sub-03_ses-test_T1w -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[0..$] -++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 2.1 s +cp /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D sub_03.results/stimuli +3dcopy /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz sub_03.results/sub-03_ses-test_T1w +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[0..$] +++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ elapsed time = 0.8 s set tr_counts = ( 238 ) cd sub_03.results touch out.pre_ss_warn.txt foreach run ( 01 ) 3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig -++ 3dToutcount: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dToutcount: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -49,7 +49,7 @@ end cat outcount.r01.1D foreach run ( 01 ) 3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig -++ 3dTshift: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTshift: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -62,7 +62,7 @@ foreach run ( 01 ) *+ WARNING: ==>> output dataset is just a copy of input dataset end 3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] -++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off #++ align_epi_anat version: 1.57 #++ turning off volume registration @@ -80,7 +80,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf \rm -f ./__tt_sub-03_ses-test_T1w* #Script is running (command trimmed): 3dcopy ./sub-03_ses-test_T1w+orig ./__tt_sub-03_ses-test_T1w+orig -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ Removing skull from anat data #Script is running (command trimmed): 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-test_T1w+orig -prefix ./__tt_sub-03_ses-test_T1w_ns @@ -94,22 +94,21 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ Oblique dataset:./__tt_sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. #Script is running (command trimmed): 3dinfo ./__tt_sub-03_ses-test_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' -#++ Dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig is ***oblique**** +#++ Dataset /Users/mli/Desktop/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig is ***oblique**** #Script is running (command trimmed): 3dAttribute DELTA ./__tt_sub-03_ses-test_T1w_ns+orig #++ Spacing for anat to oblique epi alignment is 1.000000 #++ Matching obliquity of anat to epi #Script is running (command trimmed): 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-test_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Deobliquing original dataset before obliquing ++ Combining oblique transformations -++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob+orig.BRIK #++ using 0th sub-brick because only one found #Script is running (command trimmed): 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' -++ 3dbucket: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ resampling epi to match anat data #Script is running (command trimmed): 3dresample -master ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu @@ -124,7 +123,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf #++ removing skull or area outside brain #Script is running (command trimmed): 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig -++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAutomask: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset ./__tt_vr_base_ts_rs+orig ++ Forming automask @@ -152,21 +151,19 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ last 36 z-planes are zero [from S] ++ applying mask to original data ++ Writing masked data -++ Output dataset ./__tt_vr_base_ts_rs_ns+orig.BRIK -++ CPU time = 3.570000 sec +++ CPU time = 3.610000 sec #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1890.000000 on /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1890.000000 on /Users/mli/Desktop/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig #Script is running (command trimmed): 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1890.000000))' -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__tt_vr_base_ts_rs_ns_wt+orig.BRIK #++ Aligning anat data to epi data #Script is running (command trimmed): 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns_ob+orig.HEAD ++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD @@ -174,7 +171,6 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ 1350442 voxels in -source_automask+4 ++ Zero-pad: not needed ++ 1155874 voxels [7.0%] in weight mask -++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal+orig.BRIK ++ Number of points for matching = 1155874 ++ Local correlation: blok type = 'RHDD(6.54321)' ++ shift param auto-range: -89.2..89.2 -69.3..69.3 -86.7..86.7 @@ -188,7 +184,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ Normalized convergence radius = 0.001000 ++ OpenMP thread count = 4 ++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= -++ ========== sub-brick #0 ========== [total CPU to here=9.8 s] +++ ========== sub-brick #0 ========== [total CPU to here=9.4 s] ++ *** Fine pass begins *** + * Enter alignment setup routine + - copying base image @@ -208,12 +204,11 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf z-angle=-0.6314 x-angle= 4.7459 y-angle=-1.0126 x-scale= 0.9677 y-scale= 0.9751 z-scale= 1.0200 y/x-shear=-0.0038 z/x-shear= 0.0093 z/y-shear= 0.0929 - + - Fine net CPU time = 51.8 s + + - Fine net CPU time = 48.8 s ++ Computing output image ++ image warp: parameters = 0.2099 -0.6560 -1.7075 -0.6314 4.7459 -1.0126 0.9677 0.9751 1.0200 -0.0038 0.0093 0.0929 -++ Output dataset ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk+orig.BRIK ++ Wrote -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 64.0 sec Elapsed = 38.0 +++ 3dAllineate: total CPU time = 60.4 sec Elapsed = 35.4 ++ ########################################################### ++ # Please check results visually for alignment quality # ++ ########################################################### @@ -225,7 +220,7 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf #++ Combining anat to epi and oblique transformations #Script is running (command trimmed): 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-test_T1w_al_junk -input ./__tt_sub-03_ses-test_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__tt_sub-03_ses-test_T1w_ns+orig.BRIK, @@ -256,14 +251,13 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ using -1Dmatrix_apply ++ Computing output image ++ image warp: parameters = 0.9643 -0.0770 -0.0643 8.3030 0.0414 0.9701 -0.0701 -8.0767 0.0578 0.0003 1.0212 -4.7196 -++ Output dataset ./sub-03_ses-test_T1w_al_junk+orig.BRIK -++ 3dAllineate: total CPU time = 2.4 sec Elapsed = 5.6 +++ 3dAllineate: total CPU time = 2.4 sec Elapsed = 1.8 ++ ########################################################### #++ Creating final output: skullstripped anat data -copying from dataset /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/monicali/Google-Drive/IBRAIN/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig +copying from dataset /Users/mli/Desktop/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/mli/Desktop/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig #Script is running (command trimmed): 3dcopy ./__tt_sub-03_ses-test_T1w_ns+orig sub-03_ses-test_T1w_ns -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #++ Creating final output: anat data aligned to epi # copy is not necessary #++ Saving history @@ -310,7 +304,7 @@ to your @auto_tlrc command. ********************************* Padding ... -++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dZeropad: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK Resampling ... *+ WARNING: If you are performing spatial transformations on an oblique dset, @@ -321,9 +315,8 @@ Resampling ... on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__ats_tmp__resamp_step+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -332,9 +325,8 @@ Resampling ... on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 6.455733 degrees from plumb. -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-test_T1w_ns+orig.BRIK, or viewing/combining it with volumes of differing obliquity, @@ -344,26 +336,25 @@ Resampling ... See 3dWarp -help for details. ++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. Clipping -0.000100 1158.000100 ... -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ./__ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.BRIK -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets Registration (linear final interpolation) ... -++ 3dWarpDrive: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarpDrive: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Initial scale factor set to 0.30/273.95=9.2e+02 RMS[0] = 0.384861 0.16449 ITER = 6/137 @@ -371,8 +362,8 @@ RMS[0] = 0.384861 0.16449 ITER = 6/137 Warping has converged. -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-test_T1w_ns+orig.BRIK, @@ -385,21 +376,19 @@ Warping has converged. ++ 6.455733 degrees from plumb. *+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations Applying brain mask -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK -++ 3dWarp: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox -++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drename: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.HEAD -++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.BRIK -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK.gz -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.BRIK.gz +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands -++ Output dataset ././__ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK Unpadding ... -++ 3dZeropad: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dZeropad: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ output dataset: ./__ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.BRIK -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig *+ WARNING: Changing the space of an ORIG view dataset may cause confusion! @@ -407,17 +396,17 @@ Unpadding ... *+ WARNING: Consider changing the view of the dataset to TLRC view also ++ 3drefit processed 1 datasets Changing view of transformed anatomy -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.HEAD + Changed dataset view type and filenames. ++ 3drefit processed 1 datasets Setting parent with 3drefit -wset sub-03_ses-test_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc -++ 3drefit: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc ++ 3drefit processed 1 datasets -++ 3drename: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3drename: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Warning: ignoring +tlrc on new_prefix. ++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.HEAD -> sub-03_ses-test_T1w_ns+tlrc.HEAD ++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.BRIK -> sub-03_ses-test_T1w_ns+tlrc.BRIK @@ -426,7 +415,7 @@ cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then foreach run ( 01 ) 3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig -++ 3dvolreg: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dvolreg: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base+orig.BRIK, @@ -445,7 +434,7 @@ foreach run ( 01 ) + 3319 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=9.58 s [=0.0403 s/sub-brick] +++ CPU time for realignment=9.03 s [=0.0379 s/sub-brick] ++ Min : roll=-0.125 pitch=-0.838 yaw=-0.100 dS=-1.314 dL=-0.122 dP=-0.602 ++ Mean: roll=+0.244 pitch=-0.353 yaw=+1.492 dS=+1.594 dL=+0.625 dP=-0.273 ++ Max : roll=+0.752 pitch=+0.977 yaw=+2.780 dS=+2.627 dL=+1.582 dP=+0.307 @@ -455,13 +444,12 @@ foreach run ( 01 ) ++ Max delta displ in automask = 3.75 (mm) at sub-brick 57 ++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK 3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression -++ Output dataset ./rm.epi.all1+orig.BRIK cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.sub_03.r01.tshift+orig.BRIK, @@ -480,11 +468,11 @@ cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1 ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 ++ ========== Applying transformation to 238 sub-bricks ========== -volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ð++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 6.0 sec Elapsed = 4.9 +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 5.9 sec Elapsed = 3.8 ++ ########################################################### 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./rm.epi.all1+orig.BRIK, @@ -496,25 +484,23 @@ volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20. ++ Oblique dataset:./rm.epi.all1+orig.BRIK is 6.153038 degrees from plumb. ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ Output dataset ./rm.epi.1.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 4.1 +++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 3.1 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox -++ Output dataset ./rm.epi.min.r01+tlrc.BRIK end cat dfile.r01.1D 3dcopy rm.epi.min.r01+tlrc mask_epi_extents -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] foreach run ( 01 ) 3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK end cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base+orig.BRIK, @@ -533,14 +519,14 @@ cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1 ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 ++ ========== Applying transformation to 1 sub-bricks ========== -volume 0Ð++ Output dataset ./final_epi_vr_base+tlrc.BRIK -++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.2 +volume 0Ø++ Output dataset ./final_epi_vr_base+tlrc.BRIK +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.1 ++ ########################################################### 3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.sub_03 -++ 3dcopy: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] 3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc tee out.allcostX.txt -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./anat_final.sub_03+tlrc.HEAD ++ Base dataset: ./final_epi_vr_base+tlrc.HEAD @@ -555,7 +541,7 @@ tee out.allcostX.txt ++ Local correlation: blok type = 'RHDD(14.76)' *+ WARNING: No output dataset will be calculated ++ OpenMP thread count = 4 -volume 0Ð + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +volume 0Ø + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 ++ allcost output: init #0 ls = 0.183754 sp = 0.30567 @@ -571,10 +557,10 @@ volume 0 lpa = 0.660406 lpc+ = 0.540057 ncd = 0.974675 -++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.5 +++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 ++ ########################################################### 3dAllineate -source sub-03_ses-test_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped -++ 3dAllineate: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sub-03_ses-test_T1w+orig.BRIK, @@ -590,7 +576,7 @@ volume 0 ++ Loading datasets ++ OpenMP thread count = 4 ++ ========== Applying transformation to 1 sub-bricks ========== -volume 0Ð++ wsinc5 interpolation setup: +volume 0Ø++ wsinc5 interpolation setup: + taper function = Min sidelobe 3 term + taper cut point = 0.000 + window radius = 5 voxels @@ -599,11 +585,11 @@ volume 0 + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + wsinc5 CUBE(5) mask has 1000 points ++ Output dataset ./anat_w_skull_warped+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.1 sec Elapsed = 2.0 +++ 3dAllineate: total CPU time = 3.1 sec Elapsed = 1.3 ++ ########################################################### foreach run ( 01 ) 3dmerge -1blur_fwhm 3.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc -++ 3dmerge: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dmerge: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ default -1dindex = 0 ++ default -1tindex = 1 Program 3dmerge @@ -614,7 +600,7 @@ Program 3dmerge end foreach run ( 01 ) 3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc -++ 3dAutomask: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dAutomask: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset pb03.sub_03.r01.blur+tlrc ++ Forming automask @@ -642,7 +628,6 @@ foreach run ( 01 ) ++ last 3 y-planes are zero [from A] ++ first 3 z-planes are zero [from I] ++ last 3 z-planes are zero [from S] -++ Output dataset ./rm.mask_r01+tlrc.BRIK ++ CPU time = 0.280000 sec end 3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 @@ -651,7 +636,6 @@ end ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 33064 survived, 76286 were zero ++ writing result full_mask.sub_03... -++ Output dataset ./full_mask.sub_03+tlrc.BRIK 3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-test_T1w_ns+tlrc -prefix rm.resam.anat 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 ++ no -frac option: defaulting to -union @@ -661,17 +645,16 @@ end ++ voxel limits: 0 clipped, 30704 survived, 78646 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_anat.sub_03... -++ Output dataset ./mask_anat.sub_03+tlrc.BRIK 3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_overlap.txt -++ 3dOverlap: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dOverlap: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK #A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) 33064 30704 35830 27938 5126 2766 15.5033 9.0086 0.9518 0.9265 0.9782 3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_dice.txt 0.876239 -3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/monicali/abin/MNI_avg152T1+tlrc +3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/mli/abin/MNI_avg152T1+tlrc 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ no -frac option: defaulting to -union ++ processing 1 input datasets... @@ -680,14 +663,13 @@ tee out.mask_ae_dice.txt ++ voxel limits: 0 clipped, 30980 survived, 78370 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_group... -++ Output dataset ./mask_group+tlrc.BRIK foreach run ( 01 ) 3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.mean_r01+tlrc.BRIK 3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK end @@ -698,9 +680,8 @@ total number of censored TRs (simple form) = 21 set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D -show_trs_uncensored encoded` 1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 -++ 3dDeconvolve: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +++ 3dDeconvolve: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD ++ STAT automask has 97119 voxels (out of 109350 = 88.8%) @@ -715,10 +696,11 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D ++ ** GUESSED ** -stim_times 3 using LOCAL times ++ ** GUESSED ** -stim_times 4 using LOCAL times ++ ** GUESSED ** -stim_times 5 using LOCAL times +*+ WARNING: -gltsym: Can't interpret '*' scale factor in '-*Response_Control' -- replaced by 1 +*+ WARNING: -gltsym: '*' scale factor in '-*Response_Control' not at start of string? ------------------------------------------------------------ -GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control': - 0 0 0 0 0 0.333 0.333 -0.5 0.333 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 +GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': + 0 0 0 0 0 0.5 0.5 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 ++ Number of time points: 238 (before censor) ; 217 (after) + Number of parameters: 22 [17 baseline ; 5 signal] @@ -743,10 +725,10 @@ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task ++ ----- stim_base-only matrix condition [X] (217x12): 6.17475 ++ VERY GOOD ++ ++ ----- polort-only matrix condition [X] (217x5): 1.09587 ++ VERY GOOD ++ ++ +++++ Matrix inverse average error = 1.12762e-14 ++ VERY GOOD ++ -++ Matrix setup time = 0.77 s -++ Calculations starting; elapsed time=1.314 +++ Matrix setup time = 0.60 s +++ Calculations starting; elapsed time=1.258 ++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=14.889 +++ Calculations finished; elapsed time=14.994 ++ Smallest FDR q [0 Full_Fstat] = 1.54028e-12 ++ Smallest FDR q [2 Correct_Task#0_Tstat] = 7.9356e-11 ++ Smallest FDR q [3 Correct_Task_Fstat] = 7.9356e-11 @@ -758,8 +740,8 @@ GLT matrix from 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task ++ Smallest FDR q [12 No_Response_Task_Fstat] = 1.38372e-11 ++ Smallest FDR q [14 Response_Control#0_Tstat] = 4.43676e-05 ++ Smallest FDR q [15 Response_Control_Fstat] = 4.43706e-05 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.000204818 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.000204822 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 8.17121e-11 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 8.17159e-11 ++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + created 13 FDR curves in bucket header ++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK @@ -776,40 +758,40 @@ Warnings regarding Correlation Matrix: X.xmat.1D medium: 0.566 0.642 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD -++ 3dTcat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] -++ elapsed time = 0.9 s +++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ elapsed time = 0.3 s 3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.signal.all+tlrc.BRIK 3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.noise.all+tlrc.BRIK 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./TSNR.sub_03+tlrc.BRIK 3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc -++ 3dTnorm: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTnorm: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RW Cox ++ Output dataset ./rm.errts.unit+tlrc.BRIK 3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc -++ 3dmaskave: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dmaskave: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ 33064 voxels survive the mask 3dTstat -sos -prefix - gmean.errts.unit.1D' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D -- GCOR = 0.0653973 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP -++ 3dcalc: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./rm.DP+tlrc.BRIK 3dTstat -sum -prefix corr_brain rm.DP+tlrc -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./corr_brain+tlrc.BRIK 1dcat X.nocensor.xmat.1D[5] @@ -820,7 +802,7 @@ cat out.gcor.1D set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` 1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 ++ Output dataset ./sum_ideal.1D @@ -834,22 +816,22 @@ set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 if ( 2..50,60,61,68..101,104..160,163..237 == ) continue 3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] -++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob ++ Number of voxels in mask = 33064 *+ WARNING: removed 254 voxels from mask because they are constant in time ++ detrending start: 17 baseline funcs, 217 time points - + detrending done (2.33 CPU s thus far) + + detrending done (2.57 CPU s thus far) ++ start ACF calculations out to radius = 18.97 mm - + ACF done (32.36 CPU s thus far) + + ACF done (34.29 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D -++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png end set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) 3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 @@ -858,13 +840,13 @@ average epits FWHM blurs: 0 0 0 0 echo 0 0 0 0 # epits FWHM blur estimates set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) 3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.834334 3.52471 15.2586 9.03233 -average epits ACF blurs: 0.834334 3.52471 15.2586 9.03233 -echo 0.834334 3.52471 15.2586 9.03233 # epits ACF blur estimates +echo average epits ACF blurs: 0.834327 3.5247 15.2579 9.03231 +average epits ACF blurs: 0.834327 3.5247 15.2579 9.03231 +echo 0.834327 3.5247 15.2579 9.03231 # epits ACF blur estimates touch blur.errts.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded @@ -872,22 +854,22 @@ set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 if ( 2..50,60,61,68..101,104..160,163..237 == ) continue 3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] -++ 3dFWHMx: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob ++ Number of voxels in mask = 33064 *+ WARNING: removed 254 voxels from mask because they are constant in time ++ detrending start: 17 baseline funcs, 217 time points - + detrending done (2.27 CPU s thus far) + + detrending done (2.57 CPU s thus far) ++ start ACF calculations out to radius = 18.90 mm - + ACF done (32.31 CPU s thus far) + + ACF done (35.14 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D -++ 1dplot: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png end set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) 3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 @@ -896,19 +878,19 @@ average errts FWHM blurs: 0 0 0 0 echo 0 0 0 0 # errts FWHM blur estimates set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) 3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' -++ 3dTstat: AFNI version=AFNI_17.2.04 (Jul 21 2017) [64-bit] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.86343 3.55309 16.3317 9.01111 -average errts ACF blurs: 0.86343 3.55309 16.3317 9.01111 -echo 0.86343 3.55309 16.3317 9.01111 # errts ACF blur estimates +echo average errts ACF blurs: 0.863438 3.55309 16.3324 9.0111 +average errts ACF blurs: 0.863438 3.55309 16.3324 9.0111 +echo 0.863438 3.55309 16.3324 9.0111 # errts ACF blur estimates gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD gen_ss_review_scripts.py -mot_limit 0.5 -exit0 ++ writing ss review basic: @ss_review_basic ++ writing ss review driver: @ss_review_driver ++ writing ss review drive commands: @ss_review_driver_commands -rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK.gz rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK.gz rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK.gz rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK.gz rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD tee out.ss_review.sub_03.txt if ( -e @ss_review_basic ) ./@ss_review_basic ./@ss_review_basic @@ -953,7 +935,7 @@ TSNR average : 135.813 global correlation (GCOR) : 0.0653973 anat/EPI mask Dice coef : 0.876239 maximum F-stat (masked) : 42.6934 -blur estimates (ACF) : 0.86343 3.55309 16.3317 +blur estimates (ACF) : 0.863438 3.55309 16.3324 blur estimates (FWHM) : 0 0 0 ** TR #0 outliers: possible pre-steady state TRs in run 01 @@ -961,4 +943,4 @@ blur estimates (FWHM) : 0 0 0 cd .. echo execution finished: `date` date -execution finished: Thu Aug 3 22:35:55 EDT 2017 +execution finished: Fri Aug 4 12:55:19 EDT 2017 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 old mode 100755 new mode 100644 index 7e92ab6..b6d0da4 --- a/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 +++ b/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Thu Aug 3 22:21:48 2017" +echo "auto-generated by afni_proc.py, Fri Aug 4 12:51:09 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -45,24 +45,23 @@ mkdir $output_dir mkdir $output_dir/stimuli # copy stim files into stimulus directory -cp \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ - /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ +cp /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D \ + /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D \ $output_dir/stimuli # copy anatomy to results dir -3dcopy \ - /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ +3dcopy \ + /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ $output_dir/sub-03_ses-test_T1w # ============================ auto block: tcat ============================ # apply 3dTcat to copy input dsets to results dir, while # removing the first 0 TRs 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ - /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' + /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' # and make note of repetitions (TRs) per run set tr_counts = ( 238 ) @@ -240,7 +239,7 @@ end # ---- create group anatomy mask, mask_group+tlrc ---- # (resampled from tlrc base anat, MNI_avg152T1+tlrc) 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group \ - -input /Users/monicali/abin/MNI_avg152T1+tlrc + -input /Users/mli/abin/MNI_avg152T1+tlrc # convert to binary group mask; fill gaps and holes 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc \ @@ -305,8 +304,7 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ - -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task \ - +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -457,23 +455,22 @@ echo "execution finished: `date`" # ========================================================================== # script generated by the command: # -# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ -# tshift align tlrc volreg blur mask scale regress -copy_anat \ -# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ -# -tcat_remove_first_trs 0 -dsets \ -# /Users/monicali/Google-Drive/IBRAIN/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ -# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ -# -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Correct_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Control.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_No_Response_Task.1D \ -# /Users/monicali/Google-Drive/IBRAIN/playground/timing_sub-03_ses-test_Response_Control.1D \ -# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ -# No_Response_Task Response_Control -regress_basis GAM \ -# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ -# -regress_opts_3dD -gltsym 'SYM: 0.333*Correct_Task \ -# +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control \ -# -0.5*No_Response_Control' -glt_label 1 Landmark-Detection \ -# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ +# afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ +# tshift align tlrc volreg blur mask scale regress -copy_anat \ +# /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ +# -tcat_remove_first_trs 0 -dsets \ +# /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ +# -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ +# -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D \ +# /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D \ +# -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control \ +# No_Response_Task Response_Control -regress_basis GAM \ +# -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ +# -regress_opts_3dD -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ +# -*Response_Control' -glt_label 1 Landmark-Detection \ +# -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ # -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err b/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err deleted file mode 100644 index 6aceed6..0000000 --- a/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/3dDeconvolve.err +++ /dev/null @@ -1,2 +0,0 @@ -*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.123923 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.123702 ==> few true single voxel detections diff --git a/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd b/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd deleted file mode 100644 index 968b10b..0000000 --- a/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/stats.REML_cmd +++ /dev/null @@ -1,5 +0,0 @@ -# 3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 'motion_demean.1D[0]' -stim_base 6 -stim_label 6 roll_01 -stim_file 7 'motion_demean.1D[1]' -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 'motion_demean.1D[2]' -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 'motion_demean.1D[3]' -stim_base 9 -stim_label 9 dS_01 -stim_file 10 'motion_demean.1D[4]' -stim_base 10 -stim_label 10 dL_01 -stim_file 11 'motion_demean.1D[5]' -stim_base 11 -stim_label 11 dP_01 -stim_file 12 'motion_deriv.1D[0]' -stim_base 12 -stim_label 12 roll_02 -stim_file 13 'motion_deriv.1D[1]' -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 'motion_deriv.1D[2]' -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 'motion_deriv.1D[3]' -stim_base 15 -stim_label 15 dS_02 -stim_file 16 'motion_deriv.1D[4]' -stim_base 16 -stim_label 16 dL_02 -stim_file 17 'motion_deriv.1D[5]' -stim_base 17 -stim_label 17 dP_02 -gltsym 'SYM: 0.333*Correct_Task +0.333*Incorrect_Task +0.333*No_Response_Task -0.5*Response_Control -0.5*No_Response_Control' -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 - -3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ - -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ - -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb $* From 200610b0b87c4ff2c676c8e28b467196fe4bfe43 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Fri, 4 Aug 2017 13:28:57 -0400 Subject: [PATCH 09/18] add homework response --- HomeworkAnswers.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 HomeworkAnswers.md diff --git a/HomeworkAnswers.md b/HomeworkAnswers.md new file mode 100644 index 0000000..851d0c1 --- /dev/null +++ b/HomeworkAnswers.md @@ -0,0 +1,12 @@ +# Dice Coefficient Output +## Experiment 1 (smoothing FWHM = 6 mm) ++++ 30980 voxels in the mask +0.584105 + +## Experiment 2 (smoothing FWHM = 3 mm) ++++ 30980 voxels in the mask +0.491035 + +# Interpretation +The Dice coefficient is larger when the smoothing kernel is larger. +This is because there is less noise when the data is more smoothed, resulting in higher reliability between test and retest sessions due to more robust signal. From 16d687b84bf6b614718b1aeaedf4762b205fb3dd Mon Sep 17 00:00:00 2001 From: Monica Li Date: Sat, 5 Aug 2017 15:59:29 -0400 Subject: [PATCH 10/18] discard the first TR (2.5 sec) from timing files --- timing.py | 2 +- timing_sub-03_ses-retest_Correct_Task.1D | 2 +- timing_sub-03_ses-retest_Incorrect_Task.1D | 2 +- timing_sub-03_ses-retest_No_Response_Control.1D | 2 +- timing_sub-03_ses-retest_No_Response_Task.1D | 2 +- timing_sub-03_ses-retest_Response_Control.1D | 2 +- timing_sub-03_ses-test_Correct_Task.1D | 2 +- timing_sub-03_ses-test_Incorrect_Task.1D | 2 +- timing_sub-03_ses-test_No_Response_Control.1D | 2 +- timing_sub-03_ses-test_No_Response_Task.1D | 2 +- timing_sub-03_ses-test_Response_Control.1D | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/timing.py b/timing.py index 2f9875e..2a6d3b1 100644 --- a/timing.py +++ b/timing.py @@ -22,7 +22,7 @@ matches = regex.finditer(s) for m in matches: - timing_dic[m.groups()[3]].append(m.groups()[0]) + timing_dic[m.groups()[3]].append(str(float(m.groups()[0])-2.5)) for x in timing_dic: with open("timing_sub-%s_ses-%s_%s.1D" %(subj, ses, x),"w") as f: diff --git a/timing_sub-03_ses-retest_Correct_Task.1D b/timing_sub-03_ses-retest_Correct_Task.1D index 56893c0..e4a912e 100644 --- a/timing_sub-03_ses-retest_Correct_Task.1D +++ b/timing_sub-03_ses-retest_Correct_Task.1D @@ -1 +1 @@ -24.3064 27.5864 29.2264 30.8664 32.5064 35.7863 37.4263 39.0663 89.6393 91.2793 92.9193 96.1992 99.4792 101.1192 102.7592 104.3992 156.6121 158.2521 159.8921 164.8121 166.4521 169.732 223.585 225.225 228.5049 230.1449 231.7849 235.0649 285.6379 288.9178 290.5578 295.4778 297.1178 298.7578 350.9707 352.6107 354.2507 355.8907 360.8106 362.4506 364.0906 365.7306 417.9436 419.5836 422.8635 424.5035 426.1435 427.7835 429.4235 431.0635 483.2764 484.9164 488.1964 489.8364 491.4764 493.1164 494.7564 496.3963 \ No newline at end of file +21.8064 25.0864 26.7264 28.3664 30.0064 33.2863 34.9263 36.5663 87.1393 88.7793 90.4193 93.6992 96.9792 98.6192 100.2592 101.8992 154.1121 155.7521 157.3921 162.3121 163.9521 167.232 221.085 222.725 226.0049 227.6449 229.2849 232.5649 283.1379 286.4178 288.0578 292.9778 294.6178 296.2578 348.4707 350.1107 351.7507 353.3907 358.3106 359.9506 361.5906 363.2306 415.4436 417.0836 420.3635 422.0035 423.6435 425.2835 426.9235 428.5635 480.7764 482.4164 485.6964 487.3364 488.9764 490.6164 492.2564 493.8963 \ No newline at end of file diff --git a/timing_sub-03_ses-retest_Incorrect_Task.1D b/timing_sub-03_ses-retest_Incorrect_Task.1D index 80909d7..7b8760b 100644 --- a/timing_sub-03_ses-retest_Incorrect_Task.1D +++ b/timing_sub-03_ses-retest_Incorrect_Task.1D @@ -1 +1 @@ -25.9464 34.1464 94.5592 97.8392 154.9721 161.5321 163.1721 168.092 220.305 233.4249 292.1978 300.3977 357.5307 359.1707 416.3036 421.2235 486.5564 \ No newline at end of file +23.4464 31.6464 92.0592 95.3392 152.4721 159.0321 160.6721 165.592 217.805 230.9249 289.6978 297.8977 355.0307 356.6707 413.8036 418.7235 484.0564 \ No newline at end of file diff --git a/timing_sub-03_ses-retest_No_Response_Control.1D b/timing_sub-03_ses-retest_No_Response_Control.1D index 7d9f053..1b15c00 100644 --- a/timing_sub-03_ses-retest_No_Response_Control.1D +++ b/timing_sub-03_ses-retest_No_Response_Control.1D @@ -1 +1 @@ -61.8928 71.7327 137.0656 202.3985 267.7313 333.0642 398.397 455.53 460.4499 463.7299 517.5828 527.4228 \ No newline at end of file +59.3928 69.2327 134.5656 199.8985 265.2313 330.5642 395.897 453.03 457.9499 461.2299 515.0828 524.9228 \ No newline at end of file diff --git a/timing_sub-03_ses-retest_No_Response_Task.1D b/timing_sub-03_ses-retest_No_Response_Task.1D index d114df0..5531ed9 100644 --- a/timing_sub-03_ses-retest_No_Response_Task.1D +++ b/timing_sub-03_ses-retest_No_Response_Task.1D @@ -1 +1 @@ -221.945 226.8649 287.2778 293.8378 481.6365 \ No newline at end of file +219.445 224.3649 284.7778 291.3378 479.1365 \ No newline at end of file diff --git a/timing_sub-03_ses-retest_Response_Control.1D b/timing_sub-03_ses-retest_Response_Control.1D index ae4d19f..c02fa29 100644 --- a/timing_sub-03_ses-retest_Response_Control.1D +++ b/timing_sub-03_ses-retest_Response_Control.1D @@ -1 +1 @@ -56.9728 58.6128 60.2528 63.5328 65.1728 66.8128 68.4528 70.0928 122.3057 123.9457 125.5857 127.2257 128.8657 130.5056 132.1456 133.7856 135.4256 187.6386 189.2785 190.9185 192.5585 194.1985 195.8385 197.4785 199.1185 200.7585 252.9714 254.6114 256.2514 257.8914 259.5314 261.1714 262.8114 264.4513 266.0913 318.3043 319.9443 321.5843 323.2243 324.8642 326.5042 328.1442 329.7842 331.4242 383.6372 385.2771 386.9171 388.5571 390.1971 391.8371 393.4771 395.1171 396.7571 448.97 450.61 452.25 453.89 457.17 458.8099 462.0899 514.3029 515.9429 519.2228 520.8628 522.5028 524.1428 525.7828 529.0628 \ No newline at end of file +54.4728 56.1128 57.7528 61.0328 62.6728 64.3128 65.9528 67.5928 119.8057 121.4457 123.0857 124.7257 126.3657 128.0056 129.6456 131.2856 132.9256 185.1386 186.7785 188.4185 190.0585 191.6985 193.3385 194.9785 196.6185 198.2585 250.4714 252.1114 253.7514 255.3914 257.0314 258.6714 260.3114 261.9513 263.5913 315.8043 317.4443 319.0843 320.7243 322.3642 324.0042 325.6442 327.2842 328.9242 381.1372 382.7771 384.4171 386.0571 387.6971 389.3371 390.9771 392.6171 394.2571 446.47 448.11 449.75 451.39 454.67 456.3099 459.5899 511.8029 513.4429 516.7228 518.3628 520.0028 521.6428 523.2828 526.5628 \ No newline at end of file diff --git a/timing_sub-03_ses-test_Correct_Task.1D b/timing_sub-03_ses-test_Correct_Task.1D index 5a3791a..3c7c10a 100644 --- a/timing_sub-03_ses-test_Correct_Task.1D +++ b/timing_sub-03_ses-test_Correct_Task.1D @@ -1 +1 @@ -24.3062 27.5862 29.2262 30.8662 32.5061 34.1461 35.7861 37.4261 39.066 89.6386 91.2786 94.5586 99.4785 102.7585 104.3984 220.3035 223.5834 225.2234 226.8634 228.5033 231.7833 233.4233 235.0632 287.2758 290.5558 292.1958 295.4757 300.3956 350.9683 352.6082 354.2482 355.8882 359.1681 360.8081 362.4481 364.0881 417.9406 419.5806 421.2206 422.8606 424.5005 426.1405 427.7805 429.4205 431.0604 481.6331 483.273 486.553 488.193 489.8329 491.4729 493.1129 496.3928 \ No newline at end of file +21.8062 25.0862 26.7262 28.3662 30.0061 31.6461 33.2861 34.9261 36.566 87.1386 88.7786 92.0586 96.9785 100.2585 101.8984 217.8035 221.0834 222.7234 224.3634 226.0033 229.2833 230.9233 232.5632 284.7758 288.0558 289.6958 292.9757 297.8956 348.4683 350.1082 351.7482 353.3882 356.6681 358.3081 359.9481 361.5881 415.4406 417.0806 418.7206 420.3606 422.0005 423.6405 425.2805 426.9205 428.5604 479.1331 480.773 484.053 485.693 487.3329 488.9729 490.6129 493.8928 \ No newline at end of file diff --git a/timing_sub-03_ses-test_Incorrect_Task.1D b/timing_sub-03_ses-test_Incorrect_Task.1D index e9408ac..75cb793 100644 --- a/timing_sub-03_ses-test_Incorrect_Task.1D +++ b/timing_sub-03_ses-test_Incorrect_Task.1D @@ -1 +1 @@ -25.9462 96.1986 101.1185 221.9434 288.9158 297.1157 298.7557 357.5282 365.728 416.3007 484.913 494.7529 \ No newline at end of file +23.4462 93.6986 98.6185 219.4434 286.4158 294.6157 296.2557 355.0282 363.228 413.8007 482.413 492.2529 \ No newline at end of file diff --git a/timing_sub-03_ses-test_No_Response_Control.1D b/timing_sub-03_ses-test_No_Response_Control.1D index 8675af9..ec0d343 100644 --- a/timing_sub-03_ses-test_No_Response_Control.1D +++ b/timing_sub-03_ses-test_No_Response_Control.1D @@ -1 +1 @@ -61.8924 66.8123 71.7322 122.3049 128.8648 130.5047 132.1447 137.0646 194.1972 200.7571 254.6096 256.2496 261.1695 331.4219 391.8343 398.3942 450.6068 455.5268 458.8067 463.7266 517.5792 522.4991 529.059 \ No newline at end of file +59.3924 64.3123 69.2322 119.8049 126.3648 128.0047 129.6447 134.5646 191.6972 198.2571 252.1096 253.7496 258.6695 328.9219 389.3343 395.8942 448.1068 453.0268 456.3067 461.2266 515.0792 519.9991 526.559 \ No newline at end of file diff --git a/timing_sub-03_ses-test_No_Response_Task.1D b/timing_sub-03_ses-test_No_Response_Task.1D index 1bf176f..1969074 100644 --- a/timing_sub-03_ses-test_No_Response_Task.1D +++ b/timing_sub-03_ses-test_No_Response_Task.1D @@ -1 +1 @@ -92.9186 97.8385 154.9711 156.611 158.251 159.891 161.531 163.1709 164.8109 166.4509 168.0909 169.7308 230.1433 285.6359 293.8357 \ No newline at end of file +90.4186 95.3385 152.4711 154.111 155.751 157.391 159.031 160.6709 162.3109 163.9509 165.5909 167.2308 227.6433 283.1359 291.3357 \ No newline at end of file diff --git a/timing_sub-03_ses-test_Response_Control.1D b/timing_sub-03_ses-test_Response_Control.1D index e6788d7..294cfcc 100644 --- a/timing_sub-03_ses-test_Response_Control.1D +++ b/timing_sub-03_ses-test_Response_Control.1D @@ -1 +1 @@ -56.9724 58.6124 60.2524 63.5324 65.1723 68.4523 70.0923 123.9448 125.5848 127.2248 133.7847 135.4247 187.6373 189.2772 190.9172 192.5572 195.8371 197.4771 199.1171 202.397 252.9697 257.8896 259.5296 262.8095 264.4495 266.0895 267.7294 318.3021 319.942 321.582 323.222 324.862 326.5019 328.1419 329.7819 333.0618 383.6345 385.2744 386.9144 388.5544 390.1944 393.4743 395.1143 396.7543 448.9669 452.2468 453.8868 457.1667 460.4467 462.0867 514.2993 515.9392 519.2192 520.8592 524.1391 525.7791 527.4191 \ No newline at end of file +54.4724 56.1124 57.7524 61.0324 62.6723 65.9523 67.5923 121.4448 123.0848 124.7248 131.2847 132.9247 185.1373 186.7772 188.4172 190.0572 193.3371 194.9771 196.6171 199.897 250.4697 255.3896 257.0296 260.3095 261.9495 263.5895 265.2294 315.8021 317.442 319.082 320.722 322.362 324.0019 325.6419 327.2819 330.5618 381.1345 382.7744 384.4144 386.0544 387.6944 390.9743 392.6143 394.2543 446.4669 449.7468 451.3868 454.6667 457.9467 459.5867 511.7993 513.4392 516.7192 518.3592 521.6391 523.2791 524.9191 \ No newline at end of file From 2102cebc56d777ed92e9fce0e56c7112f2399144 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Sat, 5 Aug 2017 16:45:22 -0400 Subject: [PATCH 11/18] drop first TR; add -tpattern alt+z; fix GLM typo --- .../group.retest/subj.sub_03/cmd.ap.sub_03 | 7 +- .../subj.sub_03/output.cmd.ap.sub_03 | 10 +- .../subj.sub_03/output.proc.sub_03 | 337 ++++--- .../group.retest/subj.sub_03/proc.sub_03 | 15 +- .../group.test/subj.sub_03/cmd.ap.sub_03 | 5 +- .../subj.sub_03/output.cmd.ap.sub_03 | 10 +- .../group.test/subj.sub_03/output.proc.sub_03 | 930 +++++++++++++++++- .../group.test/subj.sub_03/proc.sub_03 | 15 +- .../group.retest/subj.sub_03/cmd.ap.sub_03 | 5 +- .../subj.sub_03/output.cmd.ap.sub_03 | 10 +- .../subj.sub_03/output.proc.sub_03 | 339 ++++--- .../group.retest/subj.sub_03/proc.sub_03 | 15 +- .../group.test/subj.sub_03/cmd.ap.sub_03 | 5 +- .../subj.sub_03/output.cmd.ap.sub_03 | 10 +- .../group.test/subj.sub_03/output.proc.sub_03 | 355 ++++--- .../group.test/subj.sub_03/proc.sub_03 | 15 +- HomeworkAnswers.md | 4 +- 17 files changed, 1500 insertions(+), 587 deletions(-) mode change 100644 => 100755 Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 mode change 100644 => 100755 Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 mode change 100644 => 100755 Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 mode change 100644 => 100755 Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 index 876ffcd..c1ce29f 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 @@ -17,8 +17,9 @@ afni_proc.py -subj_id $subj \ -script proc.$subj -scr_overwrite \ -blocks tshift align tlrc volreg blur mask scale regress \ -copy_anat $anat_dir/sub-03_ses-retest_T1w.nii.gz \ - -tcat_remove_first_trs 0 \ - -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ + -tcat_remove_first_trs 1 \ + -tshift_opts_ts -tpattern alt+z \ + -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ -tlrc_base MNI_avg152T1+tlrc \ -volreg_align_to third \ -volreg_align_e2a \ @@ -38,7 +39,7 @@ afni_proc.py -subj_id $subj \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ - -*Response_Control' -glt_label 1 Landmark-Detection \ + -Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 index 725babe..ecb6f3a 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 @@ -3,11 +3,13 @@ set anat_dir = /Users/mli/Desktop/playground/sub-03/ses-retest/anat set epi_dir = /Users/mli/Desktop/playground/sub-03/ses-retest/func set subj = sub_03 set group_id = retest -afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task - -*Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 1 -tshift_opts_ts -tpattern alt+z -dsets /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task + -Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig --- tcat: reps is now 238 -++ updating polort to 4, from run len 595.0 s +** warning: removing first 1 TRs from beginning of each run + --> the stimulus timing files must reflect the removal of these TRs +-- tcat: reps is now 237 +++ updating polort to 4, from run len 592.5 s -- volreg: using base dset vr_base+orig ++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 4 mm tlrc voxels -- applying anat warps to 1 dataset(s): sub-03_ses-retest_T1w diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 index 363e30f..f0b205d 100644 --- a/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/output.proc.sub_03 @@ -1,10 +1,10 @@ -echo auto-generated by afni_proc.py, Fri Aug 4 12:45:31 2017 -auto-generated by afni_proc.py, Fri Aug 4 12:45:31 2017 +echo auto-generated by afni_proc.py, Sat Aug 5 16:05:00 2017 +auto-generated by afni_proc.py, Sat Aug 5 16:05:00 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Fri Aug 4 12:45:35 EDT 2017 +execution started: Sat Aug 5 16:05:08 EDT 2017 afni -ver Precompiled binary macosx_10.7_local: Jul 27 2017 (Version AFNI_17.2.05) afni_history -check_date 23 Sep 2016 @@ -23,10 +23,10 @@ mkdir sub_03.results/stimuli cp /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D sub_03.results/stimuli 3dcopy /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz sub_03.results/sub-03_ses-retest_T1w ++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[1..$] ++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ elapsed time = 0.8 s -set tr_counts = ( 238 ) +set tr_counts = ( 237 ) cd sub_03.results touch out.pre_ss_warn.txt foreach run ( 01 ) @@ -40,15 +40,13 @@ foreach run ( 01 ) on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. -++ 18031 voxels passed mask/clip +++ 18027 voxels passed mask/clip if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then 1deval -a outcount.r01.1D{0} -expr step(a-0.4) -echo ** TR #0 outliers: possible pre-steady state TRs in run 01 -endif end cat outcount.r01.1D foreach run ( 01 ) -3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig +3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift -tpattern alt+z pb00.sub_03.r01.tcat+orig ++ 3dTshift: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, @@ -58,8 +56,6 @@ foreach run ( 01 ) on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. -*+ WARNING: dataset is already aligned in time! -*+ WARNING: ==>> output dataset is just a copy of input dataset end 3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] ++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -127,22 +123,22 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Authored by: Emperor Zhark ++ Loading dataset ./__tt_vr_base_ts_rs+orig ++ Forming automask - + Fixed clip level = 708.019226 - + Used gradual clip level = 621.023193 .. 754.463989 - + Number voxels above clip level = 1151758 + + Fixed clip level = 707.124390 + + Used gradual clip level = 618.551697 .. 753.626404 + + Number voxels above clip level = 1151477 + Clustering voxels ... - + Largest cluster has 1151071 voxels + + Largest cluster has 1150847 voxels + Clustering voxels ... - + Largest cluster has 1150607 voxels - + Filled 381 voxels in small holes; now have 1150988 voxels - + Filled 16522 voxels in large holes; now have 1167510 voxels + + Largest cluster has 1150422 voxels + + Filled 414 voxels in small holes; now have 1150836 voxels + + Filled 16701 voxels in large holes; now have 1167537 voxels + Clustering voxels ... - + Largest cluster has 1167476 voxels + + Largest cluster has 1167504 voxels + Clustering non-brain voxels ... + Clustering voxels ... - + Largest cluster has 14352028 voxels - + Mask now has 1167476 voxels -++ 1167476 voxels in the mask [out of 15519504: 7.52%] + + Largest cluster has 14352000 voxels + + Mask now has 1167504 voxels +++ 1167504 voxels in the mask [out of 15519504: 7.52%] ++ first 64 x-planes are zero [from R] ++ last 68 x-planes are zero [from L] ++ first 30 y-planes are zero [from A] @@ -151,13 +147,13 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ last 48 z-planes are zero [from S] ++ applying mask to original data ++ Writing masked data -++ CPU time = 3.660000 sec +++ CPU time = 3.710000 sec #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1728.000000 on /Users/mli/Desktop/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1723.000000 on /Users/mli/Desktop/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig #Script is running (command trimmed): - 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1728.000000))' + 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1723.000000))' ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands #++ Aligning anat data to epi data @@ -170,8 +166,8 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Loading datasets ++ 1356008 voxels in -source_automask+4 ++ Zero-pad: not needed -++ 1167476 voxels [7.5%] in weight mask -++ Number of points for matching = 1167476 +++ 1167504 voxels [7.5%] in weight mask +++ Number of points for matching = 1167504 ++ Local correlation: blok type = 'RHDD(6.54321)' ++ shift param auto-range: -84.4..84.4 -70.6..70.6 -85.1..85.1 + Range param#4 [z-angle] = -6.000000 .. 6.000000 @@ -184,31 +180,31 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Normalized convergence radius = 0.001000 ++ OpenMP thread count = 4 ++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= -++ ========== sub-brick #0 ========== [total CPU to here=8.5 s] +++ ========== sub-brick #0 ========== [total CPU to here=8.9 s] ++ *** Fine pass begins *** + * Enter alignment setup routine + - copying base image + - copying source image + - copying weight image - + - using 1167476 points from base image [use_all=0] + + - using 1167504 points from base image [use_all=0] + * Exit alignment setup routine - + 1097666 total points stored in 2068 'RHDD(6.54321)' bloks - + - Initial cost = -0.053122 + + 1097341 total points stored in 2067 'RHDD(6.54321)' bloks + + - Initial cost = -0.051994 + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 -********************************************************************************************************************************************** - + - Finalish cost = -0.295415 ; 350 funcs -********** - + - Final cost = -0.295420 ; 136 funcs +***************************************************************************************************************************************************************** + + - Finalish cost = -0.289529 ; 377 funcs +**** + + - Final cost = -0.289531 ; 107 funcs + Final fine fit Parameters: - x-shift= 0.2981 y-shift=-0.5136 z-shift=-1.2234 - z-angle= 0.4394 x-angle= 1.9668 y-angle=-5.3161 - x-scale= 0.9674 y-scale= 0.9725 z-scale= 1.0191 - y/x-shear= 0.0000 z/x-shear= 0.0099 z/y-shear= 0.0534 - + - Fine net CPU time = 33.9 s + x-shift= 0.2825 y-shift=-0.4994 z-shift=-1.2123 + z-angle= 0.4322 x-angle= 2.0209 y-angle=-5.2935 + x-scale= 0.9675 y-scale= 0.9734 z-scale= 1.0197 + y/x-shear=-0.0002 z/x-shear= 0.0099 z/y-shear= 0.0544 + + - Fine net CPU time = 35.9 s ++ Computing output image -++ image warp: parameters = 0.2981 -0.5136 -1.2234 0.4394 1.9668 -5.3161 0.9674 0.9725 1.0191 0.0000 0.0099 0.0534 +++ image warp: parameters = 0.2825 -0.4994 -1.2123 0.4322 2.0209 -5.2935 0.9675 0.9734 1.0197 -0.0002 0.0099 0.0544 ++ Wrote -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 44.8 sec Elapsed = 27.6 +++ 3dAllineate: total CPU time = 47.4 sec Elapsed = 32.3 ++ ########################################################### ++ # Please check results visually for alignment quality # ++ ########################################################### @@ -250,8 +246,8 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s + * Exit alignment setup routine ++ using -1Dmatrix_apply ++ Computing output image -++ image warp: parameters = 0.9618 0.0448 -0.0985 14.5442 -0.0314 0.9711 -0.0538 -1.5252 0.0911 0.0281 1.0141 -11.6150 -++ 3dAllineate: total CPU time = 2.2 sec Elapsed = 1.7 +++ image warp: parameters = 0.9620 0.0446 -0.0982 14.5110 -0.0314 0.9721 -0.0546 -1.5054 0.0907 0.0280 1.0148 -11.6331 +++ 3dAllineate: total CPU time = 2.4 sec Elapsed = 1.7 ++ ########################################################### #++ Creating final output: skullstripped anat data copying from dataset /Users/mli/Desktop/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/mli/Desktop/playground/Exp-1/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig @@ -423,15 +419,15 @@ foreach run ( 01 ) + Automask has 19058 voxels + 3364 voxels left in -maxdisp mask after erosion ++ Initializing alignment base -++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=6.37 s [=0.0268 s/sub-brick] -++ Min : roll=-0.200 pitch=-0.367 yaw=-0.118 dS=-1.139 dL=-0.157 dP=-0.055 -++ Mean: roll=-0.094 pitch=-0.011 yaw=+0.456 dS=-0.124 dL=+0.184 dP=+0.074 -++ Max : roll=+0.027 pitch=+0.449 yaw=+0.935 dS=+0.523 dL=+0.640 dP=+0.245 +++ Starting final pass on 237 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236.. +++ CPU time for realignment=6.46 s [=0.0273 s/sub-brick] +++ Min : roll=-0.181 pitch=-0.341 yaw=-0.016 dS=-0.709 dL=-0.130 dP=-0.130 +++ Mean: roll=-0.081 pitch=+0.020 yaw=+0.496 dS=-0.184 dL=+0.212 dP=+0.033 +++ Max : roll=+0.032 pitch=+0.458 yaw=+0.971 dS=+0.453 dL=+0.674 dP=+0.194 ++ Max displacements (mm) for each sub-brick: - 1.41(0.00) 0.17(1.52) 0.00(0.17) 0.33(0.33) 0.34(0.10) 0.45(0.12) 0.41(0.06) 0.20(0.28) 0.21(0.16) 0.22(0.05) 0.31(0.29) 0.37(0.19) 0.50(0.19) 0.61(0.12) 0.87(0.29) 0.94(0.10) 1.05(0.18) 1.12(0.12) 1.07(0.11) 0.82(0.28) 0.67(0.28) 0.69(0.13) 0.57(0.16) 0.70(0.22) 0.67(0.04) 0.75(0.13) 0.63(0.15) 0.68(0.19) 0.59(0.12) 0.66(0.09) 0.67(0.04) 0.78(0.19) 0.61(0.19) 0.59(0.05) 0.51(0.16) 0.62(0.22) 0.63(0.12) 0.66(0.12) 0.70(0.10) 0.69(0.04) 0.70(0.03) 0.77(0.07) 0.70(0.16) 0.65(0.14) 0.72(0.10) 0.74(0.16) 0.71(0.08) 0.68(0.10) 0.74(0.12) 0.70(0.13) 0.74(0.19) 0.60(0.21) 0.54(0.09) 0.50(0.12) 0.46(0.11) 0.45(0.08) 0.44(0.09) 0.50(0.23) 0.46(0.11) 0.50(0.15) 0.49(0.11) 0.56(0.15) 0.52(0.11) 0.57(0.17) 0.63(0.15) 0.56(0.12) 0.69(0.13) 0.64(0.26) 0.67(0.18) 0.62(0.07) 0.68(0.18) 0.76(0.27) 0.58(0.33) 0.80(0.22) 0.67(0.15) 0.65(0.08) 0.70(0.08) 0.77(0.08) 0.70(0.12) 0.70(0.14) 0.66(0.08) 0.68(0.12) 0.83(0.18) 0.74(0.22) 0.64(0.22) 0.72(0.14) 0.74(0.13) 0.81(0.14) 0.75(0.10) 0.72(0.07) 0.73(0.07) 0.69(0.16) 0.69(0.12) 0.69(0.17) 0.70(0.13) 0.64(0.16) 0.68(0.16) 0.65(0.10) 0.73(0.17) 0.74(0.06) 0.69(0.10) 0.67(0.05) 0.65(0.15) 0.72(0.12) 0.63(0.25) 0.70(0.15) 0.68(0.14) 0.70(0.17) 0.63(0.21) 0.60(0.07) 0.64(0.08) 0.76(0.16) 0.72(0.14) 0.69(0.15) 0.57(0.24) 0.58(0.06) 0.59(0.04) 0.63(0.08) 0.58(0.07) 0.60(0.07) 0.67(0.10) 0.67(0.25) 0.81(0.23) 0.79(0.06) 0.72(0.11) 0.74(0.04) 0.68(0.15) 0.71(0.14) 0.69(0.04) 0.69(0.09) 0.70(0.11) 0.68(0.11) 0.75(0.16) 0.70(0.12) 0.81(0.19) 0.73(0.10) 0.85(0.14) 0.78(0.10) 0.85(0.07) 0.84(0.05) 0.84(0.04) 0.77(0.09) 0.78(0.09) 0.80(0.06) 0.81(0.03) 0.77(0.11) 0.86(0.13) 0.80(0.16) 0.91(0.15) 0.86(0.10) 0.90(0.07) 0.98(0.08) 1.10(0.14) 1.13(0.06) 1.03(0.12) 1.14(0.17) 1.06(0.09) 1.18(0.12) 1.10(0.11) 1.13(0.07) 1.08(0.14) 1.18(0.15) 1.23(0.07) 1.07(0.19) 1.17(0.13) 1.14(0.10) 1.18(0.07) 1.20(0.05) 1.22(0.07) 1.20(0.07) 1.14(0.13) 1.22(0.14) 1.14(0.14) 1.29(0.18) 1.19(0.11) 1.32(0.17) 1.27(0.10) 1.34(0.16) 1.38(0.05) 1.28(0.19) 1.31(0.09) 1.33(0.05) 1.37(0.10) 1.36(0.05) 1.42(0.14) 1.39(0.10) 1.40(0.06) 1.36(0.08) 1.36(0.03) 1.49(0.13) 1.42(0.09) 1.48(0.10) 1.30(0.24) 1.20(0.16) 1.24(0.10) 1.23(0.11) 1.25(0.03) 1.24(0.08) 1.19(0.11) 1.25(0.11) 1.18(0.08) 1.19(0.04) 1.21(0.06) 1.40(0.25) 1.31(0.26) 1.36(0.14) 1.47(0.11) 1.51(0.07) 1.53(0.06) 1.58(0.06) 1.60(0.08) 1.58(0.11) 1.65(0.10) 1.64(0.11) 1.65(0.13) 1.72(0.09) 1.79(0.07) 1.76(0.09) 1.80(0.13) 1.96(0.20) 1.94(0.03) 1.82(0.16) 1.72(0.20) 1.55(0.33) 1.60(0.32) 1.57(0.14) 1.37(0.21) 1.38(0.20) 1.14(0.38) 1.18(0.25) 1.21(0.30) 0.70(0.63) 0.81(0.24) 0.91(0.13) 1.00(0.10) 1.12(0.13) 1.02(0.23) 1.19(0.19) -++ Max displacement in automask = 1.96 (mm) at sub-brick 219 -++ Max delta displ in automask = 1.52 (mm) at sub-brick 1 + 0.30(0.00) 0.20(0.44) 0.00(0.20) 0.23(0.23) 0.26(0.09) 0.39(0.15) 0.18(0.32) 0.23(0.16) 0.35(0.15) 0.20(0.21) 0.26(0.16) 0.36(0.13) 0.47(0.18) 0.64(0.20) 0.80(0.18) 0.89(0.10) 1.01(0.17) 0.97(0.08) 0.92(0.09) 0.59(0.48) 0.64(0.07) 0.54(0.11) 0.54(0.13) 0.60(0.11) 0.60(0.06) 0.61(0.07) 0.56(0.15) 0.56(0.09) 0.53(0.05) 0.62(0.09) 0.65(0.14) 0.60(0.08) 0.52(0.10) 0.48(0.09) 0.45(0.08) 0.54(0.18) 0.56(0.12) 0.61(0.07) 0.60(0.07) 0.62(0.07) 0.65(0.04) 0.69(0.06) 0.58(0.24) 0.63(0.06) 0.66(0.12) 0.68(0.08) 0.63(0.15) 0.64(0.03) 0.64(0.10) 0.67(0.08) 0.59(0.11) 0.52(0.13) 0.45(0.11) 0.44(0.09) 0.44(0.12) 0.42(0.07) 0.53(0.13) 0.57(0.05) 0.56(0.07) 0.61(0.07) 0.61(0.05) 0.66(0.11) 0.57(0.22) 0.66(0.13) 0.69(0.05) 0.70(0.07) 0.74(0.11) 0.71(0.12) 0.75(0.24) 0.68(0.19) 0.82(0.15) 0.74(0.28) 0.81(0.21) 0.90(0.13) 0.72(0.18) 0.79(0.08) 0.81(0.04) 0.86(0.08) 0.78(0.18) 0.79(0.04) 0.74(0.06) 0.84(0.12) 0.94(0.34) 0.75(0.20) 0.78(0.08) 0.83(0.09) 0.88(0.06) 0.90(0.04) 0.81(0.14) 0.83(0.09) 0.78(0.10) 0.80(0.05) 0.70(0.11) 0.75(0.09) 0.74(0.06) 0.72(0.04) 0.75(0.07) 0.72(0.10) 0.87(0.23) 0.80(0.07) 0.80(0.13) 0.73(0.16) 0.80(0.06) 0.75(0.08) 0.73(0.08) 0.77(0.05) 0.78(0.08) 0.77(0.05) 0.67(0.16) 0.68(0.06) 0.68(0.19) 0.70(0.16) 0.68(0.13) 0.64(0.17) 0.64(0.09) 0.67(0.05) 0.66(0.04) 0.63(0.07) 0.67(0.14) 0.64(0.14) 0.73(0.18) 0.83(0.22) 1.01(0.23) 0.85(0.19) 0.87(0.05) 0.81(0.14) 0.81(0.07) 0.85(0.07) 0.78(0.09) 0.84(0.09) 0.77(0.12) 0.85(0.08) 0.85(0.03) 0.87(0.05) 0.90(0.06) 0.91(0.04) 0.97(0.09) 0.92(0.09) 1.01(0.09) 0.95(0.07) 0.95(0.04) 0.86(0.10) 0.95(0.11) 0.92(0.07) 0.92(0.10) 0.95(0.06) 0.97(0.04) 0.94(0.10) 1.07(0.14) 0.97(0.13) 1.11(0.16) 1.14(0.08) 1.31(0.19) 1.19(0.15) 1.24(0.11) 1.24(0.05) 1.25(0.06) 1.31(0.06) 1.23(0.10) 1.28(0.10) 1.20(0.09) 1.40(0.21) 1.25(0.17) 1.23(0.08) 1.32(0.10) 1.26(0.11) 1.34(0.12) 1.31(0.11) 1.39(0.13) 1.27(0.15) 1.32(0.07) 1.29(0.04) 1.35(0.06) 1.37(0.03) 1.39(0.05) 1.46(0.07) 1.41(0.06) 1.52(0.20) 1.46(0.14) 1.42(0.07) 1.44(0.07) 1.49(0.09) 1.49(0.07) 1.51(0.06) 1.56(0.06) 1.52(0.08) 1.55(0.09) 1.45(0.10) 1.58(0.13) 1.58(0.03) 1.59(0.07) 1.57(0.15) 1.34(0.33) 1.36(0.09) 1.34(0.09) 1.40(0.11) 1.36(0.05) 1.37(0.05) 1.33(0.06) 1.36(0.11) 1.30(0.09) 1.33(0.05) 1.45(0.19) 1.51(0.09) 1.42(0.18) 1.56(0.21) 1.63(0.07) 1.66(0.05) 1.67(0.04) 1.75(0.13) 1.71(0.10) 1.75(0.04) 1.77(0.07) 1.79(0.12) 1.80(0.09) 1.90(0.11) 1.91(0.05) 1.90(0.12) 2.01(0.13) 2.12(0.15) 2.00(0.15) 1.91(0.16) 1.74(0.26) 1.70(0.32) 1.75(0.18) 1.58(0.19) 1.53(0.17) 1.41(0.23) 1.23(0.22) 1.43(0.44) 1.00(0.47) 0.85(0.20) 1.02(0.28) 1.09(0.09) 1.24(0.15) 1.18(0.15) 1.21(0.11) +++ Max displacement in automask = 2.12 (mm) at sub-brick 219 +++ Max delta displ in automask = 0.48 (mm) at sub-brick 19 ++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK 3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -457,9 +453,9 @@ cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retes ++ master dataset for output = base ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 -++ ========== Applying transformation to 238 sub-bricks ========== -volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 6.1 sec Elapsed = 3.8 +++ ========== Applying transformation to 237 sub-bricks ========== +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 6.1 sec Elapsed = 3.9 ++ ########################################################### 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 ++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -474,7 +470,7 @@ volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20. ++ Oblique dataset:./rm.epi.all1+orig.BRIK is 4.947676 degrees from plumb. ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ 3dAllineate: total CPU time = 3.6 sec Elapsed = 3.1 +++ 3dAllineate: total CPU time = 3.6 sec Elapsed = 3.2 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox @@ -526,26 +522,26 @@ tee out.allcostX.txt ++ Zero-pad: ybot=0 ytop=1 ++ Zero-pad: zbot=2 ztop=1 ++ Computing -autobox -++ 113297 voxels [89.4%] in weight mask -++ Number of points for matching = 53249 +++ 113307 voxels [89.4%] in weight mask +++ Number of points for matching = 53254 ++ Local correlation: blok type = 'RHDD(14.76)' *+ WARNING: No output dataset will be calculated ++ OpenMP thread count = 4 volume 0Ø + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 ++ allcost output: init #0 - ls = 0.184126 - sp = 0.307224 - mi = -0.531581 - crM = 0.0790675 - nmi = 0.868615 - je = 3.51437 - hel = -0.106047 - crA = 0.2819 - crU = 0.301908 - lss = 0.815874 - lpc = 0.296009 - lpa = 0.703991 - lpc+ = 0.494411 + ls = 0.183506 + sp = 0.306723 + mi = -0.532442 + crM = 0.0787207 + nmi = 0.868505 + je = 3.51671 + hel = -0.106397 + crA = 0.281314 + crU = 0.301726 + lss = 0.816494 + lpc = 0.300018 + lpa = 0.699982 + lpc+ = 0.497814 ncd = 1 ++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 ++ ########################################################### @@ -584,8 +580,8 @@ foreach run ( 01 ) ++ default -1tindex = 1 Program 3dmerge 3dmerge: edit and combine 3D datasets, by RW Cox -++ editing input dataset in memory (49.6 MB) -..............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK +++ editing input dataset in memory (49.4 MB) +.............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK end foreach run ( 01 ) @@ -594,24 +590,24 @@ foreach run ( 01 ) ++ Authored by: Emperor Zhark ++ Loading dataset pb03.sub_03.r01.blur+tlrc ++ Forming automask - + Fixed clip level = 698.003235 - + Used gradual clip level = 617.152649 .. 742.589600 - + Number voxels above clip level = 28220 + + Fixed clip level = 697.172363 + + Used gradual clip level = 616.337708 .. 741.789307 + + Number voxels above clip level = 28281 + Clustering voxels ... - + Largest cluster has 28219 voxels + + Largest cluster has 28280 voxels + Clustering voxels ... - + Largest cluster has 28153 voxels - + Filled 52 voxels in small holes; now have 28205 voxels + + Largest cluster has 28217 voxels + + Filled 55 voxels in small holes; now have 28272 voxels + Clustering voxels ... - + Largest cluster has 28205 voxels + + Largest cluster has 28272 voxels + Clustering non-brain voxels ... + Clustering voxels ... - + Largest cluster has 81145 voxels - + Mask now has 28205 voxels + + Largest cluster has 81078 voxels + + Mask now has 28272 voxels ++ Dilating automask + Clustering voxels ... - + Largest cluster has 76109 voxels -++ 33241 voxels in the mask [out of 109350: 30.40%] + + Largest cluster has 76021 voxels +++ 33329 voxels in the mask [out of 109350: 30.48%] ++ first 4 x-planes are zero [from L] ++ last 3 x-planes are zero [from R] ++ first 4 y-planes are zero [from P] @@ -624,7 +620,7 @@ end ++ processing 1 input datasets... ++ padding all datasets by 0 (for dilations) ++ frac 0 over 1 volumes gives min count 0 -++ voxel limits: 0 clipped, 33241 survived, 76109 were zero +++ voxel limits: 0 clipped, 33329 survived, 76021 were zero ++ writing result full_mask.sub_03... 3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-retest_T1w_ns+tlrc -prefix rm.resam.anat 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 @@ -640,10 +636,10 @@ tee out.mask_ae_overlap.txt ++ 3dOverlap: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK #A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) -33241 30574 35745 28070 5171 2504 15.5561 8.1900 0.9405 0.9263 0.9667 +33329 30574 35778 28125 5204 2449 15.6140 8.0101 0.9411 0.9238 0.9653 3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_dice.txt -0.87973 +0.88024 3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/mli/abin/MNI_avg152T1+tlrc 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ no -frac option: defaulting to -union @@ -666,17 +662,17 @@ end 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 -total number of censored TRs (simple form) = 2 +total number of censored TRs (simple form) = 0 set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D -show_trs_uncensored encoded` 1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 ++ 3dDeconvolve: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD -++ STAT automask has 100184 voxels (out of 109350 = 91.6%) +++ STAT automask has 100230 voxels (out of 109350 = 91.7%) ++ Skipping check for initial transients -++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ +++ Input polort=4; Longest run=592.5 s; Recommended minimum polort=4 ++ OK ++ ++ -stim_times using TR=2.5 s for stimulus timing conversion ++ -stim_times using TR=2.5 s for any -iresp output datasets ++ [you can alter the -iresp TR via the -TR_times option] @@ -686,15 +682,13 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D ++ ** GUESSED ** -stim_times 3 using LOCAL times ++ ** GUESSED ** -stim_times 4 using LOCAL times ++ ** GUESSED ** -stim_times 5 using LOCAL times -*+ WARNING: -gltsym: Can't interpret '*' scale factor in '-*Response_Control' -- replaced by 1 -*+ WARNING: -gltsym: '*' scale factor in '-*Response_Control' not at start of string? ------------------------------------------------------------ -GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': - 0 0 0 0 0 0.5 0.5 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 +GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control': + 0 0 0 0 0 0.5 0.5 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 -++ Number of time points: 238 (before censor) ; 236 (after) +++ Number of time points: 237 (no censoring) + Number of parameters: 22 [17 baseline ; 5 signal] -++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) +++ Memory required for output bricks = 215,638,200 bytes (about 216 million [mega]) ++ Wrote matrix image to file X.jpg ++ Wrote matrix values to file X.xmat.1D ++ ========= Things you can do with the matrix file ========= @@ -709,34 +703,34 @@ GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': ++ (c) Synthesis of sub-model datasets using 3dSynthesize ++ ========================================================== ++ Wrote matrix values to file X.nocensor.xmat.1D -++ ----- Signal+Baseline matrix condition [X] (236x22): 5.23887 ++ VERY GOOD ++ -++ ----- Signal-only matrix condition [X] (236x5): 1.40108 ++ VERY GOOD ++ -++ ----- Baseline-only matrix condition [X] (236x17): 5.1314 ++ VERY GOOD ++ -++ ----- stim_base-only matrix condition [X] (236x12): 3.87376 ++ VERY GOOD ++ -++ ----- polort-only matrix condition [X] (236x5): 1.05506 ++ VERY GOOD ++ -++ +++++ Matrix inverse average error = 2.74977e-15 ++ VERY GOOD ++ +++ ----- Signal+Baseline matrix condition [X] (237x22): 5.15025 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (237x5): 1.40108 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (237x17): 5.05637 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (237x12): 3.89229 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (237x5): 1.01409 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 2.52458e-15 ++ VERY GOOD ++ ++ Matrix setup time = 0.64 s -++ Calculations starting; elapsed time=1.346 +++ Calculations starting; elapsed time=1.336 ++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=15.873 -++ Smallest FDR q [0 Full_Fstat] = 2.20611e-13 -++ Smallest FDR q [2 Correct_Task#0_Tstat] = 4.23368e-12 -++ Smallest FDR q [3 Correct_Task_Fstat] = 4.23389e-12 -++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 1.38672e-05 -++ Smallest FDR q [6 Incorrect_Task_Fstat] = 1.38678e-05 -++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.000272278 -++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.000272271 -++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 0.00181556 -++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.0018156 -++ Smallest FDR q [14 Response_Control#0_Tstat] = 7.47239e-13 -++ Smallest FDR q [15 Response_Control_Fstat] = 7.47258e-13 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 3.58106e-13 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 3.58045e-13 +++ Calculations finished; elapsed time=16.363 +++ Smallest FDR q [0 Full_Fstat] = 8.19701e-14 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 5.99871e-13 +++ Smallest FDR q [3 Correct_Task_Fstat] = 5.99903e-13 +++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 9.32686e-06 +++ Smallest FDR q [6 Incorrect_Task_Fstat] = 9.32779e-06 +++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.000445298 +++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.000445278 +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 0.000323183 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.000323173 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 2.49688e-13 +++ Smallest FDR q [15 Response_Control_Fstat] = 2.49674e-13 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.0019913 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.00199136 ++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + created 13 FDR curves in bucket header ++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK ++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK -++ #Flops=4.31862e+10 Average Dot Product=37.4801 +++ #Flops=4.33688e+10 Average Dot Product=37.4925 if ( 0 != 0 ) then 1d_tool.py -show_cormat_warnings -infile X.xmat.1D tee out.cormat_warn.txt @@ -749,12 +743,12 @@ Warnings regarding Correlation Matrix: X.xmat.1D 3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD ++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -++ elapsed time = 0.4 s -3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..237] +++ elapsed time = 0.3 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[0..236] ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.signal.all+tlrc.BRIK -3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..237] +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[0..236] ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.noise.all+tlrc.BRIK @@ -768,14 +762,14 @@ Warnings regarding Correlation Matrix: X.xmat.1D ++ Output dataset ./rm.errts.unit+tlrc.BRIK 3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc ++ 3dmaskave: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -+++ 33241 voxels survive the mask ++++ 33329 voxels survive the mask 3dTstat -sos -prefix - gmean.errts.unit.1D' ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D --- GCOR = 0.109705 +-- GCOR = 0.123131 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands @@ -804,16 +798,16 @@ foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..237] +if ( 0..236 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[0..236] ++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 33241 -*+ WARNING: removed 220 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 236 time points - + detrending done (2.92 CPU s thus far) -++ start ACF calculations out to radius = 27.83 mm - + ACF done (63.36 CPU s thus far) +++ Number of voxels in mask = 33329 +*+ WARNING: removed 218 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 237 time points + + detrending done (2.83 CPU s thus far) +++ start ACF calculations out to radius = 28.17 mm + + ACF done (66.11 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. @@ -834,24 +828,24 @@ set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.631007 5.37466 12.7311 13.5952 -average epits ACF blurs: 0.631007 5.37466 12.7311 13.5952 -echo 0.631007 5.37466 12.7311 13.5952 # epits ACF blur estimates +echo average epits ACF blurs: 0.595014 5.44304 12.6085 13.8182 +average epits ACF blurs: 0.595014 5.44304 12.6085 13.8182 +echo 0.595014 5.44304 12.6085 13.8182 # epits ACF blur estimates touch blur.errts.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..237] +if ( 0..236 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[0..236] ++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 33241 -*+ WARNING: removed 220 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 236 time points - + detrending done (3.01 CPU s thus far) -++ start ACF calculations out to radius = 27.36 mm - + ACF done (63.19 CPU s thus far) +++ Number of voxels in mask = 33329 +*+ WARNING: removed 218 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 237 time points + + detrending done (2.86 CPU s thus far) +++ start ACF calculations out to radius = 27.61 mm + + ACF done (64.28 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. @@ -872,9 +866,9 @@ set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.694842 5.25419 13.1836 13.2188 -average errts ACF blurs: 0.694842 5.25419 13.1836 13.2188 -echo 0.694842 5.25419 13.1836 13.2188 # errts ACF blur estimates +echo average errts ACF blurs: 0.677865 5.3313 12.8334 13.3773 +average errts ACF blurs: 0.677865 5.3313 12.8334 13.3773 +echo 0.677865 5.3313 12.8334 13.3773 # errts ACF blur estimates gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD gen_ss_review_scripts.py -mot_limit 0.5 -exit0 ++ writing ss review basic: @ss_review_basic @@ -886,51 +880,50 @@ if ( -e @ss_review_basic ) ./@ss_review_basic ./@ss_review_basic subject ID : sub_03 -TRs removed (per run) : 0 +TRs removed (per run) : 1 num stim classes provided : 5 final anatomy dset : anat_final.sub_03+tlrc.HEAD final stats dset : stats.sub_03+tlrc.HEAD final voxel resolution : 4.000000 4.000000 4.000000 motion limit : 0.5 -num TRs above mot limit : 1 -average motion (per TR) : 0.0937926 -average censored motion : 0.0889158 -max motion displacement : 1.69106 -max censored displacement : 1.69012 +num TRs above mot limit : 0 +average motion (per TR) : 0.0785451 +average censored motion : 0.0785451 +max motion displacement : 1.72403 +max censored displacement : 1.72403 outlier limit : 0.1 -average outlier frac (TR) : 0.00559353 -num TRs above out limit : 1 +average outlier frac (TR) : 0.0019311 +num TRs above out limit : 0 num runs found : 1 -num TRs per run : 238 -num TRs per run (applied) : 236 -num TRs per run (censored): 2 -fraction censored per run : 0.00840336 -TRs total (uncensored) : 238 -TRs total : 236 +num TRs per run : 237 +num TRs per run (applied) : 237 +num TRs per run (censored): 0 +fraction censored per run : 0 +TRs total (uncensored) : 237 +TRs total : 237 degrees of freedom used : 22 -degrees of freedom left : 214 +degrees of freedom left : 215 -TRs censored : 2 -censor fraction : 0.008403 +TRs censored : 0 +censor fraction : 0.000000 num regs of interest : 5 num TRs per stim (orig) : 78 56 46 19 79 num TRs censored per stim : 0 0 0 0 0 fraction TRs censored : 0.000 0.000 0.000 0.000 0.000 -ave mot per sresp (orig) : 0.086607 0.082908 0.080591 0.071212 0.078827 -ave mot per sresp (cens) : 0.086607 0.082908 0.080591 0.071212 0.078827 +ave mot per sresp (orig) : 0.074047 0.073782 0.065246 0.067506 0.063698 +ave mot per sresp (cens) : 0.074047 0.073782 0.065246 0.067506 0.063698 -TSNR average : 234.187 -global correlation (GCOR) : 0.109705 -anat/EPI mask Dice coef : 0.87973 -maximum F-stat (masked) : 48.3344 -blur estimates (ACF) : 0.694842 5.25419 13.1836 +TSNR average : 254.187 +global correlation (GCOR) : 0.123131 +anat/EPI mask Dice coef : 0.88024 +maximum F-stat (masked) : 82.8417 +blur estimates (ACF) : 0.677865 5.3313 12.8334 blur estimates (FWHM) : 0 0 0 -** TR #0 outliers: possible pre-steady state TRs in run 01 cd .. echo execution finished: `date` date -execution finished: Fri Aug 4 12:49:48 EDT 2017 +execution finished: Sat Aug 5 16:09:40 EDT 2017 diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 b/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 old mode 100644 new mode 100755 index dc0c6f0..14b69d7 --- a/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 +++ b/Exp-1/subject_results/group.retest/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Fri Aug 4 12:45:31 2017" +echo "auto-generated by afni_proc.py, Sat Aug 5 16:05:00 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -59,12 +59,12 @@ cp /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D # ============================ auto block: tcat ============================ # apply 3dTcat to copy input dsets to results dir, while -# removing the first 0 TRs +# removing the first 1 TRs 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ - /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' + /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[1..$]' # and make note of repetitions (TRs) per run -set tr_counts = ( 238 ) +set tr_counts = ( 237 ) # ------------------------------------------------------- # enter the results directory (can begin processing data) @@ -92,6 +92,7 @@ cat outcount.r*.1D > outcount_rall.1D # time shift data so all slice timing is the same foreach run ( $runs ) 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + -tpattern alt+z \ pb00.$subj.r$run.tcat+orig end @@ -305,7 +306,7 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ - -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control' \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -459,7 +460,7 @@ echo "execution finished: `date`" # afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ # tshift align tlrc volreg blur mask scale regress -copy_anat \ # /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ -# -tcat_remove_first_trs 0 -dsets \ +# -tcat_remove_first_trs 1 -tshift_opts_ts -tpattern alt+z -dsets \ # /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ # -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ # -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ @@ -472,6 +473,6 @@ echo "execution finished: `date`" # No_Response_Task Response_Control -regress_basis GAM \ # -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ # -regress_opts_3dD -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ -# -*Response_Control' -glt_label 1 Landmark-Detection \ +# -Response_Control' -glt_label 1 Landmark-Detection \ # -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ # -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 index 98608cd..6240d91 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 @@ -17,7 +17,8 @@ afni_proc.py -subj_id $subj \ -script proc.$subj -scr_overwrite \ -blocks tshift align tlrc volreg blur mask scale regress \ -copy_anat $anat_dir/sub-03_ses-test_T1w.nii.gz \ - -tcat_remove_first_trs 0 \ + -tcat_remove_first_trs 1 \ + -tshift_opts_ts -tpattern alt+z \ -dsets $epi_dir/sub-03_ses-test_task-linebisection_bold.nii.gz \ -tlrc_base MNI_avg152T1+tlrc \ -volreg_align_to third \ @@ -38,7 +39,7 @@ afni_proc.py -subj_id $subj \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ - -*Response_Control' -glt_label 1 Landmark-Detection \ + -Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 index 930c067..bb288d0 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 @@ -3,11 +3,13 @@ set anat_dir = /Users/mli/Desktop/playground/sub-03/ses-test/anat set epi_dir = /Users/mli/Desktop/playground/sub-03/ses-test/func set subj = sub_03 set group_id = test -afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task - -*Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 1 -tshift_opts_ts -tpattern alt+z -dsets /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task + -Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig --- tcat: reps is now 238 -++ updating polort to 4, from run len 595.0 s +** warning: removing first 1 TRs from beginning of each run + --> the stimulus timing files must reflect the removal of these TRs +-- tcat: reps is now 237 +++ updating polort to 4, from run len 592.5 s -- volreg: using base dset vr_base+orig ++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 4 mm tlrc voxels -- applying anat warps to 1 dataset(s): sub-03_ses-test_T1w diff --git a/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 index 45b7b68..0fc01ea 100644 --- a/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/output.proc.sub_03 @@ -1,10 +1,10 @@ -echo auto-generated by afni_proc.py, Fri Aug 4 12:43:15 2017 -auto-generated by afni_proc.py, Fri Aug 4 12:43:15 2017 +echo auto-generated by afni_proc.py, Sat Aug 5 16:29:05 2017 +auto-generated by afni_proc.py, Sat Aug 5 16:29:05 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Fri Aug 4 12:43:28 EDT 2017 +execution started: Sat Aug 5 16:29:06 EDT 2017 afni -ver Precompiled binary macosx_10.7_local: Jul 27 2017 (Version AFNI_17.2.05) afni_history -check_date 23 Sep 2016 @@ -16,6 +16,924 @@ set subj = sub_03 endif set output_dir = sub_03.results if ( -d sub_03.results ) then -echo output dir sub_03.results already exists -output dir sub_03.results already exists -exit +set runs = ( `count -digits 2 1 1` ) +count -digits 2 1 1 +mkdir sub_03.results +mkdir sub_03.results/stimuli +cp /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D sub_03.results/stimuli +3dcopy /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz sub_03.results/sub-03_ses-test_T1w +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[1..$] +++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ elapsed time = 0.8 s +set tr_counts = ( 237 ) +cd sub_03.results +touch out.pre_ss_warn.txt +foreach run ( 01 ) +3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_03.r01.tcat+orig +++ 3dToutcount: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. +++ 17835 voxels passed mask/clip +if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then +1deval -a outcount.r01.1D{0} -expr step(a-0.4) +end +cat outcount.r01.1D +foreach run ( 01 ) +3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift -tpattern alt+z pb00.sub_03.r01.tcat+orig +++ 3dTshift: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb00.sub_03.r01.tcat+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. +end +3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] +++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off +#++ align_epi_anat version: 1.57 +#++ turning off volume registration +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./vr_base+orig +#Script is running (command trimmed): + 3dAttribute DELTA ./sub-03_ses-test_T1w+orig +#++ Multi-cost is lpc +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-test_T1w* +#Script is running (command trimmed): + 3dcopy ./sub-03_ses-test_T1w+orig ./__tt_sub-03_ses-test_T1w+orig +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +#++ Removing skull from anat data +#Script is running (command trimmed): + 3dSkullStrip -orig_vol -input ./__tt_sub-03_ses-test_T1w+orig -prefix ./__tt_sub-03_ses-test_T1w_ns +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-test_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. +#Script is running (command trimmed): + 3dinfo ./__tt_sub-03_ses-test_T1w_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' +#++ Dataset /Users/mli/Desktop/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig is ***oblique**** +#Script is running (command trimmed): + 3dAttribute DELTA ./__tt_sub-03_ses-test_T1w_ns+orig +#++ Spacing for anat to oblique epi alignment is 1.000000 +#++ Matching obliquity of anat to epi +#Script is running (command trimmed): + 3dWarp -verb -card2oblique ./vr_base+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob -newgrid 1.000000 ./__tt_sub-03_ses-test_T1w_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Deobliquing original dataset before obliquing +++ Combining oblique transformations +#++ using 0th sub-brick because only one found +#Script is running (command trimmed): + 3dbucket -prefix ./__tt_vr_base_ts ./vr_base+orig'[0]' +++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +#++ resampling epi to match anat data +#Script is running (command trimmed): + 3dresample -master ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_vr_base_ts+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_vr_base_ts+orig.BRIK is 6.153038 degrees from plumb. +#++ removing skull or area outside brain +#Script is running (command trimmed): + 3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig +++ 3dAutomask: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset ./__tt_vr_base_ts_rs+orig +++ Forming automask + + Fixed clip level = 720.187500 + + Used gradual clip level = 622.540100 .. 825.700012 + + Number voxels above clip level = 1139151 + + Clustering voxels ... + + Largest cluster has 1137868 voxels + + Clustering voxels ... + + Largest cluster has 1137453 voxels + + Filled 420 voxels in small holes; now have 1137873 voxels + + Filled 17758 voxels in large holes; now have 1155631 voxels + + Clustering voxels ... + + Largest cluster has 1155621 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 15251532 voxels + + Mask now has 1155621 voxels +++ 1155621 voxels in the mask [out of 16407153: 7.04%] +++ first 71 x-planes are zero [from R] +++ last 75 x-planes are zero [from L] +++ first 33 y-planes are zero [from A] +++ last 17 y-planes are zero [from P] +++ first 123 z-planes are zero [from I] +++ last 36 z-planes are zero [from S] +++ applying mask to original data +++ Writing masked data +++ CPU time = 3.600000 sec +#++ Computing weight mask +#Script is running (command trimmed): + 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1884.000000 on /Users/mli/Desktop/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#Script is running (command trimmed): + 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1884.000000))' +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +#++ Aligning anat data to epi data +#Script is running (command trimmed): + 3dAllineate -lpc -wtprefix ./__tt_sub-03_ses-test_T1w_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_sub-03_ses-test_T1w_ns_ob+orig -prefix ./__tt_sub-03_ses-test_T1w_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns_ob+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets +++ 1350442 voxels in -source_automask+4 +++ Zero-pad: not needed +++ 1155621 voxels [7.0%] in weight mask +++ Number of points for matching = 1155621 +++ Local correlation: blok type = 'RHDD(6.54321)' +++ shift param auto-range: -89.2..89.2 -69.3..69.3 -86.7..86.7 + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 + + 12 free parameters +++ Normalized convergence radius = 0.001000 +++ OpenMP thread count = 4 +++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= +++ ========== sub-brick #0 ========== [total CPU to here=9.9 s] +++ *** Fine pass begins *** + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - copying weight image + + - using 1155621 points from base image [use_all=0] + + * Exit alignment setup routine + + 1095318 total points stored in 2076 'RHDD(6.54321)' bloks + + - Initial cost = -0.091164 + + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +************************************************************************************************************************************************************************************************************** + + - Finalish cost = -0.223788 ; 478 funcs +* + + - Final cost = -0.223788 ; 109 funcs + + Final fine fit Parameters: + x-shift= 0.1988 y-shift=-0.6640 z-shift=-1.7061 + z-angle=-0.6160 x-angle= 4.7517 y-angle=-1.0181 + x-scale= 0.9680 y-scale= 0.9748 z-scale= 1.0199 + y/x-shear=-0.0035 z/x-shear= 0.0100 z/y-shear= 0.0924 + + - Fine net CPU time = 39.7 s +++ Computing output image +++ image warp: parameters = 0.1988 -0.6640 -1.7061 -0.6160 4.7517 -1.0181 0.9680 0.9748 1.0199 -0.0035 0.0100 0.0924 +++ Wrote -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D +++ 3dAllineate: total CPU time = 52.3 sec Elapsed = 35.0 +++ ########################################################### +++ # Please check results visually for alignment quality # +++ ########################################################### +++ # '-autoweight' is recommended when using -lpc or -lpa # +++ # If your results are not good, please try again. # +++ ########################################################### +#Script is running (command trimmed): + cat_matvec -ONELINE ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D ./__tt_sub-03_ses-test_T1w_ns_obla2e_mat.1D -I > ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D +#++ Combining anat to epi and oblique transformations +#Script is running (command trimmed): + 3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./sub-03_ses-test_T1w_al_junk_mat.aff12.1D -prefix ./sub-03_ses-test_T1w_al_junk -input ./__tt_sub-03_ses-test_T1w_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__tt_sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__tt_sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ Source dataset: ./__tt_sub-03_ses-test_T1w_ns+orig.HEAD +++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD +++ Loading datasets + + Range param#4 [z-angle] = -6.000000 .. 6.000000 + + Range param#5 [x-angle] = -6.000000 .. 6.000000 + + Range param#6 [y-angle] = -6.000000 .. 6.000000 + + Range param#1 [x-shift] = -10.000000 .. 10.000000 + + Range param#2 [y-shift] = -10.000000 .. 10.000000 + + Range param#3 [z-shift] = -10.000000 .. 10.000000 +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +++ ========== sub-brick #0 ========== [total CPU to here=0.1 s] + + * Enter alignment setup routine + + - copying base image + + - copying source image + + - no weight image + + - using 11 points from base image [use_all=0] + + * Exit alignment setup routine +++ using -1Dmatrix_apply +++ Computing output image +++ image warp: parameters = 0.9647 -0.0767 -0.0644 8.2560 0.0414 0.9697 -0.0702 -8.0361 0.0573 0.0012 1.0210 -4.6777 +++ 3dAllineate: total CPU time = 2.3 sec Elapsed = 1.9 +++ ########################################################### +#++ Creating final output: skullstripped anat data +copying from dataset /Users/mli/Desktop/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/mli/Desktop/playground/Exp-1/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig +#Script is running (command trimmed): + 3dcopy ./__tt_sub-03_ses-test_T1w_ns+orig sub-03_ses-test_T1w_ns +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +#++ Creating final output: anat data aligned to epi +# copy is not necessary +#++ Saving history +#Script is running (command trimmed): + 3dNotes -h "align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig \ + -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 \ + -epi_strip 3dAutomask -volreg off -tshift off" \ + ./sub-03_ses-test_T1w_al_junk+orig + +#++ Removing all the temporary files +#Script is running: + \rm -f ./__tt_vr_base* +#Script is running: + \rm -f ./__tt_sub-03_ses-test_T1w* + +# Finished alignment successfully + +@auto_tlrc -base MNI_avg152T1+tlrc -input sub-03_ses-test_T1w_ns+orig -no_ss +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. + +*********** Warning ************* +Dataset centers are 52.843487 mm +apart. If registration fails, or if +parts of the original anatomy gets +cropped, try adding option + -init_xform AUTO_CENTER +to your @auto_tlrc command. + +********************************* + +Padding ... +++ 3dZeropad: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_40pad+tlrc.BRIK +Resampling ... +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./__ats_tmp__resamp_step+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./__ats_tmp__resamp_step+orig.BRIK is 6.455733 degrees from plumb. +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +Clipping -0.000100 1158.000100 ... +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___rs_sub-03_ses-test_T1w_ns+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Registration (linear final interpolation) ... +++ 3dWarpDrive: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Initial scale factor set to 0.30/273.95=9.2e+02 +RMS[0] = 0.384861 0.16449 ITER = 6/137 +0.384861 + +Warping has converged. + +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w_ns+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w_ns+orig.BRIK is 6.455733 degrees from plumb. +++ 6.455733 degrees from plumb. +*+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations +Applying brain mask +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +++ 3dWarp: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ 3drename: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.HEAD -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___pad40_sub-03_ses-test_T1w_ns+orig.BRIK.gz -> __ats_tmp___pad40_sub-03_ses-test_T1w_ns.skl+orig.BRIK.gz +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +Unpadding ... +++ 3dZeropad: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ output dataset: ./__ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.BRIK +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig +*+ WARNING: Changing the space of an ORIG view dataset may cause confusion! +*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space). +*+ WARNING: Consider changing the view of the dataset to TLRC view also +++ 3drefit processed 1 datasets +Changing view of transformed anatomy +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+orig.HEAD + + Changed dataset view type and filenames. +++ 3drefit processed 1 datasets +Setting parent with 3drefit -wset sub-03_ses-test_T1w_ns+orig __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc +++ 3drefit: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Processing AFNI dataset __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc +++ 3drefit processed 1 datasets +++ 3drename: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Warning: ignoring +tlrc on new_prefix. +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.HEAD -> sub-03_ses-test_T1w_ns+tlrc.HEAD +++ THD_rename_dataset_files: rename __ats_tmp___upad40_sub-03_ses-test_T1w_ns+tlrc.BRIK -> sub-03_ses-test_T1w_ns+tlrc.BRIK +Cleanup ... +cat_matvec sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I +if ( ! -f sub-03_ses-test_T1w_ns+tlrc.HEAD ) then +foreach run ( 01 ) +3dvolreg -verbose -zpad 1 -base vr_base+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub_03.r01.tshift+orig +++ 3dvolreg: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 6.153038 degrees from plumb. +++ Reading in base dataset ./vr_base+orig.BRIK +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 6.153038 degrees from plumb. +++ Reading input dataset ./pb01.sub_03.r01.tshift+orig.BRIK +++ Edging: x=3 y=3 z=2 +++ Creating mask for -maxdisp + + Automask has 18925 voxels + + 3320 voxels left in -maxdisp mask after erosion +++ Initializing alignment base +++ Starting final pass on 237 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236.. +++ CPU time for realignment=9.23 s [=0.0389 s/sub-brick] +++ Min : roll=-0.099 pitch=-0.764 yaw=-0.000 dS=-0.132 dL=-0.087 dP=-0.636 +++ Mean: roll=+0.252 pitch=-0.320 yaw=+1.503 dS=+1.540 dL=+0.638 dP=-0.281 +++ Max : roll=+0.752 pitch=+1.091 yaw=+2.787 dS=+2.524 dL=+1.597 dP=+0.138 +++ Max displacements (mm) for each sub-brick: + 0.39(0.00) 0.36(0.73) 0.00(0.36) 0.63(0.63) 0.68(0.12) 0.32(0.39) 0.49(0.19) 0.69(0.22) 0.80(0.17) 0.77(0.07) 0.87(0.11) 1.05(0.21) 1.19(0.18) 1.18(0.10) 1.20(0.06) 1.23(0.03) 1.31(0.12) 1.33(0.10) 1.29(0.05) 1.34(0.08) 1.30(0.16) 1.25(0.18) 1.38(0.16) 1.41(0.06) 1.39(0.05) 1.47(0.08) 1.44(0.10) 1.57(0.15) 1.50(0.11) 1.56(0.08) 1.52(0.08) 1.57(0.08) 1.57(0.11) 1.70(0.15) 1.78(0.09) 1.83(0.09) 1.93(0.10) 1.96(0.05) 2.01(0.12) 2.07(0.10) 2.02(0.15) 2.12(0.14) 2.12(0.08) 2.15(0.06) 2.19(0.17) 2.21(0.08) 2.19(0.10) 2.18(0.12) 1.95(0.43) 1.65(1.28) 1.81(1.18) 0.91(1.59) 0.84(0.26) 1.58(1.54) 1.51(1.33) 2.08(1.14) 2.54(2.35) 4.01(2.10) 3.02(1.06) 3.51(0.78) 3.27(0.29) 3.24(0.12) 2.33(1.09) 2.04(0.58) 2.77(1.27) 2.07(0.91) 1.23(1.41) 2.13(1.65) 2.55(0.48) 2.61(0.10) 2.79(0.21) 2.87(0.10) 2.69(0.63) 2.86(0.46) 2.78(0.20) 2.80(0.09) 2.86(0.10) 2.74(0.19) 2.71(0.23) 2.69(0.07) 2.77(0.09) 2.81(0.09) 2.84(0.06) 3.03(0.22) 2.87(0.20) 3.06(0.19) 3.20(0.15) 3.24(0.05) 3.37(0.18) 3.40(0.05) 3.51(0.12) 3.48(0.05) 3.62(0.16) 3.55(0.08) 3.53(0.16) 3.33(0.44) 3.18(0.42) 3.17(0.09) 3.29(0.30) 3.36(0.08) 3.42(0.11) 3.09(0.86) 3.16(0.30) 3.64(0.63) 3.61(0.19) 3.70(0.14) 3.81(0.18) 3.81(0.09) 3.82(0.05) 3.78(0.13) 3.72(0.11) 3.57(0.23) 3.56(0.07) 3.63(0.12) 3.78(0.23) 3.90(0.18) 3.95(0.11) 4.10(0.18) 3.99(0.23) 4.25(0.31) 4.11(0.21) 4.14(0.07) 4.20(0.15) 3.91(0.41) 3.78(0.20) 3.72(0.13) 3.61(0.37) 3.73(0.29) 3.84(0.14) 3.84(0.03) 4.10(0.33) 4.06(0.10) 4.12(0.08) 4.08(0.14) 4.05(0.12) 4.20(0.20) 4.04(0.21) 4.41(0.43) 4.12(0.54) 4.20(0.16) 4.38(0.22) 4.53(0.19) 4.86(0.35) 4.55(0.38) 4.62(0.12) 4.52(0.17) 4.57(0.11) 4.52(0.18) 4.52(0.11) 4.77(0.38) 4.63(0.18) 4.55(0.20) 4.40(0.22) 4.57(0.23) 4.59(0.02) 4.52(0.07) 4.65(0.14) 4.57(0.13) 4.72(0.18) 4.82(0.10) 4.90(0.24) 5.30(0.79) 5.50(0.43) 4.99(1.04) 5.21(0.24) 5.46(0.32) 5.64(0.36) 5.66(0.07) 5.83(0.19) 5.76(0.14) 5.76(0.16) 5.73(0.05) 5.73(0.12) 5.58(0.27) 5.46(0.28) 5.45(0.40) 5.46(0.25) 5.37(0.21) 5.32(0.09) 5.45(0.18) 5.51(0.08) 5.68(0.25) 5.56(0.16) 5.63(0.07) 5.66(0.05) 5.57(0.25) 5.19(0.64) 5.48(0.78) 5.32(0.22) 4.57(1.04) 4.55(0.14) 4.88(0.39) 5.27(0.59) 5.64(0.60) 5.82(0.26) 5.70(0.27) 5.88(0.33) 5.87(0.05) 5.80(0.19) 5.75(0.11) 5.78(0.23) 5.98(0.27) 5.96(0.11) 5.92(0.10) 6.02(0.29) 6.04(0.11) 6.10(0.12) 6.10(0.10) 6.10(0.06) 6.10(0.08) 6.11(0.03) 6.03(0.13) 6.13(0.13) 6.12(0.15) 6.07(0.13) 6.13(0.15) 6.03(0.17) 6.10(0.14) 6.03(0.09) 6.01(0.05) 6.16(0.23) 5.98(0.22) 5.86(0.22) 5.94(0.10) 5.83(0.15) 5.68(0.26) 5.88(0.46) 6.00(0.25) 5.97(0.26) 6.05(0.12) 6.24(0.32) 6.26(0.17) 6.33(0.24) 6.15(0.32) 5.98(0.38) 6.01(0.05) 6.10(0.15) +++ Max displacement in automask = 6.33 (mm) at sub-brick 232 +++ Max delta displ in automask = 2.35 (mm) at sub-brick 56 +++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK +3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +*+ WARNING: input 'a' is not used in the expression +cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input pb01.sub_03.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -prefix rm.epi.nomask.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./pb01.sub_03.r01.tshift+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./pb01.sub_03.r01.tshift+orig.BRIK is 6.153038 degrees from plumb. +++ Source dataset: ./pb01.sub_03.r01.tshift+orig.HEAD +++ Base dataset: ./sub-03_ses-test_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 237 sub-bricks ========== +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 6.0 sec Elapsed = 4.1 +++ ########################################################### +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./rm.epi.all1+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./rm.epi.all1+orig.BRIK is 6.153038 degrees from plumb. +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 3.1 +3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +end +cat dfile.r01.1D +3dcopy rm.epi.min.r01+tlrc mask_epi_extents +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +foreach run ( 01 ) +3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_03.r01.volreg +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb02.sub_03.r01.volreg+tlrc.BRIK +end +cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1w_al_junk_mat.aff12.1D -I +3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input vr_base+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 4 -prefix final_epi_vr_base +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./vr_base+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./vr_base+orig.BRIK is 6.153038 degrees from plumb. +++ Source dataset: ./vr_base+orig.HEAD +++ Base dataset: ./sub-03_ses-test_T1w_ns+tlrc.HEAD +++ Loading datasets +++ NOTE: base and source coordinate systems have different handedness + + Orientations: base=Right handed (LPI); source=Left handed (RPI) +++ master dataset for output = base +++ changing output grid spacing to 4.0000 mm +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ø++ Output dataset ./final_epi_vr_base+tlrc.BRIK +++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.1 +++ ########################################################### +3dcopy sub-03_ses-test_T1w_ns+tlrc anat_final.sub_03 +++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +3dAllineate -base final_epi_vr_base+tlrc -allcostX -input anat_final.sub_03+tlrc +tee out.allcostX.txt +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Zhark the Registrator +++ Source dataset: ./anat_final.sub_03+tlrc.HEAD +++ Base dataset: ./final_epi_vr_base+tlrc.HEAD +++ Loading datasets +++ 223015 voxels in source_automask+0 +++ Zero-pad: xbot=1 xtop=2 +++ Zero-pad: ybot=0 ytop=1 +++ Zero-pad: zbot=1 ztop=1 +++ Computing -autobox +++ 111006 voxels [89.5%] in weight mask +++ Number of points for matching = 52172 +++ Local correlation: blok type = 'RHDD(14.76)' +*+ WARNING: No output dataset will be calculated +++ OpenMP thread count = 4 +volume 0Ø + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 +++ allcost output: init #0 + ls = 0.18269 + sp = 0.302214 + mi = -0.542443 + crM = 0.0831465 + nmi = 0.868037 + je = 3.5681 + hel = -0.108642 + crA = 0.288642 + crU = 0.301598 + lss = 0.81731 + lpc = 0.373345 + lpa = 0.626655 + lpc+ = 0.57125 + ncd = 0.966558 +++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 +++ ########################################################### +3dAllineate -source sub-03_ses-test_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped +++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Zhark the Registrator +*+ WARNING: If you are performing spatial transformations on an oblique dset, + such as ./sub-03_ses-test_T1w+orig.BRIK, + or viewing/combining it with volumes of differing obliquity, + you should consider running: + 3dWarp -deoblique + on this and other oblique datasets in the same session. + See 3dWarp -help for details. +++ Oblique dataset:./sub-03_ses-test_T1w+orig.BRIK is 6.455733 degrees from plumb. +++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers +++ Source dataset: ./sub-03_ses-test_T1w+orig.HEAD +++ Base dataset: (not given) +++ Loading datasets +++ OpenMP thread count = 4 +++ ========== Applying transformation to 1 sub-bricks ========== +volume 0Ø++ wsinc5 interpolation setup: + + taper function = Min sidelobe 3 term + + taper cut point = 0.000 + + window radius = 5 voxels + + window shape = Cubical + + The above can be altered via the AFNI_WSINC5_* environment variables. + + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + + wsinc5 CUBE(5) mask has 1000 points +++ Output dataset ./anat_w_skull_warped+tlrc.BRIK +++ 3dAllineate: total CPU time = 3.1 sec Elapsed = 1.3 +++ ########################################################### +foreach run ( 01 ) +3dmerge -1blur_fwhm 6.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc +++ 3dmerge: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ default -1dindex = 0 +++ default -1tindex = 1 +Program 3dmerge +3dmerge: edit and combine 3D datasets, by RW Cox +++ editing input dataset in memory (49.4 MB) +.............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK + +end +foreach run ( 01 ) +3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub_03.r01.blur+tlrc +++ 3dAutomask: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: Emperor Zhark +++ Loading dataset pb03.sub_03.r01.blur+tlrc +++ Forming automask + + Fixed clip level = 709.231506 + + Used gradual clip level = 629.214294 .. 792.803772 + + Number voxels above clip level = 28213 + + Clustering voxels ... + + Largest cluster has 28213 voxels + + Clustering voxels ... + + Largest cluster has 28129 voxels + + Filled 49 voxels in small holes; now have 28178 voxels + + Clustering voxels ... + + Largest cluster has 28178 voxels + + Clustering non-brain voxels ... + + Clustering voxels ... + + Largest cluster has 81172 voxels + + Mask now has 28178 voxels +++ Dilating automask + + Clustering voxels ... + + Largest cluster has 76144 voxels +++ 33206 voxels in the mask [out of 109350: 30.37%] +++ first 4 x-planes are zero [from L] +++ last 3 x-planes are zero [from R] +++ first 4 y-planes are zero [from P] +++ last 3 y-planes are zero [from A] +++ first 3 z-planes are zero [from I] +++ last 3 z-planes are zero [from S] +++ CPU time = 0.240000 sec +end +3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 +++ processing 1 input datasets... +++ padding all datasets by 0 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 33206 survived, 76144 were zero +++ writing result full_mask.sub_03... +3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-test_T1w_ns+tlrc -prefix rm.resam.anat +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30704 survived, 78646 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_anat.sub_03... +3dABoverlap -no_automask full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_overlap.txt +++ 3dOverlap: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +#A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK +#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) +33206 30704 35986 27924 5282 2780 15.9068 9.0542 0.9454 0.9214 0.9826 +3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc +tee out.mask_ae_dice.txt +0.873854 +3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/mli/abin/MNI_avg152T1+tlrc +3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group +++ no -frac option: defaulting to -union +++ processing 1 input datasets... +++ padding all datasets by 5 (for dilations) +++ frac 0 over 1 volumes gives min count 0 +++ voxel limits: 0 clipped, 30980 survived, 78370 were zero +++ filled 0 holes (0 voxels) +++ writing result mask_group... +foreach run ( 01 ) +3dTstat -prefix rm.mean_r01 pb03.sub_03.r01.blur+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.mean_r01+tlrc.BRIK +3dcalc -a pb03.sub_03.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_03.r01.scale +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./pb04.sub_03.r01.scale+tlrc.BRIK +end +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D +1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 +total number of censored TRs (simple form) = 22 +set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D + -show_trs_uncensored encoded` +1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +++ 3dDeconvolve: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: B. Douglas Ward, et al. +++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD +++ STAT automask has 97106 voxels (out of 109350 = 88.8%) +++ Skipping check for initial transients +++ Input polort=4; Longest run=592.5 s; Recommended minimum polort=4 ++ OK ++ +++ -stim_times using TR=2.5 s for stimulus timing conversion +++ -stim_times using TR=2.5 s for any -iresp output datasets +++ [you can alter the -iresp TR via the -TR_times option] +++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise +++ ** GUESSED ** -stim_times 1 using LOCAL times +++ ** GUESSED ** -stim_times 2 using LOCAL times +++ ** GUESSED ** -stim_times 3 using LOCAL times +++ ** GUESSED ** -stim_times 4 using LOCAL times +++ ** GUESSED ** -stim_times 5 using LOCAL times +------------------------------------------------------------ +GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control': + 0 0 0 0 0 0.5 0.5 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 + +++ Number of time points: 237 (before censor) ; 215 (after) + + Number of parameters: 22 [17 baseline ; 5 signal] +++ Memory required for output bricks = 215,638,200 bytes (about 216 million [mega]) +++ Wrote matrix image to file X.jpg +++ Wrote matrix values to file X.xmat.1D +++ ========= Things you can do with the matrix file ========= +++ (a) Linear regression with ARMA(1,1) modeling of serial correlation: + +3dREMLfit -matrix X.xmat.1D -input pb04.sub_03.r01.scale+tlrc.HEAD \ + -fout -tout -Rbuck stats.sub_03_REML -Rvar stats.sub_03_REMLvar \ + -Rfitts fitts.sub_03_REML -Rerrts errts.sub_03_REML -verb + +++ N.B.: 3dREMLfit command above written to file stats.REML_cmd +++ (b) Visualization/analysis of the matrix via ExamineXmat.R +++ (c) Synthesis of sub-model datasets using 3dSynthesize +++ ========================================================== +++ Wrote matrix values to file X.nocensor.xmat.1D +++ ----- Signal+Baseline matrix condition [X] (215x22): 7.47726 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (215x5): 1.47181 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (215x17): 7.3131 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (215x12): 6.12753 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (215x5): 1.09962 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 9.39256e-15 ++ VERY GOOD ++ +++ Matrix setup time = 0.57 s +++ Calculations starting; elapsed time=1.180 +++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. +++ Calculations finished; elapsed time=15.307 +++ Smallest FDR q [0 Full_Fstat] = 3.64156e-13 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 3.53829e-12 +++ Smallest FDR q [3 Correct_Task_Fstat] = 3.53752e-12 +++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.0769233 +++ Smallest FDR q [6 Incorrect_Task_Fstat] = 0.0769143 +++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.000784632 +++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.000784632 +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 8.9263e-12 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 8.92772e-12 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 2.6772e-11 +++ Smallest FDR q [15 Response_Control_Fstat] = 2.67706e-11 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.0684832 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.068483 +++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + + created 13 FDR curves in bucket header +++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK +++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK +++ #Flops=3.93533e+10 Average Dot Product=37.1935 +if ( 0 != 0 ) then +1d_tool.py -show_cormat_warnings -infile X.xmat.1D +tee out.cormat_warn.txt + +Warnings regarding Correlation Matrix: X.xmat.1D + + severity correlation cosine regressor pair + -------- ----------- ------ ---------------------------------------- + medium: 0.570 0.649 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 + +3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD +++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ elapsed time = 0.5 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[0..47,59,60,68..161,164..187,190..236] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.signal.all+tlrc.BRIK +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[0..47,59,60,68..161,164..187,190..236] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./rm.noise.all+tlrc.BRIK +3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.sub_03+tlrc -expr c*a/b -prefix TSNR.sub_03 +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./TSNR.sub_03+tlrc.BRIK +3dTnorm -norm2 -prefix rm.errts.unit errts.sub_03+tlrc +++ 3dTnorm: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RW Cox +++ Output dataset ./rm.errts.unit+tlrc.BRIK +3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc +++ 3dmaskave: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++++ 33206 voxels survive the mask +3dTstat -sos -prefix - gmean.errts.unit.1D' +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo -- GCOR = `cat out.gcor.1D` +cat out.gcor.1D +-- GCOR = 0.158995 +3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP +++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: A cast of thousands +++ Output dataset ./rm.DP+tlrc.BRIK +3dTstat -sum -prefix corr_brain rm.DP+tlrc +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +++ Output dataset ./corr_brain+tlrc.BRIK +1dcat X.nocensor.xmat.1D[5] +1dcat X.nocensor.xmat.1D[6] +1dcat X.nocensor.xmat.1D[7] +1dcat X.nocensor.xmat.1D[8] +1dcat X.nocensor.xmat.1D[9] +set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest` +1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest +3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[5..9] +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +++ Output dataset ./sum_ideal.1D +1dcat X.nocensor.xmat.1D[5..9] +touch blur_est.sub_03.1D +mkdir files_ACF +touch blur.epits.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 0..47,59,60,68..161,164..187,190..236 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[0..47,59,60,68..161,164..187,190..236] +++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 33206 +*+ WARNING: removed 236 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 215 time points + + detrending done (2.53 CPU s thus far) +++ start ACF calculations out to radius = 28.19 mm + + ACF done (58.93 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits FWHM blurs: 0 0 0 0 +average epits FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # epits FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.epits.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average epits ACF blurs: 0.600388 5.30928 13.65 13.7777 +average epits ACF blurs: 0.600388 5.30928 13.65 13.7777 +echo 0.600388 5.30928 13.65 13.7777 # epits ACF blur estimates +touch blur.errts.1D +foreach run ( 01 ) +set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded + -show_trs_run $run` +1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 +if ( 0..47,59,60,68..161,164..187,190..236 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[0..47,59,60,68..161,164..187,190..236] +++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: The Bob +++ Number of voxels in mask = 33206 +*+ WARNING: removed 236 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 215 time points + + detrending done (2.59 CPU s thus far) +++ start ACF calculations out to radius = 27.70 mm + + ACF done (58.17 CPU s thus far) +++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D +++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: RWC et al. + + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png +end +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{0..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts FWHM blurs: 0 0 0 0 +average errts FWHM blurs: 0 0 0 0 +echo 0 0 0 0 # errts FWHM blur estimates +set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) +3dTstat -mean -prefix - blur.errts.1D{1..$(2)}' +++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] +++ Authored by: KR Hammett & RW Cox +*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off +*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 +echo average errts ACF blurs: 0.669971 5.25102 13.8287 13.4065 +average errts ACF blurs: 0.669971 5.25102 13.8287 13.4065 +echo 0.669971 5.25102 13.8287 13.4065 # errts ACF blur estimates +gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD +gen_ss_review_scripts.py -mot_limit 0.5 -exit0 +++ writing ss review basic: @ss_review_basic +++ writing ss review driver: @ss_review_driver +++ writing ss review drive commands: @ss_review_driver_commands +rm -f rm.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK.gz rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK.gz rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK.gz rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK.gz rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD +tee out.ss_review.sub_03.txt +if ( -e @ss_review_basic ) ./@ss_review_basic +./@ss_review_basic + +subject ID : sub_03 +TRs removed (per run) : 1 +num stim classes provided : 5 +final anatomy dset : anat_final.sub_03+tlrc.HEAD +final stats dset : stats.sub_03+tlrc.HEAD +final voxel resolution : 4.000000 4.000000 4.000000 + +motion limit : 0.5 +num TRs above mot limit : 16 +average motion (per TR) : 0.160024 +average censored motion : 0.115175 +max motion displacement : 4.03483 +max censored displacement : 4.03483 +outlier limit : 0.1 +average outlier frac (TR) : 0.0119293 +num TRs above out limit : 8 + +num runs found : 1 +num TRs per run : 237 +num TRs per run (applied) : 215 +num TRs per run (censored): 22 +fraction censored per run : 0.092827 +TRs total (uncensored) : 237 +TRs total : 215 +degrees of freedom used : 22 +degrees of freedom left : 193 + +TRs censored : 22 +censor fraction : 0.092827 +num regs of interest : 5 +num TRs per stim (orig) : 71 43 64 28 79 +num TRs censored per stim : 0 0 13 7 11 +fraction TRs censored : 0.000 0.000 0.203 0.250 0.139 +ave mot per sresp (orig) : 0.105296 0.103826 0.216156 0.210735 0.179376 +ave mot per sresp (cens) : 0.105296 0.103826 0.108428 0.100787 0.100622 + +TSNR average : 210.84 +global correlation (GCOR) : 0.158995 +anat/EPI mask Dice coef : 0.873854 +maximum F-stat (masked) : 61.5622 +blur estimates (ACF) : 0.669971 5.25102 13.8287 +blur estimates (FWHM) : 0 0 0 + + +cd .. +echo execution finished: `date` +date +execution finished: Sat Aug 5 16:33:35 EDT 2017 diff --git a/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 b/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 old mode 100644 new mode 100755 index f3cc349..96f1d92 --- a/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 +++ b/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Fri Aug 4 12:43:15 2017" +echo "auto-generated by afni_proc.py, Sat Aug 5 16:29:05 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -59,12 +59,12 @@ cp /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D # ============================ auto block: tcat ============================ # apply 3dTcat to copy input dsets to results dir, while -# removing the first 0 TRs +# removing the first 1 TRs 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ - /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' + /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[1..$]' # and make note of repetitions (TRs) per run -set tr_counts = ( 238 ) +set tr_counts = ( 237 ) # ------------------------------------------------------- # enter the results directory (can begin processing data) @@ -92,6 +92,7 @@ cat outcount.r*.1D > outcount_rall.1D # time shift data so all slice timing is the same foreach run ( $runs ) 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + -tpattern alt+z \ pb00.$subj.r$run.tcat+orig end @@ -304,7 +305,7 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ - -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control' \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -458,7 +459,7 @@ echo "execution finished: `date`" # afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ # tshift align tlrc volreg blur mask scale regress -copy_anat \ # /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ -# -tcat_remove_first_trs 0 -dsets \ +# -tcat_remove_first_trs 1 -tshift_opts_ts -tpattern alt+z -dsets \ # /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ # -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ # -volreg_tlrc_warp -blur_size 6.0 -regress_stim_times \ @@ -471,6 +472,6 @@ echo "execution finished: `date`" # No_Response_Task Response_Control -regress_basis GAM \ # -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ # -regress_opts_3dD -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ -# -*Response_Control' -glt_label 1 Landmark-Detection \ +# -Response_Control' -glt_label 1 Landmark-Detection \ # -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ # -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 index 9b568a9..c2e5946 100644 --- a/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 @@ -17,7 +17,8 @@ afni_proc.py -subj_id $subj \ -script proc.$subj -scr_overwrite \ -blocks tshift align tlrc volreg blur mask scale regress \ -copy_anat $anat_dir/sub-03_ses-retest_T1w.nii.gz \ - -tcat_remove_first_trs 0 \ + -tcat_remove_first_trs 1 \ + -tshift_opts_ts -tpattern alt+z \ -dsets $epi_dir/sub-03_ses-retest_task-linebisection_bold.nii.gz \ -tlrc_base MNI_avg152T1+tlrc \ -volreg_align_to third \ @@ -38,7 +39,7 @@ afni_proc.py -subj_id $subj \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ - -*Response_Control' -glt_label 1 Landmark-Detection \ + -Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 index 06b29a0..106d34d 100644 --- a/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 @@ -3,11 +3,13 @@ set anat_dir = /Users/mli/Desktop/playground/sub-03/ses-retest/anat set epi_dir = /Users/mli/Desktop/playground/sub-03/ses-retest/func set subj = sub_03 set group_id = retest -afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task - -*Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz -tcat_remove_first_trs 1 -tshift_opts_ts -tpattern alt+z -dsets /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task + -Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig --- tcat: reps is now 238 -++ updating polort to 4, from run len 595.0 s +** warning: removing first 1 TRs from beginning of each run + --> the stimulus timing files must reflect the removal of these TRs +-- tcat: reps is now 237 +++ updating polort to 4, from run len 592.5 s -- volreg: using base dset vr_base+orig ++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 4 mm tlrc voxels -- applying anat warps to 1 dataset(s): sub-03_ses-retest_T1w diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 index 64e976f..b6a975a 100644 --- a/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 +++ b/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 @@ -1,10 +1,10 @@ -echo auto-generated by afni_proc.py, Fri Aug 4 12:55:45 2017 -auto-generated by afni_proc.py, Fri Aug 4 12:55:45 2017 +echo auto-generated by afni_proc.py, Sat Aug 5 16:37:42 2017 +auto-generated by afni_proc.py, Sat Aug 5 16:37:42 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Fri Aug 4 12:55:48 EDT 2017 +execution started: Sat Aug 5 16:37:43 EDT 2017 afni -ver Precompiled binary macosx_10.7_local: Jul 27 2017 (Version AFNI_17.2.05) afni_history -check_date 23 Sep 2016 @@ -23,10 +23,10 @@ mkdir sub_03.results/stimuli cp /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Response_Control.1D sub_03.results/stimuli 3dcopy /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz sub_03.results/sub-03_ses-retest_T1w ++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[0..$] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz[1..$] ++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -++ elapsed time = 0.9 s -set tr_counts = ( 238 ) +++ elapsed time = 0.8 s +set tr_counts = ( 237 ) cd sub_03.results touch out.pre_ss_warn.txt foreach run ( 01 ) @@ -40,15 +40,13 @@ foreach run ( 01 ) on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. -++ 18031 voxels passed mask/clip +++ 18027 voxels passed mask/clip if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then 1deval -a outcount.r01.1D{0} -expr step(a-0.4) -echo ** TR #0 outliers: possible pre-steady state TRs in run 01 -endif end cat outcount.r01.1D foreach run ( 01 ) -3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig +3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift -tpattern alt+z pb00.sub_03.r01.tcat+orig ++ 3dTshift: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, @@ -58,8 +56,6 @@ foreach run ( 01 ) on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 4.947676 degrees from plumb. -*+ WARNING: dataset is already aligned in time! -*+ WARNING: ==>> output dataset is just a copy of input dataset end 3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] ++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -127,22 +123,22 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Authored by: Emperor Zhark ++ Loading dataset ./__tt_vr_base_ts_rs+orig ++ Forming automask - + Fixed clip level = 708.019226 - + Used gradual clip level = 621.023193 .. 754.463989 - + Number voxels above clip level = 1151758 + + Fixed clip level = 707.124390 + + Used gradual clip level = 618.551697 .. 753.626404 + + Number voxels above clip level = 1151477 + Clustering voxels ... - + Largest cluster has 1151071 voxels + + Largest cluster has 1150847 voxels + Clustering voxels ... - + Largest cluster has 1150607 voxels - + Filled 381 voxels in small holes; now have 1150988 voxels - + Filled 16522 voxels in large holes; now have 1167510 voxels + + Largest cluster has 1150422 voxels + + Filled 414 voxels in small holes; now have 1150836 voxels + + Filled 16701 voxels in large holes; now have 1167537 voxels + Clustering voxels ... - + Largest cluster has 1167476 voxels + + Largest cluster has 1167504 voxels + Clustering non-brain voxels ... + Clustering voxels ... - + Largest cluster has 14352028 voxels - + Mask now has 1167476 voxels -++ 1167476 voxels in the mask [out of 15519504: 7.52%] + + Largest cluster has 14352000 voxels + + Mask now has 1167504 voxels +++ 1167504 voxels in the mask [out of 15519504: 7.52%] ++ first 64 x-planes are zero [from R] ++ last 68 x-planes are zero [from L] ++ first 30 y-planes are zero [from A] @@ -151,13 +147,13 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ last 48 z-planes are zero [from S] ++ applying mask to original data ++ Writing masked data -++ CPU time = 3.970000 sec +++ CPU time = 4.020000 sec #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1728.000000 on /Users/mli/Desktop/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1723.000000 on /Users/mli/Desktop/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig #Script is running (command trimmed): - 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1728.000000))' + 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1723.000000))' ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands #++ Aligning anat data to epi data @@ -170,8 +166,8 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Loading datasets ++ 1356008 voxels in -source_automask+4 ++ Zero-pad: not needed -++ 1167476 voxels [7.5%] in weight mask -++ Number of points for matching = 1167476 +++ 1167504 voxels [7.5%] in weight mask +++ Number of points for matching = 1167504 ++ Local correlation: blok type = 'RHDD(6.54321)' ++ shift param auto-range: -84.4..84.4 -70.6..70.6 -85.1..85.1 + Range param#4 [z-angle] = -6.000000 .. 6.000000 @@ -184,31 +180,31 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s ++ Normalized convergence radius = 0.001000 ++ OpenMP thread count = 4 ++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= -++ ========== sub-brick #0 ========== [total CPU to here=10.3 s] +++ ========== sub-brick #0 ========== [total CPU to here=9.5 s] ++ *** Fine pass begins *** + * Enter alignment setup routine + - copying base image + - copying source image + - copying weight image - + - using 1167476 points from base image [use_all=0] + + - using 1167504 points from base image [use_all=0] + * Exit alignment setup routine - + 1097666 total points stored in 2068 'RHDD(6.54321)' bloks - + - Initial cost = -0.053122 + + 1097341 total points stored in 2067 'RHDD(6.54321)' bloks + + - Initial cost = -0.051994 + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 -********************************************************************************************************************************************** - + - Finalish cost = -0.295415 ; 350 funcs -********** - + - Final cost = -0.295420 ; 136 funcs +***************************************************************************************************************************************************************** + + - Finalish cost = -0.289529 ; 377 funcs +**** + + - Final cost = -0.289531 ; 107 funcs + Final fine fit Parameters: - x-shift= 0.2981 y-shift=-0.5136 z-shift=-1.2234 - z-angle= 0.4394 x-angle= 1.9668 y-angle=-5.3161 - x-scale= 0.9674 y-scale= 0.9725 z-scale= 1.0191 - y/x-shear= 0.0000 z/x-shear= 0.0099 z/y-shear= 0.0534 - + - Fine net CPU time = 36.5 s + x-shift= 0.2825 y-shift=-0.4994 z-shift=-1.2123 + z-angle= 0.4322 x-angle= 2.0209 y-angle=-5.2935 + x-scale= 0.9675 y-scale= 0.9734 z-scale= 1.0197 + y/x-shear=-0.0002 z/x-shear= 0.0099 z/y-shear= 0.0544 + + - Fine net CPU time = 37.4 s ++ Computing output image -++ image warp: parameters = 0.2981 -0.5136 -1.2234 0.4394 1.9668 -5.3161 0.9674 0.9725 1.0191 0.0000 0.0099 0.0534 +++ image warp: parameters = 0.2825 -0.4994 -1.2123 0.4322 2.0209 -5.2935 0.9675 0.9734 1.0197 -0.0002 0.0099 0.0544 ++ Wrote -1Dmatrix_save ./sub-03_ses-retest_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 49.5 sec Elapsed = 36.2 +++ 3dAllineate: total CPU time = 49.5 sec Elapsed = 32.5 ++ ########################################################### ++ # Please check results visually for alignment quality # ++ ########################################################### @@ -250,8 +246,8 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-retest_T1w+orig -save_skullstrip -s + * Exit alignment setup routine ++ using -1Dmatrix_apply ++ Computing output image -++ image warp: parameters = 0.9618 0.0448 -0.0985 14.5442 -0.0314 0.9711 -0.0538 -1.5252 0.0911 0.0281 1.0141 -11.6150 -++ 3dAllineate: total CPU time = 2.2 sec Elapsed = 1.9 +++ image warp: parameters = 0.9620 0.0446 -0.0982 14.5110 -0.0314 0.9721 -0.0546 -1.5054 0.0907 0.0280 1.0148 -11.6331 +++ 3dAllineate: total CPU time = 2.2 sec Elapsed = 1.7 ++ ########################################################### #++ Creating final output: skullstripped anat data copying from dataset /Users/mli/Desktop/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/__tt_sub-03_ses-retest_T1w_ns+orig to /Users/mli/Desktop/playground/Exp-2/subject_results/group.retest/subj.sub_03/sub_03.results/sub-03_ses-retest_T1w_ns+orig @@ -423,15 +419,15 @@ foreach run ( 01 ) + Automask has 19058 voxels + 3364 voxels left in -maxdisp mask after erosion ++ Initializing alignment base -++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=6.75 s [=0.0284 s/sub-brick] -++ Min : roll=-0.200 pitch=-0.367 yaw=-0.118 dS=-1.139 dL=-0.157 dP=-0.055 -++ Mean: roll=-0.094 pitch=-0.011 yaw=+0.456 dS=-0.124 dL=+0.184 dP=+0.074 -++ Max : roll=+0.027 pitch=+0.449 yaw=+0.935 dS=+0.523 dL=+0.640 dP=+0.245 +++ Starting final pass on 237 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236.. +++ CPU time for realignment=6.8 s [=0.0287 s/sub-brick] +++ Min : roll=-0.181 pitch=-0.341 yaw=-0.016 dS=-0.709 dL=-0.130 dP=-0.130 +++ Mean: roll=-0.081 pitch=+0.020 yaw=+0.496 dS=-0.184 dL=+0.212 dP=+0.033 +++ Max : roll=+0.032 pitch=+0.458 yaw=+0.971 dS=+0.453 dL=+0.674 dP=+0.194 ++ Max displacements (mm) for each sub-brick: - 1.41(0.00) 0.17(1.52) 0.00(0.17) 0.33(0.33) 0.34(0.10) 0.45(0.12) 0.41(0.06) 0.20(0.28) 0.21(0.16) 0.22(0.05) 0.31(0.29) 0.37(0.19) 0.50(0.19) 0.61(0.12) 0.87(0.29) 0.94(0.10) 1.05(0.18) 1.12(0.12) 1.07(0.11) 0.82(0.28) 0.67(0.28) 0.69(0.13) 0.57(0.16) 0.70(0.22) 0.67(0.04) 0.75(0.13) 0.63(0.15) 0.68(0.19) 0.59(0.12) 0.66(0.09) 0.67(0.04) 0.78(0.19) 0.61(0.19) 0.59(0.05) 0.51(0.16) 0.62(0.22) 0.63(0.12) 0.66(0.12) 0.70(0.10) 0.69(0.04) 0.70(0.03) 0.77(0.07) 0.70(0.16) 0.65(0.14) 0.72(0.10) 0.74(0.16) 0.71(0.08) 0.68(0.10) 0.74(0.12) 0.70(0.13) 0.74(0.19) 0.60(0.21) 0.54(0.09) 0.50(0.12) 0.46(0.11) 0.45(0.08) 0.44(0.09) 0.50(0.23) 0.46(0.11) 0.50(0.15) 0.49(0.11) 0.56(0.15) 0.52(0.11) 0.57(0.17) 0.63(0.15) 0.56(0.12) 0.69(0.13) 0.64(0.26) 0.67(0.18) 0.62(0.07) 0.68(0.18) 0.76(0.27) 0.58(0.33) 0.80(0.22) 0.67(0.15) 0.65(0.08) 0.70(0.08) 0.77(0.08) 0.70(0.12) 0.70(0.14) 0.66(0.08) 0.68(0.12) 0.83(0.18) 0.74(0.22) 0.64(0.22) 0.72(0.14) 0.74(0.13) 0.81(0.14) 0.75(0.10) 0.72(0.07) 0.73(0.07) 0.69(0.16) 0.69(0.12) 0.69(0.17) 0.70(0.13) 0.64(0.16) 0.68(0.16) 0.65(0.10) 0.73(0.17) 0.74(0.06) 0.69(0.10) 0.67(0.05) 0.65(0.15) 0.72(0.12) 0.63(0.25) 0.70(0.15) 0.68(0.14) 0.70(0.17) 0.63(0.21) 0.60(0.07) 0.64(0.08) 0.76(0.16) 0.72(0.14) 0.69(0.15) 0.57(0.24) 0.58(0.06) 0.59(0.04) 0.63(0.08) 0.58(0.07) 0.60(0.07) 0.67(0.10) 0.67(0.25) 0.81(0.23) 0.79(0.06) 0.72(0.11) 0.74(0.04) 0.68(0.15) 0.71(0.14) 0.69(0.04) 0.69(0.09) 0.70(0.11) 0.68(0.11) 0.75(0.16) 0.70(0.12) 0.81(0.19) 0.73(0.10) 0.85(0.14) 0.78(0.10) 0.85(0.07) 0.84(0.05) 0.84(0.04) 0.77(0.09) 0.78(0.09) 0.80(0.06) 0.81(0.03) 0.77(0.11) 0.86(0.13) 0.80(0.16) 0.91(0.15) 0.86(0.10) 0.90(0.07) 0.98(0.08) 1.10(0.14) 1.13(0.06) 1.03(0.12) 1.14(0.17) 1.06(0.09) 1.18(0.12) 1.10(0.11) 1.13(0.07) 1.08(0.14) 1.18(0.15) 1.23(0.07) 1.07(0.19) 1.17(0.13) 1.14(0.10) 1.18(0.07) 1.20(0.05) 1.22(0.07) 1.20(0.07) 1.14(0.13) 1.22(0.14) 1.14(0.14) 1.29(0.18) 1.19(0.11) 1.32(0.17) 1.27(0.10) 1.34(0.16) 1.38(0.05) 1.28(0.19) 1.31(0.09) 1.33(0.05) 1.37(0.10) 1.36(0.05) 1.42(0.14) 1.39(0.10) 1.40(0.06) 1.36(0.08) 1.36(0.03) 1.49(0.13) 1.42(0.09) 1.48(0.10) 1.30(0.24) 1.20(0.16) 1.24(0.10) 1.23(0.11) 1.25(0.03) 1.24(0.08) 1.19(0.11) 1.25(0.11) 1.18(0.08) 1.19(0.04) 1.21(0.06) 1.40(0.25) 1.31(0.26) 1.36(0.14) 1.47(0.11) 1.51(0.07) 1.53(0.06) 1.58(0.06) 1.60(0.08) 1.58(0.11) 1.65(0.10) 1.64(0.11) 1.65(0.13) 1.72(0.09) 1.79(0.07) 1.76(0.09) 1.80(0.13) 1.96(0.20) 1.94(0.03) 1.82(0.16) 1.72(0.20) 1.55(0.33) 1.60(0.32) 1.57(0.14) 1.37(0.21) 1.38(0.20) 1.14(0.38) 1.18(0.25) 1.21(0.30) 0.70(0.63) 0.81(0.24) 0.91(0.13) 1.00(0.10) 1.12(0.13) 1.02(0.23) 1.19(0.19) -++ Max displacement in automask = 1.96 (mm) at sub-brick 219 -++ Max delta displ in automask = 1.52 (mm) at sub-brick 1 + 0.30(0.00) 0.20(0.44) 0.00(0.20) 0.23(0.23) 0.26(0.09) 0.39(0.15) 0.18(0.32) 0.23(0.16) 0.35(0.15) 0.20(0.21) 0.26(0.16) 0.36(0.13) 0.47(0.18) 0.64(0.20) 0.80(0.18) 0.89(0.10) 1.01(0.17) 0.97(0.08) 0.92(0.09) 0.59(0.48) 0.64(0.07) 0.54(0.11) 0.54(0.13) 0.60(0.11) 0.60(0.06) 0.61(0.07) 0.56(0.15) 0.56(0.09) 0.53(0.05) 0.62(0.09) 0.65(0.14) 0.60(0.08) 0.52(0.10) 0.48(0.09) 0.45(0.08) 0.54(0.18) 0.56(0.12) 0.61(0.07) 0.60(0.07) 0.62(0.07) 0.65(0.04) 0.69(0.06) 0.58(0.24) 0.63(0.06) 0.66(0.12) 0.68(0.08) 0.63(0.15) 0.64(0.03) 0.64(0.10) 0.67(0.08) 0.59(0.11) 0.52(0.13) 0.45(0.11) 0.44(0.09) 0.44(0.12) 0.42(0.07) 0.53(0.13) 0.57(0.05) 0.56(0.07) 0.61(0.07) 0.61(0.05) 0.66(0.11) 0.57(0.22) 0.66(0.13) 0.69(0.05) 0.70(0.07) 0.74(0.11) 0.71(0.12) 0.75(0.24) 0.68(0.19) 0.82(0.15) 0.74(0.28) 0.81(0.21) 0.90(0.13) 0.72(0.18) 0.79(0.08) 0.81(0.04) 0.86(0.08) 0.78(0.18) 0.79(0.04) 0.74(0.06) 0.84(0.12) 0.94(0.34) 0.75(0.20) 0.78(0.08) 0.83(0.09) 0.88(0.06) 0.90(0.04) 0.81(0.14) 0.83(0.09) 0.78(0.10) 0.80(0.05) 0.70(0.11) 0.75(0.09) 0.74(0.06) 0.72(0.04) 0.75(0.07) 0.72(0.10) 0.87(0.23) 0.80(0.07) 0.80(0.13) 0.73(0.16) 0.80(0.06) 0.75(0.08) 0.73(0.08) 0.77(0.05) 0.78(0.08) 0.77(0.05) 0.67(0.16) 0.68(0.06) 0.68(0.19) 0.70(0.16) 0.68(0.13) 0.64(0.17) 0.64(0.09) 0.67(0.05) 0.66(0.04) 0.63(0.07) 0.67(0.14) 0.64(0.14) 0.73(0.18) 0.83(0.22) 1.01(0.23) 0.85(0.19) 0.87(0.05) 0.81(0.14) 0.81(0.07) 0.85(0.07) 0.78(0.09) 0.84(0.09) 0.77(0.12) 0.85(0.08) 0.85(0.03) 0.87(0.05) 0.90(0.06) 0.91(0.04) 0.97(0.09) 0.92(0.09) 1.01(0.09) 0.95(0.07) 0.95(0.04) 0.86(0.10) 0.95(0.11) 0.92(0.07) 0.92(0.10) 0.95(0.06) 0.97(0.04) 0.94(0.10) 1.07(0.14) 0.97(0.13) 1.11(0.16) 1.14(0.08) 1.31(0.19) 1.19(0.15) 1.24(0.11) 1.24(0.05) 1.25(0.06) 1.31(0.06) 1.23(0.10) 1.28(0.10) 1.20(0.09) 1.40(0.21) 1.25(0.17) 1.23(0.08) 1.32(0.10) 1.26(0.11) 1.34(0.12) 1.31(0.11) 1.39(0.13) 1.27(0.15) 1.32(0.07) 1.29(0.04) 1.35(0.06) 1.37(0.03) 1.39(0.05) 1.46(0.07) 1.41(0.06) 1.52(0.20) 1.46(0.14) 1.42(0.07) 1.44(0.07) 1.49(0.09) 1.49(0.07) 1.51(0.06) 1.56(0.06) 1.52(0.08) 1.55(0.09) 1.45(0.10) 1.58(0.13) 1.58(0.03) 1.59(0.07) 1.57(0.15) 1.34(0.33) 1.36(0.09) 1.34(0.09) 1.40(0.11) 1.36(0.05) 1.37(0.05) 1.33(0.06) 1.36(0.11) 1.30(0.09) 1.33(0.05) 1.45(0.19) 1.51(0.09) 1.42(0.18) 1.56(0.21) 1.63(0.07) 1.66(0.05) 1.67(0.04) 1.75(0.13) 1.71(0.10) 1.75(0.04) 1.77(0.07) 1.79(0.12) 1.80(0.09) 1.90(0.11) 1.91(0.05) 1.90(0.12) 2.01(0.13) 2.12(0.15) 2.00(0.15) 1.91(0.16) 1.74(0.26) 1.70(0.32) 1.75(0.18) 1.58(0.19) 1.53(0.17) 1.41(0.23) 1.23(0.22) 1.43(0.44) 1.00(0.47) 0.85(0.20) 1.02(0.28) 1.09(0.09) 1.24(0.15) 1.18(0.15) 1.21(0.11) +++ Max displacement in automask = 2.12 (mm) at sub-brick 219 +++ Max delta displ in automask = 0.48 (mm) at sub-brick 19 ++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK 3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -457,9 +453,9 @@ cat_matvec -ONELINE sub-03_ses-retest_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-retes ++ master dataset for output = base ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 -++ ========== Applying transformation to 238 sub-bricks ========== -volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 6.2 sec Elapsed = 3.8 +++ ========== Applying transformation to 237 sub-bricks ========== +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 6.2 sec Elapsed = 4.2 ++ ########################################################### 3dAllineate -base sub-03_ses-retest_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 ++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -474,7 +470,7 @@ volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20. ++ Oblique dataset:./rm.epi.all1+orig.BRIK is 4.947676 degrees from plumb. ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ 3dAllineate: total CPU time = 3.6 sec Elapsed = 3.1 +++ 3dAllineate: total CPU time = 3.7 sec Elapsed = 3.7 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox @@ -526,26 +522,26 @@ tee out.allcostX.txt ++ Zero-pad: ybot=0 ytop=1 ++ Zero-pad: zbot=2 ztop=1 ++ Computing -autobox -++ 113297 voxels [89.4%] in weight mask -++ Number of points for matching = 53249 +++ 113307 voxels [89.4%] in weight mask +++ Number of points for matching = 53254 ++ Local correlation: blok type = 'RHDD(14.76)' *+ WARNING: No output dataset will be calculated ++ OpenMP thread count = 4 volume 0Ø + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 ++ allcost output: init #0 - ls = 0.184126 - sp = 0.307224 - mi = -0.531581 - crM = 0.0790675 - nmi = 0.868615 - je = 3.51437 - hel = -0.106047 - crA = 0.2819 - crU = 0.301908 - lss = 0.815874 - lpc = 0.296009 - lpa = 0.703991 - lpc+ = 0.494411 + ls = 0.183506 + sp = 0.306723 + mi = -0.532442 + crM = 0.0787207 + nmi = 0.868505 + je = 3.51671 + hel = -0.106397 + crA = 0.281314 + crU = 0.301726 + lss = 0.816494 + lpc = 0.300018 + lpa = 0.699982 + lpc+ = 0.497814 ncd = 1 ++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 ++ ########################################################### @@ -575,7 +571,7 @@ volume 0 + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + wsinc5 CUBE(5) mask has 1000 points ++ Output dataset ./anat_w_skull_warped+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.1 sec Elapsed = 1.6 +++ 3dAllineate: total CPU time = 3.2 sec Elapsed = 1.5 ++ ########################################################### foreach run ( 01 ) 3dmerge -1blur_fwhm 3.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc @@ -584,8 +580,8 @@ foreach run ( 01 ) ++ default -1tindex = 1 Program 3dmerge 3dmerge: edit and combine 3D datasets, by RW Cox -++ editing input dataset in memory (49.6 MB) -..............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK +++ editing input dataset in memory (49.4 MB) +.............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK end foreach run ( 01 ) @@ -594,37 +590,37 @@ foreach run ( 01 ) ++ Authored by: Emperor Zhark ++ Loading dataset pb03.sub_03.r01.blur+tlrc ++ Forming automask - + Fixed clip level = 705.332397 - + Used gradual clip level = 626.181824 .. 751.003906 - + Number voxels above clip level = 28040 + + Fixed clip level = 704.767273 + + Used gradual clip level = 625.530457 .. 750.232300 + + Number voxels above clip level = 28088 + Clustering voxels ... - + Largest cluster has 28006 voxels + + Largest cluster has 28054 voxels + Clustering voxels ... - + Largest cluster has 27881 voxels - + Filled 94 voxels in small holes; now have 27975 voxels + + Largest cluster has 27922 voxels + + Filled 97 voxels in small holes; now have 28019 voxels + Clustering voxels ... - + Largest cluster has 27975 voxels + + Largest cluster has 28019 voxels + Clustering non-brain voxels ... + Clustering voxels ... - + Largest cluster has 81375 voxels - + Mask now has 27975 voxels + + Largest cluster has 81331 voxels + + Mask now has 28019 voxels ++ Dilating automask + Clustering voxels ... - + Largest cluster has 76204 voxels -++ 33146 voxels in the mask [out of 109350: 30.31%] + + Largest cluster has 76177 voxels +++ 33173 voxels in the mask [out of 109350: 30.34%] ++ first 4 x-planes are zero [from L] ++ last 3 x-planes are zero [from R] ++ first 4 y-planes are zero [from P] ++ last 3 y-planes are zero [from A] ++ first 3 z-planes are zero [from I] ++ last 3 z-planes are zero [from S] -++ CPU time = 0.290000 sec +++ CPU time = 0.300000 sec end 3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 ++ processing 1 input datasets... ++ padding all datasets by 0 (for dilations) ++ frac 0 over 1 volumes gives min count 0 -++ voxel limits: 0 clipped, 33146 survived, 76204 were zero +++ voxel limits: 0 clipped, 33173 survived, 76177 were zero ++ writing result full_mask.sub_03... 3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-retest_T1w_ns+tlrc -prefix rm.resam.anat 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 @@ -640,10 +636,10 @@ tee out.mask_ae_overlap.txt ++ 3dOverlap: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK #A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) -33146 30574 35621 28099 5047 2475 15.2266 8.0951 0.9461 0.9329 0.9590 +33173 30574 35634 28113 5060 2461 15.2534 8.0493 0.9466 0.9314 0.9581 3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_dice.txt -0.881952 +0.882018 3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/mli/abin/MNI_avg152T1+tlrc 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ no -frac option: defaulting to -union @@ -666,17 +662,17 @@ end 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 -total number of censored TRs (simple form) = 2 +total number of censored TRs (simple form) = 0 set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D -show_trs_uncensored encoded` 1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-retest_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-retest_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-retest_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-retest_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-retest_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 ++ 3dDeconvolve: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD -++ STAT automask has 100184 voxels (out of 109350 = 91.6%) +++ STAT automask has 100230 voxels (out of 109350 = 91.7%) ++ Skipping check for initial transients -++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ +++ Input polort=4; Longest run=592.5 s; Recommended minimum polort=4 ++ OK ++ ++ -stim_times using TR=2.5 s for stimulus timing conversion ++ -stim_times using TR=2.5 s for any -iresp output datasets ++ [you can alter the -iresp TR via the -TR_times option] @@ -686,15 +682,13 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D ++ ** GUESSED ** -stim_times 3 using LOCAL times ++ ** GUESSED ** -stim_times 4 using LOCAL times ++ ** GUESSED ** -stim_times 5 using LOCAL times -*+ WARNING: -gltsym: Can't interpret '*' scale factor in '-*Response_Control' -- replaced by 1 -*+ WARNING: -gltsym: '*' scale factor in '-*Response_Control' not at start of string? ------------------------------------------------------------ -GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': - 0 0 0 0 0 0.5 0.5 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 +GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control': + 0 0 0 0 0 0.5 0.5 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 -++ Number of time points: 238 (before censor) ; 236 (after) +++ Number of time points: 237 (no censoring) + Number of parameters: 22 [17 baseline ; 5 signal] -++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) +++ Memory required for output bricks = 215,638,200 bytes (about 216 million [mega]) ++ Wrote matrix image to file X.jpg ++ Wrote matrix values to file X.xmat.1D ++ ========= Things you can do with the matrix file ========= @@ -709,34 +703,34 @@ GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': ++ (c) Synthesis of sub-model datasets using 3dSynthesize ++ ========================================================== ++ Wrote matrix values to file X.nocensor.xmat.1D -++ ----- Signal+Baseline matrix condition [X] (236x22): 5.23887 ++ VERY GOOD ++ -++ ----- Signal-only matrix condition [X] (236x5): 1.40108 ++ VERY GOOD ++ -++ ----- Baseline-only matrix condition [X] (236x17): 5.1314 ++ VERY GOOD ++ -++ ----- stim_base-only matrix condition [X] (236x12): 3.87376 ++ VERY GOOD ++ -++ ----- polort-only matrix condition [X] (236x5): 1.05506 ++ VERY GOOD ++ -++ +++++ Matrix inverse average error = 2.74977e-15 ++ VERY GOOD ++ +++ ----- Signal+Baseline matrix condition [X] (237x22): 5.15025 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (237x5): 1.40108 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (237x17): 5.05637 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (237x12): 3.89229 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (237x5): 1.01409 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 2.52458e-15 ++ VERY GOOD ++ ++ Matrix setup time = 0.66 s -++ Calculations starting; elapsed time=1.556 +++ Calculations starting; elapsed time=1.251 ++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=20.792 -++ Smallest FDR q [0 Full_Fstat] = 4.80713e-13 -++ Smallest FDR q [2 Correct_Task#0_Tstat] = 8.98106e-12 -++ Smallest FDR q [3 Correct_Task_Fstat] = 8.98004e-12 -++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 1.82055e-05 -++ Smallest FDR q [6 Incorrect_Task_Fstat] = 1.82049e-05 -++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.002104 -++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.0021038 -++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 0.008893 -++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.00889248 -++ Smallest FDR q [14 Response_Control#0_Tstat] = 1.42207e-12 -++ Smallest FDR q [15 Response_Control_Fstat] = 1.422e-12 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 7.67542e-13 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 7.67601e-13 +++ Calculations finished; elapsed time=16.434 +++ Smallest FDR q [0 Full_Fstat] = 1.58949e-13 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 1.14183e-12 +++ Smallest FDR q [3 Correct_Task_Fstat] = 1.14177e-12 +++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 2.37228e-06 +++ Smallest FDR q [6 Incorrect_Task_Fstat] = 2.37223e-06 +++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.00142543 +++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.0014255 +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 0.00041271 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 0.000412699 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 4.63842e-13 +++ Smallest FDR q [15 Response_Control_Fstat] = 4.63842e-13 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 7.39797e-06 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 7.39878e-06 ++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + created 13 FDR curves in bucket header ++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK ++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK -++ #Flops=4.31862e+10 Average Dot Product=37.4801 +++ #Flops=4.33688e+10 Average Dot Product=37.4925 if ( 0 != 0 ) then 1d_tool.py -show_cormat_warnings -infile X.xmat.1D tee out.cormat_warn.txt @@ -749,12 +743,12 @@ Warnings regarding Correlation Matrix: X.xmat.1D 3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD ++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -++ elapsed time = 0.5 s -3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..237] +++ elapsed time = 0.3 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[0..236] ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.signal.all+tlrc.BRIK -3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..237] +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[0..236] ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.noise.all+tlrc.BRIK @@ -768,14 +762,14 @@ Warnings regarding Correlation Matrix: X.xmat.1D ++ Output dataset ./rm.errts.unit+tlrc.BRIK 3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc ++ 3dmaskave: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -+++ 33146 voxels survive the mask ++++ 33173 voxels survive the mask 3dTstat -sos -prefix - gmean.errts.unit.1D' ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D --- GCOR = 0.051467 +-- GCOR = 0.0592107 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands @@ -804,16 +798,16 @@ foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..237] +if ( 0..236 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[0..236] ++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 33146 +++ Number of voxels in mask = 33173 *+ WARNING: removed 239 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 236 time points - + detrending done (3.15 CPU s thus far) -++ start ACF calculations out to radius = 19.19 mm - + ACF done (39.49 CPU s thus far) +++ detrending start: 17 baseline funcs, 237 time points + + detrending done (2.92 CPU s thus far) +++ start ACF calculations out to radius = 19.39 mm + + ACF done (37.41 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. @@ -834,24 +828,24 @@ set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.824135 3.58341 14.0583 9.17803 -average epits ACF blurs: 0.824135 3.58341 14.0583 9.17803 -echo 0.824135 3.58341 14.0583 9.17803 # epits ACF blur estimates +echo average epits ACF blurs: 0.788541 3.59942 12.8144 9.29002 +average epits ACF blurs: 0.788541 3.59942 12.8144 9.29002 +echo 0.788541 3.59942 12.8144 9.29002 # epits ACF blur estimates touch blur.errts.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..237] +if ( 0..236 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[0..236] ++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 33146 +++ Number of voxels in mask = 33173 *+ WARNING: removed 239 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 236 time points - + detrending done (2.94 CPU s thus far) -++ start ACF calculations out to radius = 19.08 mm - + ACF done (38.80 CPU s thus far) +++ detrending start: 17 baseline funcs, 237 time points + + detrending done (2.86 CPU s thus far) +++ start ACF calculations out to radius = 19.25 mm + + ACF done (37.78 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. @@ -872,9 +866,9 @@ set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.863014 3.61002 15.013 9.12366 -average errts ACF blurs: 0.863014 3.61002 15.013 9.12366 -echo 0.863014 3.61002 15.013 9.12366 # errts ACF blur estimates +echo average errts ACF blurs: 0.838314 3.62939 13.5545 9.21637 +average errts ACF blurs: 0.838314 3.62939 13.5545 9.21637 +echo 0.838314 3.62939 13.5545 9.21637 # errts ACF blur estimates gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD gen_ss_review_scripts.py -mot_limit 0.5 -exit0 ++ writing ss review basic: @ss_review_basic @@ -886,51 +880,50 @@ if ( -e @ss_review_basic ) ./@ss_review_basic ./@ss_review_basic subject ID : sub_03 -TRs removed (per run) : 0 +TRs removed (per run) : 1 num stim classes provided : 5 final anatomy dset : anat_final.sub_03+tlrc.HEAD final stats dset : stats.sub_03+tlrc.HEAD final voxel resolution : 4.000000 4.000000 4.000000 motion limit : 0.5 -num TRs above mot limit : 1 -average motion (per TR) : 0.0937926 -average censored motion : 0.0889158 -max motion displacement : 1.69106 -max censored displacement : 1.69012 +num TRs above mot limit : 0 +average motion (per TR) : 0.0785451 +average censored motion : 0.0785451 +max motion displacement : 1.72403 +max censored displacement : 1.72403 outlier limit : 0.1 -average outlier frac (TR) : 0.00559353 -num TRs above out limit : 1 +average outlier frac (TR) : 0.0019311 +num TRs above out limit : 0 num runs found : 1 -num TRs per run : 238 -num TRs per run (applied) : 236 -num TRs per run (censored): 2 -fraction censored per run : 0.00840336 -TRs total (uncensored) : 238 -TRs total : 236 +num TRs per run : 237 +num TRs per run (applied) : 237 +num TRs per run (censored): 0 +fraction censored per run : 0 +TRs total (uncensored) : 237 +TRs total : 237 degrees of freedom used : 22 -degrees of freedom left : 214 +degrees of freedom left : 215 -TRs censored : 2 -censor fraction : 0.008403 +TRs censored : 0 +censor fraction : 0.000000 num regs of interest : 5 num TRs per stim (orig) : 78 56 46 19 79 num TRs censored per stim : 0 0 0 0 0 fraction TRs censored : 0.000 0.000 0.000 0.000 0.000 -ave mot per sresp (orig) : 0.086607 0.082908 0.080591 0.071212 0.078827 -ave mot per sresp (cens) : 0.086607 0.082908 0.080591 0.071212 0.078827 +ave mot per sresp (orig) : 0.074047 0.073782 0.065246 0.067506 0.063698 +ave mot per sresp (cens) : 0.074047 0.073782 0.065246 0.067506 0.063698 -TSNR average : 160.267 -global correlation (GCOR) : 0.051467 -anat/EPI mask Dice coef : 0.881952 -maximum F-stat (masked) : 48.5706 -blur estimates (ACF) : 0.863014 3.61002 15.013 +TSNR average : 176.458 +global correlation (GCOR) : 0.0592107 +anat/EPI mask Dice coef : 0.882018 +maximum F-stat (masked) : 83.3662 +blur estimates (ACF) : 0.838314 3.62939 13.5545 blur estimates (FWHM) : 0 0 0 -** TR #0 outliers: possible pre-steady state TRs in run 01 cd .. echo execution finished: `date` date -execution finished: Fri Aug 4 13:00:11 EDT 2017 +execution finished: Sat Aug 5 16:42:02 EDT 2017 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 b/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 old mode 100644 new mode 100755 index 04780a2..c782fff --- a/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 +++ b/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Fri Aug 4 12:55:45 2017" +echo "auto-generated by afni_proc.py, Sat Aug 5 16:37:42 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -59,12 +59,12 @@ cp /Users/mli/Desktop/playground/timing_sub-03_ses-retest_Correct_Task.1D # ============================ auto block: tcat ============================ # apply 3dTcat to copy input dsets to results dir, while -# removing the first 0 TRs +# removing the first 1 TRs 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ - /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[0..$]' + /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz'[1..$]' # and make note of repetitions (TRs) per run -set tr_counts = ( 238 ) +set tr_counts = ( 237 ) # ------------------------------------------------------- # enter the results directory (can begin processing data) @@ -92,6 +92,7 @@ cat outcount.r*.1D > outcount_rall.1D # time shift data so all slice timing is the same foreach run ( $runs ) 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + -tpattern alt+z \ pb00.$subj.r$run.tcat+orig end @@ -305,7 +306,7 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ - -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control' \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -459,7 +460,7 @@ echo "execution finished: `date`" # afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ # tshift align tlrc volreg blur mask scale regress -copy_anat \ # /Users/mli/Desktop/playground/sub-03/ses-retest/anat/sub-03_ses-retest_T1w.nii.gz \ -# -tcat_remove_first_trs 0 -dsets \ +# -tcat_remove_first_trs 1 -tshift_opts_ts -tpattern alt+z -dsets \ # /Users/mli/Desktop/playground/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz \ # -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ # -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times \ @@ -472,6 +473,6 @@ echo "execution finished: `date`" # No_Response_Task Response_Control -regress_basis GAM \ # -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ # -regress_opts_3dD -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ -# -*Response_Control' -glt_label 1 Landmark-Detection \ +# -Response_Control' -glt_label 1 Landmark-Detection \ # -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ # -regress_est_blur_errts -regress_run_clustsim no diff --git a/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 index aea25a4..59fa428 100644 --- a/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 +++ b/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 @@ -17,7 +17,8 @@ afni_proc.py -subj_id $subj \ -script proc.$subj -scr_overwrite \ -blocks tshift align tlrc volreg blur mask scale regress \ -copy_anat $anat_dir/sub-03_ses-test_T1w.nii.gz \ - -tcat_remove_first_trs 0 \ + -tcat_remove_first_trs 1 \ + -tshift_opts_ts -tpattern alt+z \ -dsets $epi_dir/sub-03_ses-test_task-linebisection_bold.nii.gz \ -tlrc_base MNI_avg152T1+tlrc \ -volreg_align_to third \ @@ -38,7 +39,7 @@ afni_proc.py -subj_id $subj \ -regress_apply_mot_types demean deriv \ -regress_opts_3dD \ -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ - -*Response_Control' -glt_label 1 Landmark-Detection \ + -Response_Control' -glt_label 1 Landmark-Detection \ -regress_make_ideal_sum sum_ideal.1D \ -regress_est_blur_epits \ -regress_est_blur_errts \ diff --git a/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 index 647e95b..c85d9ed 100644 --- a/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 +++ b/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 @@ -3,11 +3,13 @@ set anat_dir = /Users/mli/Desktop/playground/sub-03/ses-test/anat set epi_dir = /Users/mli/Desktop/playground/sub-03/ses-test/func set subj = sub_03 set group_id = test -afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 0 -dsets /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task - -*Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no +afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -copy_anat /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz -tcat_remove_first_trs 1 -tshift_opts_ts -tpattern alt+z -dsets /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D -regress_stim_labels Correct_Task Incorrect_Task No_Response_Control No_Response_Task Response_Control -regress_basis GAM -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv -regress_opts_3dD -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task + -Response_Control -glt_label 1 Landmark-Detection -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -- applying orig view as +orig --- tcat: reps is now 238 -++ updating polort to 4, from run len 595.0 s +** warning: removing first 1 TRs from beginning of each run + --> the stimulus timing files must reflect the removal of these TRs +-- tcat: reps is now 237 +++ updating polort to 4, from run len 592.5 s -- volreg: using base dset vr_base+orig ++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 4 mm tlrc voxels -- applying anat warps to 1 dataset(s): sub-03_ses-test_T1w diff --git a/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 index 59d69f8..6b7e8d9 100644 --- a/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 +++ b/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 @@ -1,10 +1,10 @@ -echo auto-generated by afni_proc.py, Fri Aug 4 12:51:09 2017 -auto-generated by afni_proc.py, Fri Aug 4 12:51:09 2017 +echo auto-generated by afni_proc.py, Sat Aug 5 16:33:35 2017 +auto-generated by afni_proc.py, Sat Aug 5 16:33:35 2017 echo (version 5.15, April 25, 2017) (version 5.15, April 25, 2017) echo execution started: `date` date -execution started: Fri Aug 4 12:51:13 EDT 2017 +execution started: Sat Aug 5 16:33:36 EDT 2017 afni -ver Precompiled binary macosx_10.7_local: Jul 27 2017 (Version AFNI_17.2.05) afni_history -check_date 23 Sep 2016 @@ -23,10 +23,10 @@ mkdir sub_03.results/stimuli cp /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Incorrect_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Control.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_No_Response_Task.1D /Users/mli/Desktop/playground/timing_sub-03_ses-test_Response_Control.1D sub_03.results/stimuli 3dcopy /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz sub_03.results/sub-03_ses-test_T1w ++ 3dcopy: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[0..$] +3dTcat -prefix sub_03.results/pb00.sub_03.r01.tcat /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz[1..$] ++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ elapsed time = 0.8 s -set tr_counts = ( 238 ) +set tr_counts = ( 237 ) cd sub_03.results touch out.pre_ss_warn.txt foreach run ( 01 ) @@ -40,15 +40,13 @@ foreach run ( 01 ) on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. -++ 17837 voxels passed mask/clip +++ 17835 voxels passed mask/clip if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then 1deval -a outcount.r01.1D{0} -expr step(a-0.4) -echo ** TR #0 outliers: possible pre-steady state TRs in run 01 -endif end cat outcount.r01.1D foreach run ( 01 ) -3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift pb00.sub_03.r01.tcat+orig +3dTshift -tzero 0 -quintic -prefix pb01.sub_03.r01.tshift -tpattern alt+z pb00.sub_03.r01.tcat+orig ++ 3dTshift: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub_03.r01.tcat+orig.BRIK, @@ -58,8 +56,6 @@ foreach run ( 01 ) on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub_03.r01.tcat+orig.BRIK is 6.153038 degrees from plumb. -*+ WARNING: dataset is already aligned in time! -*+ WARNING: ==>> output dataset is just a copy of input dataset end 3dbucket -prefix vr_base pb01.sub_03.r01.tshift+orig[2] ++ 3dbucket: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -127,22 +123,22 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ Authored by: Emperor Zhark ++ Loading dataset ./__tt_vr_base_ts_rs+orig ++ Forming automask - + Fixed clip level = 722.140930 - + Used gradual clip level = 624.995605 .. 827.664490 - + Number voxels above clip level = 1139938 + + Fixed clip level = 720.187500 + + Used gradual clip level = 622.540100 .. 825.700012 + + Number voxels above clip level = 1139151 + Clustering voxels ... - + Largest cluster has 1138291 voxels + + Largest cluster has 1137868 voxels + Clustering voxels ... - + Largest cluster has 1137874 voxels - + Filled 374 voxels in small holes; now have 1138248 voxels - + Filled 17631 voxels in large holes; now have 1155879 voxels + + Largest cluster has 1137453 voxels + + Filled 420 voxels in small holes; now have 1137873 voxels + + Filled 17758 voxels in large holes; now have 1155631 voxels + Clustering voxels ... - + Largest cluster has 1155874 voxels + + Largest cluster has 1155621 voxels + Clustering non-brain voxels ... + Clustering voxels ... - + Largest cluster has 15251279 voxels - + Mask now has 1155874 voxels -++ 1155874 voxels in the mask [out of 16407153: 7.04%] + + Largest cluster has 15251532 voxels + + Mask now has 1155621 voxels +++ 1155621 voxels in the mask [out of 16407153: 7.04%] ++ first 71 x-planes are zero [from R] ++ last 75 x-planes are zero [from L] ++ first 33 y-planes are zero [from A] @@ -151,13 +147,13 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ last 36 z-planes are zero [from S] ++ applying mask to original data ++ Writing masked data -++ CPU time = 3.610000 sec +++ CPU time = 3.400000 sec #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_ts_rs_ns+orig -#++ Applying threshold of 1890.000000 on /Users/mli/Desktop/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig +#++ Applying threshold of 1884.000000 on /Users/mli/Desktop/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_vr_base_ts_rs_ns+orig #Script is running (command trimmed): - 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1890.000000))' + 3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/1884.000000))' ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands #++ Aligning anat data to epi data @@ -170,8 +166,8 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ Loading datasets ++ 1350442 voxels in -source_automask+4 ++ Zero-pad: not needed -++ 1155874 voxels [7.0%] in weight mask -++ Number of points for matching = 1155874 +++ 1155621 voxels [7.0%] in weight mask +++ Number of points for matching = 1155621 ++ Local correlation: blok type = 'RHDD(6.54321)' ++ shift param auto-range: -89.2..89.2 -69.3..69.3 -86.7..86.7 + Range param#4 [z-angle] = -6.000000 .. 6.000000 @@ -184,31 +180,31 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf ++ Normalized convergence radius = 0.001000 ++ OpenMP thread count = 4 ++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= -++ ========== sub-brick #0 ========== [total CPU to here=9.4 s] +++ ========== sub-brick #0 ========== [total CPU to here=9.2 s] ++ *** Fine pass begins *** + * Enter alignment setup routine + - copying base image + - copying source image + - copying weight image - + - using 1155874 points from base image [use_all=0] + + - using 1155621 points from base image [use_all=0] + * Exit alignment setup routine - + 1095215 total points stored in 2075 'RHDD(6.54321)' bloks - + - Initial cost = -0.096907 + + 1095318 total points stored in 2076 'RHDD(6.54321)' bloks + + - Initial cost = -0.091164 + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 -*************************************************************************************************************************************************************************************************************************************************************************************************** - + - Finalish cost = -0.235911 ; 645 funcs -** - + - Final cost = -0.235912 ; 97 funcs +************************************************************************************************************************************************************************************************************** + + - Finalish cost = -0.223788 ; 478 funcs +* + + - Final cost = -0.223788 ; 109 funcs + Final fine fit Parameters: - x-shift= 0.2099 y-shift=-0.6560 z-shift=-1.7075 - z-angle=-0.6314 x-angle= 4.7459 y-angle=-1.0126 - x-scale= 0.9677 y-scale= 0.9751 z-scale= 1.0200 - y/x-shear=-0.0038 z/x-shear= 0.0093 z/y-shear= 0.0929 - + - Fine net CPU time = 48.8 s + x-shift= 0.1988 y-shift=-0.6640 z-shift=-1.7061 + z-angle=-0.6160 x-angle= 4.7517 y-angle=-1.0181 + x-scale= 0.9680 y-scale= 0.9748 z-scale= 1.0199 + y/x-shear=-0.0035 z/x-shear= 0.0100 z/y-shear= 0.0924 + + - Fine net CPU time = 38.6 s ++ Computing output image -++ image warp: parameters = 0.2099 -0.6560 -1.7075 -0.6314 4.7459 -1.0126 0.9677 0.9751 1.0200 -0.0038 0.0093 0.0929 +++ image warp: parameters = 0.1988 -0.6640 -1.7061 -0.6160 4.7517 -1.0181 0.9680 0.9748 1.0199 -0.0035 0.0100 0.0924 ++ Wrote -1Dmatrix_save ./sub-03_ses-test_T1w_al_junk_e2a_only_mat.aff12.1D -++ 3dAllineate: total CPU time = 60.4 sec Elapsed = 35.4 +++ 3dAllineate: total CPU time = 50.5 sec Elapsed = 31.9 ++ ########################################################### ++ # Please check results visually for alignment quality # ++ ########################################################### @@ -250,8 +246,8 @@ align_epi_anat.py -anat2epi -anat sub-03_ses-test_T1w+orig -save_skullstrip -suf + * Exit alignment setup routine ++ using -1Dmatrix_apply ++ Computing output image -++ image warp: parameters = 0.9643 -0.0770 -0.0643 8.3030 0.0414 0.9701 -0.0701 -8.0767 0.0578 0.0003 1.0212 -4.7196 -++ 3dAllineate: total CPU time = 2.4 sec Elapsed = 1.8 +++ image warp: parameters = 0.9647 -0.0767 -0.0644 8.2560 0.0414 0.9697 -0.0702 -8.0361 0.0573 0.0012 1.0210 -4.6777 +++ 3dAllineate: total CPU time = 2.1 sec Elapsed = 1.8 ++ ########################################################### #++ Creating final output: skullstripped anat data copying from dataset /Users/mli/Desktop/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/__tt_sub-03_ses-test_T1w_ns+orig to /Users/mli/Desktop/playground/Exp-2/subject_results/group.test/subj.sub_03/sub_03.results/sub-03_ses-test_T1w_ns+orig @@ -430,18 +426,18 @@ foreach run ( 01 ) ++ Reading input dataset ./pb01.sub_03.r01.tshift+orig.BRIK ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp - + Automask has 18932 voxels - + 3319 voxels left in -maxdisp mask after erosion + + Automask has 18925 voxels + + 3320 voxels left in -maxdisp mask after erosion ++ Initializing alignment base -++ Starting final pass on 238 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237.. -++ CPU time for realignment=9.03 s [=0.0379 s/sub-brick] -++ Min : roll=-0.125 pitch=-0.838 yaw=-0.100 dS=-1.314 dL=-0.122 dP=-0.602 -++ Mean: roll=+0.244 pitch=-0.353 yaw=+1.492 dS=+1.594 dL=+0.625 dP=-0.273 -++ Max : roll=+0.752 pitch=+0.977 yaw=+2.780 dS=+2.627 dL=+1.582 dP=+0.307 +++ Starting final pass on 237 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236.. +++ CPU time for realignment=8.6 s [=0.0363 s/sub-brick] +++ Min : roll=-0.099 pitch=-0.764 yaw=-0.000 dS=-0.132 dL=-0.087 dP=-0.636 +++ Mean: roll=+0.252 pitch=-0.320 yaw=+1.503 dS=+1.540 dL=+0.638 dP=-0.281 +++ Max : roll=+0.752 pitch=+1.091 yaw=+2.787 dS=+2.524 dL=+1.597 dP=+0.138 ++ Max displacements (mm) for each sub-brick: - 1.52(0.00) 0.25(1.43) 0.00(0.25) 0.40(0.40) 0.85(0.46) 0.73(0.21) 0.34(0.44) 0.80(0.50) 0.82(0.05) 0.97(0.22) 0.87(0.11) 1.14(0.27) 1.23(0.16) 1.37(0.28) 1.26(0.16) 1.40(0.16) 1.34(0.10) 1.53(0.22) 1.37(0.18) 1.47(0.12) 1.43(0.07) 1.39(0.23) 1.43(0.08) 1.54(0.12) 1.51(0.07) 1.54(0.05) 1.54(0.05) 1.63(0.10) 1.61(0.10) 1.65(0.10) 1.58(0.17) 1.71(0.19) 1.62(0.17) 1.77(0.19) 1.79(0.08) 1.95(0.18) 1.92(0.03) 2.10(0.19) 2.00(0.14) 2.23(0.27) 2.03(0.25) 2.26(0.23) 2.09(0.31) 2.37(0.33) 2.12(0.35) 2.37(0.41) 2.24(0.24) 2.31(0.12) 2.16(0.21) 1.75(0.92) 1.69(0.29) 1.26(0.56) 0.82(1.06) 1.02(0.77) 1.77(1.06) 2.02(2.37) 2.06(0.37) 3.95(3.75) 3.32(0.64) 3.59(1.18) 3.39(0.23) 3.42(0.10) 3.04(0.50) 2.05(1.20) 2.22(0.39) 3.63(1.92) 1.23(3.45) 1.76(1.27) 2.43(0.95) 2.71(0.28) 2.77(0.09) 3.03(0.29) 2.84(0.35) 2.83(0.31) 2.96(0.54) 2.87(0.19) 2.94(0.08) 2.89(0.08) 2.81(0.17) 2.77(0.22) 2.81(0.14) 2.95(0.14) 2.95(0.08) 3.06(0.14) 3.10(0.07) 3.01(0.16) 3.28(0.30) 3.28(0.02) 3.43(0.18) 3.45(0.06) 3.56(0.13) 3.57(0.06) 3.65(0.08) 3.70(0.08) 3.59(0.15) 3.66(0.17) 3.19(0.76) 3.37(0.22) 3.17(0.24) 3.47(0.52) 3.40(0.19) 3.40(0.24) 3.00(0.74) 3.66(1.10) 3.60(0.37) 3.73(0.37) 3.84(0.14) 3.89(0.14) 3.87(0.11) 3.89(0.14) 3.80(0.15) 3.73(0.12) 3.58(0.20) 3.69(0.13) 3.73(0.21) 3.94(0.25) 3.97(0.12) 4.13(0.21) 4.09(0.08) 4.18(0.13) 4.31(0.20) 4.11(0.27) 4.31(0.31) 4.13(0.23) 3.87(0.38) 3.82(0.12) 3.71(0.29) 3.74(0.07) 3.87(0.25) 3.89(0.04) 4.03(0.17) 4.19(0.19) 4.11(0.13) 4.27(0.21) 4.04(0.40) 4.27(0.29) 4.15(0.16) 4.26(0.14) 4.45(0.22) 4.07(0.63) 4.50(0.54) 4.38(0.16) 4.90(0.59) 4.74(0.24) 4.66(0.13) 4.65(0.20) 4.60(0.17) 4.66(0.26) 4.53(0.16) 4.73(0.26) 4.77(0.11) 4.69(0.13) 4.51(0.35) 4.52(0.15) 4.72(0.22) 4.55(0.21) 4.72(0.18) 4.65(0.12) 4.70(0.06) 4.79(0.14) 5.04(0.26) 4.95(0.48) 5.70(1.30) 5.19(0.83) 5.18(0.35) 5.42(0.26) 5.61(0.36) 5.74(0.24) 5.78(0.09) 5.89(0.15) 5.83(0.13) 5.83(0.10) 5.80(0.06) 5.73(0.25) 5.59(0.28) 5.50(0.39) 5.51(0.31) 5.49(0.23) 5.37(0.20) 5.45(0.10) 5.55(0.10) 5.64(0.17) 5.69(0.08) 5.62(0.12) 5.73(0.14) 5.69(0.09) 5.45(0.51) 5.28(0.22) 5.59(0.71) 5.03(0.73) 4.43(0.85) 4.81(0.47) 5.08(0.37) 5.55(0.73) 5.80(0.42) 5.82(0.13) 5.79(0.07) 6.03(0.40) 5.85(0.36) 5.89(0.09) 5.76(0.31) 5.95(0.23) 6.06(0.14) 5.97(0.17) 6.01(0.08) 6.11(0.29) 6.11(0.07) 6.21(0.16) 6.12(0.24) 6.18(0.07) 6.15(0.16) 6.15(0.10) 6.11(0.10) 6.23(0.23) 6.11(0.23) 6.18(0.10) 6.13(0.07) 6.12(0.08) 6.14(0.15) 6.04(0.16) 6.16(0.16) 6.15(0.11) 5.93(0.28) 6.00(0.08) 5.90(0.20) 5.86(0.40) 5.77(0.25) 6.07(0.68) 6.04(0.20) 5.99(0.20) 6.28(0.40) 6.31(0.10) 6.35(0.22) 6.33(0.19) 6.10(0.42) 6.01(0.25) 6.16(0.24) 6.13(0.07) -++ Max displacement in automask = 6.35 (mm) at sub-brick 232 -++ Max delta displ in automask = 3.75 (mm) at sub-brick 57 + 0.39(0.00) 0.36(0.73) 0.00(0.36) 0.63(0.63) 0.68(0.12) 0.32(0.39) 0.49(0.19) 0.69(0.22) 0.80(0.17) 0.77(0.07) 0.87(0.11) 1.05(0.21) 1.19(0.18) 1.18(0.10) 1.20(0.06) 1.23(0.03) 1.31(0.12) 1.33(0.10) 1.29(0.05) 1.34(0.08) 1.30(0.16) 1.25(0.18) 1.38(0.16) 1.41(0.06) 1.39(0.05) 1.47(0.08) 1.44(0.10) 1.57(0.15) 1.50(0.11) 1.56(0.08) 1.52(0.08) 1.57(0.08) 1.57(0.11) 1.70(0.15) 1.78(0.09) 1.83(0.09) 1.93(0.10) 1.96(0.05) 2.01(0.12) 2.07(0.10) 2.02(0.15) 2.12(0.14) 2.12(0.08) 2.15(0.06) 2.19(0.17) 2.21(0.08) 2.19(0.10) 2.18(0.12) 1.95(0.43) 1.65(1.28) 1.81(1.18) 0.91(1.59) 0.84(0.26) 1.58(1.54) 1.51(1.33) 2.08(1.14) 2.54(2.35) 4.01(2.10) 3.02(1.06) 3.51(0.78) 3.27(0.29) 3.24(0.12) 2.33(1.09) 2.04(0.58) 2.77(1.27) 2.07(0.91) 1.23(1.41) 2.13(1.65) 2.55(0.48) 2.61(0.10) 2.79(0.21) 2.87(0.10) 2.69(0.63) 2.86(0.46) 2.78(0.20) 2.80(0.09) 2.86(0.10) 2.74(0.19) 2.71(0.23) 2.69(0.07) 2.77(0.09) 2.81(0.09) 2.84(0.06) 3.03(0.22) 2.87(0.20) 3.06(0.19) 3.20(0.15) 3.24(0.05) 3.37(0.18) 3.40(0.05) 3.51(0.12) 3.48(0.05) 3.62(0.16) 3.55(0.08) 3.53(0.16) 3.33(0.44) 3.18(0.42) 3.17(0.09) 3.29(0.30) 3.36(0.08) 3.42(0.11) 3.09(0.86) 3.16(0.30) 3.64(0.63) 3.61(0.19) 3.70(0.14) 3.81(0.18) 3.81(0.09) 3.82(0.05) 3.78(0.13) 3.72(0.11) 3.57(0.23) 3.56(0.07) 3.63(0.12) 3.78(0.23) 3.90(0.18) 3.95(0.11) 4.10(0.18) 3.99(0.23) 4.25(0.31) 4.11(0.21) 4.14(0.07) 4.20(0.15) 3.91(0.41) 3.78(0.20) 3.72(0.13) 3.61(0.37) 3.73(0.29) 3.84(0.14) 3.84(0.03) 4.10(0.33) 4.06(0.10) 4.12(0.08) 4.08(0.14) 4.05(0.12) 4.20(0.20) 4.04(0.21) 4.41(0.43) 4.12(0.54) 4.20(0.16) 4.38(0.22) 4.53(0.19) 4.86(0.35) 4.55(0.38) 4.62(0.12) 4.52(0.17) 4.57(0.11) 4.52(0.18) 4.52(0.11) 4.77(0.38) 4.63(0.18) 4.55(0.20) 4.40(0.22) 4.57(0.23) 4.59(0.02) 4.52(0.07) 4.65(0.14) 4.57(0.13) 4.72(0.18) 4.82(0.10) 4.90(0.24) 5.30(0.79) 5.50(0.43) 4.99(1.04) 5.21(0.24) 5.46(0.32) 5.64(0.36) 5.66(0.07) 5.83(0.19) 5.76(0.14) 5.76(0.16) 5.73(0.05) 5.73(0.12) 5.58(0.27) 5.46(0.28) 5.45(0.40) 5.46(0.25) 5.37(0.21) 5.32(0.09) 5.45(0.18) 5.51(0.08) 5.68(0.25) 5.56(0.16) 5.63(0.07) 5.66(0.05) 5.57(0.25) 5.19(0.64) 5.48(0.78) 5.32(0.22) 4.57(1.04) 4.55(0.14) 4.88(0.39) 5.27(0.59) 5.64(0.60) 5.82(0.26) 5.70(0.27) 5.88(0.33) 5.87(0.05) 5.80(0.19) 5.75(0.11) 5.78(0.23) 5.98(0.27) 5.96(0.11) 5.92(0.10) 6.02(0.29) 6.04(0.11) 6.10(0.12) 6.10(0.10) 6.10(0.06) 6.10(0.08) 6.11(0.03) 6.03(0.13) 6.13(0.13) 6.12(0.15) 6.07(0.13) 6.13(0.15) 6.03(0.17) 6.10(0.14) 6.03(0.09) 6.01(0.05) 6.16(0.23) 5.98(0.22) 5.86(0.22) 5.94(0.10) 5.83(0.15) 5.68(0.26) 5.88(0.46) 6.00(0.25) 5.97(0.26) 6.05(0.12) 6.24(0.32) 6.26(0.17) 6.33(0.24) 6.15(0.32) 5.98(0.38) 6.01(0.05) 6.10(0.15) +++ Max displacement in automask = 6.33 (mm) at sub-brick 232 +++ Max delta displ in automask = 2.35 (mm) at sub-brick 56 ++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK 3dcalc -overwrite -a pb01.sub_03.r01.tshift+orig -expr 1 -prefix rm.epi.all1 ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -467,9 +463,9 @@ cat_matvec -ONELINE sub-03_ses-test_T1w_ns+tlrc::WARP_DATA -I sub-03_ses-test_T1 ++ master dataset for output = base ++ changing output grid spacing to 4.0000 mm ++ OpenMP thread count = 4 -++ ========== Applying transformation to 238 sub-bricks ========== -volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK -++ 3dAllineate: total CPU time = 5.9 sec Elapsed = 3.8 +++ ========== Applying transformation to 237 sub-bricks ========== +volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236Ø++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK +++ 3dAllineate: total CPU time = 6.0 sec Elapsed = 4.1 ++ ########################################################### 3dAllineate -base sub-03_ses-test_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 4 -final NN -quiet -prefix rm.epi.1.r01 ++ 3dAllineate: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] @@ -484,7 +480,7 @@ volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20. ++ Oblique dataset:./rm.epi.all1+orig.BRIK is 6.153038 degrees from plumb. ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (LPI); source=Left handed (RPI) -++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 3.1 +++ 3dAllineate: total CPU time = 3.5 sec Elapsed = 3.2 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox @@ -532,31 +528,31 @@ tee out.allcostX.txt ++ Base dataset: ./final_epi_vr_base+tlrc.HEAD ++ Loading datasets ++ 223015 voxels in source_automask+0 -++ Zero-pad: xbot=2 xtop=2 +++ Zero-pad: xbot=1 xtop=2 ++ Zero-pad: ybot=0 ytop=1 ++ Zero-pad: zbot=1 ztop=1 ++ Computing -autobox -++ 113223 voxels [89.4%] in weight mask -++ Number of points for matching = 53214 +++ 111006 voxels [89.5%] in weight mask +++ Number of points for matching = 52172 ++ Local correlation: blok type = 'RHDD(14.76)' *+ WARNING: No output dataset will be calculated ++ OpenMP thread count = 4 volume 0Ø + initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 ++ allcost output: init #0 - ls = 0.183754 - sp = 0.30567 - mi = -0.534639 - crM = 0.0839806 - nmi = 0.868199 - je = 3.52175 - hel = -0.107071 - crA = 0.290078 - crU = 0.302909 - lss = 0.816246 - lpc = 0.339594 - lpa = 0.660406 - lpc+ = 0.540057 - ncd = 0.974675 + ls = 0.18269 + sp = 0.302214 + mi = -0.542443 + crM = 0.0831465 + nmi = 0.868037 + je = 3.5681 + hel = -0.108642 + crA = 0.288642 + crU = 0.301598 + lss = 0.81731 + lpc = 0.373345 + lpa = 0.626655 + lpc+ = 0.57125 + ncd = 0.966558 ++ 3dAllineate: total CPU time = 0.3 sec Elapsed = 0.4 ++ ########################################################### 3dAllineate -source sub-03_ses-test_T1w+orig -master anat_final.sub_03+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped @@ -585,7 +581,7 @@ volume 0 + (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.) + wsinc5 CUBE(5) mask has 1000 points ++ Output dataset ./anat_w_skull_warped+tlrc.BRIK -++ 3dAllineate: total CPU time = 3.1 sec Elapsed = 1.3 +++ 3dAllineate: total CPU time = 3.1 sec Elapsed = 1.4 ++ ########################################################### foreach run ( 01 ) 3dmerge -1blur_fwhm 3.0 -doall -prefix pb03.sub_03.r01.blur pb02.sub_03.r01.volreg+tlrc @@ -594,8 +590,8 @@ foreach run ( 01 ) ++ default -1tindex = 1 Program 3dmerge 3dmerge: edit and combine 3D datasets, by RW Cox -++ editing input dataset in memory (49.6 MB) -..............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK +++ editing input dataset in memory (49.4 MB) +.............................................................................................................................................................................................................................................-- Wrote edited dataset: ./pb03.sub_03.r01.blur+tlrc.BRIK end foreach run ( 01 ) @@ -604,37 +600,37 @@ foreach run ( 01 ) ++ Authored by: Emperor Zhark ++ Loading dataset pb03.sub_03.r01.blur+tlrc ++ Forming automask - + Fixed clip level = 721.097839 - + Used gradual clip level = 636.466919 .. 805.468140 - + Number voxels above clip level = 27995 + + Fixed clip level = 720.255432 + + Used gradual clip level = 635.817200 .. 804.311340 + + Number voxels above clip level = 27991 + Clustering voxels ... - + Largest cluster has 27978 voxels + + Largest cluster has 27974 voxels + Clustering voxels ... - + Largest cluster has 27818 voxels - + Filled 108 voxels in small holes; now have 27926 voxels + + Largest cluster has 27811 voxels + + Filled 108 voxels in small holes; now have 27919 voxels + Clustering voxels ... - + Largest cluster has 27926 voxels + + Largest cluster has 27919 voxels + Clustering non-brain voxels ... + Clustering voxels ... - + Largest cluster has 81416 voxels - + Mask now has 27934 voxels + + Largest cluster has 81423 voxels + + Mask now has 27927 voxels ++ Dilating automask + Clustering voxels ... - + Largest cluster has 76286 voxels -++ 33064 voxels in the mask [out of 109350: 30.24%] + + Largest cluster has 76296 voxels +++ 33054 voxels in the mask [out of 109350: 30.23%] ++ first 4 x-planes are zero [from L] ++ last 3 x-planes are zero [from R] ++ first 4 y-planes are zero [from P] ++ last 3 y-planes are zero [from A] ++ first 3 z-planes are zero [from I] ++ last 3 z-planes are zero [from S] -++ CPU time = 0.280000 sec +++ CPU time = 0.250000 sec end 3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_03 ++ processing 1 input datasets... ++ padding all datasets by 0 (for dilations) ++ frac 0 over 1 volumes gives min count 0 -++ voxel limits: 0 clipped, 33064 survived, 76286 were zero +++ voxel limits: 0 clipped, 33054 survived, 76296 were zero ++ writing result full_mask.sub_03... 3dresample -master full_mask.sub_03+tlrc -input sub-03_ses-test_T1w_ns+tlrc -prefix rm.resam.anat 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_03 @@ -650,10 +646,10 @@ tee out.mask_ae_overlap.txt ++ 3dOverlap: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] #A=./full_mask.sub_03+tlrc.BRIK B=./mask_anat.sub_03+tlrc.BRIK #A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A) -33064 30704 35830 27938 5126 2766 15.5033 9.0086 0.9518 0.9265 0.9782 +33054 30704 35804 27954 5100 2750 15.4293 8.9565 0.9508 0.9280 0.9784 3ddot -dodice full_mask.sub_03+tlrc mask_anat.sub_03+tlrc tee out.mask_ae_dice.txt -0.876239 +0.876878 3dresample -master full_mask.sub_03+tlrc -prefix ./rm.resam.group -input /Users/mli/abin/MNI_avg152T1+tlrc 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ no -frac option: defaulting to -union @@ -676,17 +672,17 @@ end 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.5 motion_sub_03 -total number of censored TRs (simple form) = 21 +total number of censored TRs (simple form) = 22 set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D -show_trs_uncensored encoded` 1d_tool.py -infile motion_sub_03_censor.1D -show_trs_uncensored encoded -3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 +3dDeconvolve -input pb04.sub_03.r01.scale+tlrc.HEAD -censor motion_sub_03_censor.1D -polort 4 -num_stimts 17 -stim_times 1 stimuli/timing_sub-03_ses-test_Correct_Task.1D GAM -stim_label 1 Correct_Task -stim_times 2 stimuli/timing_sub-03_ses-test_Incorrect_Task.1D GAM -stim_label 2 Incorrect_Task -stim_times 3 stimuli/timing_sub-03_ses-test_No_Response_Control.1D GAM -stim_label 3 No_Response_Control -stim_times 4 stimuli/timing_sub-03_ses-test_No_Response_Task.1D GAM -stim_label 4 No_Response_Task -stim_times 5 stimuli/timing_sub-03_ses-test_Response_Control.1D GAM -stim_label 5 Response_Control -stim_file 6 motion_demean.1D[0] -stim_base 6 -stim_label 6 roll_01 -stim_file 7 motion_demean.1D[1] -stim_base 7 -stim_label 7 pitch_01 -stim_file 8 motion_demean.1D[2] -stim_base 8 -stim_label 8 yaw_01 -stim_file 9 motion_demean.1D[3] -stim_base 9 -stim_label 9 dS_01 -stim_file 10 motion_demean.1D[4] -stim_base 10 -stim_label 10 dL_01 -stim_file 11 motion_demean.1D[5] -stim_base 11 -stim_label 11 dP_01 -stim_file 12 motion_deriv.1D[0] -stim_base 12 -stim_label 12 roll_02 -stim_file 13 motion_deriv.1D[1] -stim_base 13 -stim_label 13 pitch_02 -stim_file 14 motion_deriv.1D[2] -stim_base 14 -stim_label 14 yaw_02 -stim_file 15 motion_deriv.1D[3] -stim_base 15 -stim_label 15 dS_02 -stim_file 16 motion_deriv.1D[4] -stim_base 16 -stim_label 16 dL_02 -stim_file 17 motion_deriv.1D[5] -stim_base 17 -stim_label 17 dP_02 -gltsym SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control -glt_label 1 Landmark-Detection -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub_03 -errts errts.sub_03 -bucket stats.sub_03 ++ 3dDeconvolve: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ loading dataset pb04.sub_03.r01.scale+tlrc.HEAD -++ STAT automask has 97119 voxels (out of 109350 = 88.8%) +++ STAT automask has 97106 voxels (out of 109350 = 88.8%) ++ Skipping check for initial transients -++ Input polort=4; Longest run=595.0 s; Recommended minimum polort=4 ++ OK ++ +++ Input polort=4; Longest run=592.5 s; Recommended minimum polort=4 ++ OK ++ ++ -stim_times using TR=2.5 s for stimulus timing conversion ++ -stim_times using TR=2.5 s for any -iresp output datasets ++ [you can alter the -iresp TR via the -TR_times option] @@ -696,15 +692,13 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D ++ ** GUESSED ** -stim_times 3 using LOCAL times ++ ** GUESSED ** -stim_times 4 using LOCAL times ++ ** GUESSED ** -stim_times 5 using LOCAL times -*+ WARNING: -gltsym: Can't interpret '*' scale factor in '-*Response_Control' -- replaced by 1 -*+ WARNING: -gltsym: '*' scale factor in '-*Response_Control' not at start of string? ------------------------------------------------------------ -GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': - 0 0 0 0 0 0.5 0.5 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 +GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control': + 0 0 0 0 0 0.5 0.5 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 -++ Number of time points: 238 (before censor) ; 217 (after) +++ Number of time points: 237 (before censor) ; 215 (after) + Number of parameters: 22 [17 baseline ; 5 signal] -++ Memory required for output bricks = 216,513,000 bytes (about 217 million [mega]) +++ Memory required for output bricks = 215,638,200 bytes (about 216 million [mega]) ++ Wrote matrix image to file X.jpg ++ Wrote matrix values to file X.xmat.1D ++ ========= Things you can do with the matrix file ========= @@ -719,34 +713,34 @@ GLT matrix from 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control': ++ (c) Synthesis of sub-model datasets using 3dSynthesize ++ ========================================================== ++ Wrote matrix values to file X.nocensor.xmat.1D -++ ----- Signal+Baseline matrix condition [X] (217x22): 7.87414 ++ VERY GOOD ++ -++ ----- Signal-only matrix condition [X] (217x5): 1.46311 ++ VERY GOOD ++ -++ ----- Baseline-only matrix condition [X] (217x17): 7.75168 ++ VERY GOOD ++ -++ ----- stim_base-only matrix condition [X] (217x12): 6.17475 ++ VERY GOOD ++ -++ ----- polort-only matrix condition [X] (217x5): 1.09587 ++ VERY GOOD ++ -++ +++++ Matrix inverse average error = 1.12762e-14 ++ VERY GOOD ++ -++ Matrix setup time = 0.60 s -++ Calculations starting; elapsed time=1.258 +++ ----- Signal+Baseline matrix condition [X] (215x22): 7.47726 ++ VERY GOOD ++ +++ ----- Signal-only matrix condition [X] (215x5): 1.47181 ++ VERY GOOD ++ +++ ----- Baseline-only matrix condition [X] (215x17): 7.3131 ++ VERY GOOD ++ +++ ----- stim_base-only matrix condition [X] (215x12): 6.12753 ++ VERY GOOD ++ +++ ----- polort-only matrix condition [X] (215x5): 1.09962 ++ VERY GOOD ++ +++ +++++ Matrix inverse average error = 9.39256e-15 ++ VERY GOOD ++ +++ Matrix setup time = 0.54 s +++ Calculations starting; elapsed time=1.143 ++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789. -++ Calculations finished; elapsed time=14.994 -++ Smallest FDR q [0 Full_Fstat] = 1.54028e-12 -++ Smallest FDR q [2 Correct_Task#0_Tstat] = 7.9356e-11 -++ Smallest FDR q [3 Correct_Task_Fstat] = 7.9356e-11 -*+ WARNING: Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.123923 ==> few true single voxel detections -*+ WARNING: Smallest FDR q [6 Incorrect_Task_Fstat] = 0.123702 ==> few true single voxel detections -++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.054463 -++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.0543708 -++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 1.38372e-11 -++ Smallest FDR q [12 No_Response_Task_Fstat] = 1.38372e-11 -++ Smallest FDR q [14 Response_Control#0_Tstat] = 4.43676e-05 -++ Smallest FDR q [15 Response_Control_Fstat] = 4.43706e-05 -++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 8.17121e-11 -++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 8.17159e-11 +++ Calculations finished; elapsed time=15.405 +++ Smallest FDR q [0 Full_Fstat] = 6.364e-13 +++ Smallest FDR q [2 Correct_Task#0_Tstat] = 4.42671e-12 +++ Smallest FDR q [3 Correct_Task_Fstat] = 4.42671e-12 +++ Smallest FDR q [5 Incorrect_Task#0_Tstat] = 0.069944 +++ Smallest FDR q [6 Incorrect_Task_Fstat] = 0.0699435 +++ Smallest FDR q [8 No_Response_Control#0_Tstat] = 0.00160631 +++ Smallest FDR q [9 No_Response_Control_Fstat] = 0.00160642 +++ Smallest FDR q [11 No_Response_Task#0_Tstat] = 3.41585e-11 +++ Smallest FDR q [12 No_Response_Task_Fstat] = 3.41585e-11 +++ Smallest FDR q [14 Response_Control#0_Tstat] = 5.26673e-10 +++ Smallest FDR q [15 Response_Control_Fstat] = 5.26673e-10 +++ Smallest FDR q [17 Landmark-Detection_GLT#0_Tstat] = 0.0192157 +++ Smallest FDR q [18 Landmark-Detection_GLT_Fstat] = 0.019215 ++ Wrote bucket dataset into ./stats.sub_03+tlrc.BRIK + created 13 FDR curves in bucket header ++ Wrote 3D+time dataset into ./fitts.sub_03+tlrc.BRIK ++ Wrote 3D+time dataset into ./errts.sub_03+tlrc.BRIK -++ #Flops=3.97183e+10 Average Dot Product=37.2229 +++ #Flops=3.93533e+10 Average Dot Product=37.1935 if ( 0 != 0 ) then 1d_tool.py -show_cormat_warnings -infile X.xmat.1D tee out.cormat_warn.txt @@ -755,16 +749,16 @@ Warnings regarding Correlation Matrix: X.xmat.1D severity correlation cosine regressor pair -------- ----------- ------ ---------------------------------------- - medium: 0.566 0.642 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 + medium: 0.570 0.649 ( 7 vs. 9) No_Response_Control#0 vs. Response_Control#0 3dTcat -prefix all_runs.sub_03 pb04.sub_03.r01.scale+tlrc.HEAD ++ 3dTcat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -++ elapsed time = 0.3 s -3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] +++ elapsed time = 0.4 s +3dTstat -mean -prefix rm.signal.all all_runs.sub_03+tlrc[0..47,59,60,68..161,164..187,190..236] ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.signal.all+tlrc.BRIK -3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] +3dTstat -stdev -prefix rm.noise.all errts.sub_03+tlrc[0..47,59,60,68..161,164..187,190..236] ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./rm.noise.all+tlrc.BRIK @@ -778,14 +772,14 @@ Warnings regarding Correlation Matrix: X.xmat.1D ++ Output dataset ./rm.errts.unit+tlrc.BRIK 3dmaskave -quiet -mask full_mask.sub_03+tlrc rm.errts.unit+tlrc ++ 3dmaskave: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] -+++ 33064 voxels survive the mask ++++ 33054 voxels survive the mask 3dTstat -sos -prefix - gmean.errts.unit.1D' ++ 3dTstat: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D --- GCOR = 0.0653973 +-- GCOR = 0.0781041 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP ++ 3dcalc: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: A cast of thousands @@ -814,16 +808,16 @@ foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..50,60,61,68..101,104..160,163..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] +if ( 0..47,59,60,68..161,164..187,190..236 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.sub_03+tlrc[0..47,59,60,68..161,164..187,190..236] ++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 33064 -*+ WARNING: removed 254 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 217 time points - + detrending done (2.57 CPU s thus far) -++ start ACF calculations out to radius = 18.97 mm - + ACF done (34.29 CPU s thus far) +++ Number of voxels in mask = 33054 +*+ WARNING: removed 255 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 215 time points + + detrending done (2.58 CPU s thus far) +++ start ACF calculations out to radius = 19.16 mm + + ACF done (34.40 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. @@ -844,24 +838,24 @@ set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average epits ACF blurs: 0.834327 3.5247 15.2579 9.03231 -average epits ACF blurs: 0.834327 3.5247 15.2579 9.03231 -echo 0.834327 3.5247 15.2579 9.03231 # epits ACF blur estimates +echo average epits ACF blurs: 0.798127 3.52816 13.8595 9.13476 +average epits ACF blurs: 0.798127 3.52816 13.8595 9.13476 +echo 0.798127 3.52816 13.8595 9.13476 # epits ACF blur estimates touch blur.errts.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 -if ( 2..50,60,61,68..101,104..160,163..237 == ) continue -3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[2..50,60,61,68..101,104..160,163..237] +if ( 0..47,59,60,68..161,164..187,190..236 == ) continue +3dFWHMx -detrend -mask full_mask.sub_03+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.sub_03+tlrc[0..47,59,60,68..161,164..187,190..236] ++ 3dFWHMx: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: The Bob -++ Number of voxels in mask = 33064 -*+ WARNING: removed 254 voxels from mask because they are constant in time -++ detrending start: 17 baseline funcs, 217 time points - + detrending done (2.57 CPU s thus far) -++ start ACF calculations out to radius = 18.90 mm - + ACF done (35.14 CPU s thus far) +++ Number of voxels in mask = 33054 +*+ WARNING: removed 255 voxels from mask because they are constant in time +++ detrending start: 17 baseline funcs, 215 time points + + detrending done (2.56 CPU s thus far) +++ start ACF calculations out to radius = 19.06 mm + + ACF done (34.59 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r01.1D ++ 1dplot: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit] ++ Authored by: RWC et al. @@ -882,9 +876,9 @@ set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` ) ++ Authored by: KR Hammett & RW Cox *+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off *+ WARNING: Input dataset is not 3D+time; assuming TR=1.0 -echo average errts ACF blurs: 0.863438 3.55309 16.3324 9.0111 -average errts ACF blurs: 0.863438 3.55309 16.3324 9.0111 -echo 0.863438 3.55309 16.3324 9.0111 # errts ACF blur estimates +echo average errts ACF blurs: 0.835807 3.5609 14.5821 9.09429 +average errts ACF blurs: 0.835807 3.5609 14.5821 9.09429 +echo 0.835807 3.5609 14.5821 9.09429 # errts ACF blur estimates gen_epi_review.py -script @epi_review.sub_03 -dsets pb00.sub_03.r01.tcat+orig.HEAD gen_ss_review_scripts.py -mot_limit 0.5 -exit0 ++ writing ss review basic: @ss_review_basic @@ -896,51 +890,50 @@ if ( -e @ss_review_basic ) ./@ss_review_basic ./@ss_review_basic subject ID : sub_03 -TRs removed (per run) : 0 +TRs removed (per run) : 1 num stim classes provided : 5 final anatomy dset : anat_final.sub_03+tlrc.HEAD final stats dset : stats.sub_03+tlrc.HEAD final voxel resolution : 4.000000 4.000000 4.000000 motion limit : 0.5 -num TRs above mot limit : 13 -average motion (per TR) : 0.179191 -average censored motion : 0.129595 -max motion displacement : 5.04394 -max censored displacement : 3.96802 +num TRs above mot limit : 16 +average motion (per TR) : 0.160024 +average censored motion : 0.115175 +max motion displacement : 4.03483 +max censored displacement : 4.03483 outlier limit : 0.1 -average outlier frac (TR) : 0.0152516 +average outlier frac (TR) : 0.0119293 num TRs above out limit : 8 num runs found : 1 -num TRs per run : 238 -num TRs per run (applied) : 217 -num TRs per run (censored): 21 -fraction censored per run : 0.0882353 -TRs total (uncensored) : 238 -TRs total : 217 +num TRs per run : 237 +num TRs per run (applied) : 215 +num TRs per run (censored): 22 +fraction censored per run : 0.092827 +TRs total (uncensored) : 237 +TRs total : 215 degrees of freedom used : 22 -degrees of freedom left : 195 +degrees of freedom left : 193 -TRs censored : 21 -censor fraction : 0.088235 +TRs censored : 22 +censor fraction : 0.092827 num regs of interest : 5 num TRs per stim (orig) : 71 43 64 28 79 -num TRs censored per stim : 0 0 13 6 12 -fraction TRs censored : 0.000 0.000 0.203 0.214 0.152 -ave mot per sresp (orig) : 0.124806 0.112975 0.230781 0.273948 0.190656 -ave mot per sresp (cens) : 0.124806 0.112975 0.122112 0.144313 0.107954 +num TRs censored per stim : 0 0 13 7 11 +fraction TRs censored : 0.000 0.000 0.203 0.250 0.139 +ave mot per sresp (orig) : 0.105296 0.103826 0.216156 0.210735 0.179376 +ave mot per sresp (cens) : 0.105296 0.103826 0.108428 0.100787 0.100622 -TSNR average : 135.813 -global correlation (GCOR) : 0.0653973 -anat/EPI mask Dice coef : 0.876239 -maximum F-stat (masked) : 42.6934 -blur estimates (ACF) : 0.863438 3.55309 16.3324 +TSNR average : 148.219 +global correlation (GCOR) : 0.0781041 +anat/EPI mask Dice coef : 0.876878 +maximum F-stat (masked) : 55.9274 +blur estimates (ACF) : 0.835807 3.5609 14.5821 blur estimates (FWHM) : 0 0 0 -** TR #0 outliers: possible pre-steady state TRs in run 01 cd .. echo execution finished: `date` date -execution finished: Fri Aug 4 12:55:19 EDT 2017 +execution finished: Sat Aug 5 16:37:42 EDT 2017 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 b/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 old mode 100644 new mode 100755 index b6d0da4..d0d55fa --- a/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 +++ b/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 @@ -1,6 +1,6 @@ #!/bin/tcsh -xef -echo "auto-generated by afni_proc.py, Fri Aug 4 12:51:09 2017" +echo "auto-generated by afni_proc.py, Sat Aug 5 16:33:35 2017" echo "(version 5.15, April 25, 2017)" echo "execution started: `date`" @@ -59,12 +59,12 @@ cp /Users/mli/Desktop/playground/timing_sub-03_ses-test_Correct_Task.1D # ============================ auto block: tcat ============================ # apply 3dTcat to copy input dsets to results dir, while -# removing the first 0 TRs +# removing the first 1 TRs 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \ - /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[0..$]' + /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz'[1..$]' # and make note of repetitions (TRs) per run -set tr_counts = ( 238 ) +set tr_counts = ( 237 ) # ------------------------------------------------------- # enter the results directory (can begin processing data) @@ -92,6 +92,7 @@ cat outcount.r*.1D > outcount_rall.1D # time shift data so all slice timing is the same foreach run ( $runs ) 3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \ + -tpattern alt+z \ pb00.$subj.r$run.tcat+orig end @@ -304,7 +305,7 @@ set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D \ -stim_file 15 motion_deriv.1D'[3]' -stim_base 15 -stim_label 15 dS_02 \ -stim_file 16 motion_deriv.1D'[4]' -stim_base 16 -stim_label 16 dL_02 \ -stim_file 17 motion_deriv.1D'[5]' -stim_base 17 -stim_label 17 dP_02 \ - -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -*Response_Control' \ + -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task -Response_Control' \ -glt_label 1 Landmark-Detection \ -fout -tout -x1D X.xmat.1D -xjpeg X.jpg \ -x1D_uncensored X.nocensor.xmat.1D \ @@ -458,7 +459,7 @@ echo "execution finished: `date`" # afni_proc.py -subj_id sub_03 -script proc.sub_03 -scr_overwrite -blocks \ # tshift align tlrc volreg blur mask scale regress -copy_anat \ # /Users/mli/Desktop/playground/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz \ -# -tcat_remove_first_trs 0 -dsets \ +# -tcat_remove_first_trs 1 -tshift_opts_ts -tpattern alt+z -dsets \ # /Users/mli/Desktop/playground/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz \ # -tlrc_base MNI_avg152T1+tlrc -volreg_align_to third -volreg_align_e2a \ # -volreg_tlrc_warp -blur_size 3.0 -regress_stim_times \ @@ -471,6 +472,6 @@ echo "execution finished: `date`" # No_Response_Task Response_Control -regress_basis GAM \ # -regress_censor_motion 0.5 -regress_apply_mot_types demean deriv \ # -regress_opts_3dD -gltsym 'SYM: 0.5*Correct_Task +0.5*Incorrect_Task \ -# -*Response_Control' -glt_label 1 Landmark-Detection \ +# -Response_Control' -glt_label 1 Landmark-Detection \ # -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \ # -regress_est_blur_errts -regress_run_clustsim no diff --git a/HomeworkAnswers.md b/HomeworkAnswers.md index 851d0c1..3292c37 100644 --- a/HomeworkAnswers.md +++ b/HomeworkAnswers.md @@ -1,11 +1,11 @@ # Dice Coefficient Output ## Experiment 1 (smoothing FWHM = 6 mm) +++ 30980 voxels in the mask -0.584105 +0.198745 ## Experiment 2 (smoothing FWHM = 3 mm) +++ 30980 voxels in the mask -0.491035 +0.161541 # Interpretation The Dice coefficient is larger when the smoothing kernel is larger. From a46d729fdeb5b114803cecc76458c604240151f2 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Fri, 18 Aug 2017 21:23:40 -0400 Subject: [PATCH 12/18] move homework 2 to subdirectory --- .gitignore | 3 - Exp-1.sh => hw2/Exp-1.sh | 0 .../subj.sub_03/.orig.cmd.ap.sub_03 | 0 .../subj.sub_03/.orig.cmd.usubj.sub_03 | 0 .../subj.sub_03/.orig.proc.sub_03 | 0 .../group.retest/subj.sub_03/cmd.ap.sub_03 | 0 .../subj.sub_03/output.cmd.ap.sub_03 | 0 .../subj.sub_03/output.proc.sub_03 | 0 .../group.retest/subj.sub_03/proc.sub_03 | 0 .../subj.sub_03/.orig.cmd.ap.sub_03 | 0 .../subj.sub_03/.orig.cmd.usubj.sub_03 | 0 .../group.test/subj.sub_03/.orig.proc.sub_03 | 0 .../group.test/subj.sub_03/cmd.ap.sub_03 | 0 .../subj.sub_03/output.cmd.ap.sub_03 | 0 .../group.test/subj.sub_03/output.proc.sub_03 | 0 .../group.test/subj.sub_03/proc.sub_03 | 0 Exp-2.sh => hw2/Exp-2.sh | 0 .../subj.sub_03/.orig.cmd.ap.sub_03 | 0 .../subj.sub_03/.orig.cmd.usubj.sub_03 | 0 .../subj.sub_03/.orig.proc.sub_03 | 0 .../group.retest/subj.sub_03/cmd.ap.sub_03 | 0 .../subj.sub_03/output.cmd.ap.sub_03 | 0 .../subj.sub_03/output.proc.sub_03 | 0 .../group.retest/subj.sub_03/proc.sub_03 | 0 .../subj.sub_03/.orig.cmd.ap.sub_03 | 0 .../subj.sub_03/.orig.cmd.usubj.sub_03 | 0 .../group.test/subj.sub_03/.orig.proc.sub_03 | 0 .../group.test/subj.sub_03/cmd.ap.sub_03 | 0 .../subj.sub_03/output.cmd.ap.sub_03 | 0 .../group.test/subj.sub_03/output.proc.sub_03 | 0 .../group.test/subj.sub_03/proc.sub_03 | 0 HomeworkAnswers.md => hw2/HomeworkAnswers.md | 0 ...3_ses-retest_task-linebisection_events.tsv | 161 ++++++++++++++++++ ...-03_ses-test_task-linebisection_events.tsv | 161 ++++++++++++++++++ timing.py => hw2/timing.py | 0 .../timing_sub-03_ses-retest_Correct_Task.1D | 0 ...timing_sub-03_ses-retest_Incorrect_Task.1D | 0 ...g_sub-03_ses-retest_No_Response_Control.1D | 0 ...ming_sub-03_ses-retest_No_Response_Task.1D | 0 ...ming_sub-03_ses-retest_Response_Control.1D | 0 .../timing_sub-03_ses-test_Correct_Task.1D | 0 .../timing_sub-03_ses-test_Incorrect_Task.1D | 0 ...ing_sub-03_ses-test_No_Response_Control.1D | 0 ...timing_sub-03_ses-test_No_Response_Task.1D | 0 ...timing_sub-03_ses-test_Response_Control.1D | 0 45 files changed, 322 insertions(+), 3 deletions(-) rename Exp-1.sh => hw2/Exp-1.sh (100%) rename {Exp-1 => hw2/Exp-1}/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 (100%) rename {Exp-1 => hw2/Exp-1}/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 (100%) rename {Exp-1 => hw2/Exp-1}/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 (100%) rename {Exp-1 => hw2/Exp-1}/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 (100%) rename {Exp-1 => hw2/Exp-1}/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 (100%) rename {Exp-1 => hw2/Exp-1}/subject_results/group.retest/subj.sub_03/output.proc.sub_03 (100%) rename {Exp-1 => hw2/Exp-1}/subject_results/group.retest/subj.sub_03/proc.sub_03 (100%) rename {Exp-1 => 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rename HomeworkAnswers.md => hw2/HomeworkAnswers.md (100%) create mode 100755 hw2/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_events.tsv create mode 100755 hw2/sub-03/ses-test/func/sub-03_ses-test_task-linebisection_events.tsv rename timing.py => hw2/timing.py (100%) rename timing_sub-03_ses-retest_Correct_Task.1D => hw2/timing_sub-03_ses-retest_Correct_Task.1D (100%) rename timing_sub-03_ses-retest_Incorrect_Task.1D => hw2/timing_sub-03_ses-retest_Incorrect_Task.1D (100%) rename timing_sub-03_ses-retest_No_Response_Control.1D => hw2/timing_sub-03_ses-retest_No_Response_Control.1D (100%) rename timing_sub-03_ses-retest_No_Response_Task.1D => hw2/timing_sub-03_ses-retest_No_Response_Task.1D (100%) rename timing_sub-03_ses-retest_Response_Control.1D => hw2/timing_sub-03_ses-retest_Response_Control.1D (100%) rename timing_sub-03_ses-test_Correct_Task.1D => hw2/timing_sub-03_ses-test_Correct_Task.1D (100%) rename timing_sub-03_ses-test_Incorrect_Task.1D => hw2/timing_sub-03_ses-test_Incorrect_Task.1D (100%) rename timing_sub-03_ses-test_No_Response_Control.1D => hw2/timing_sub-03_ses-test_No_Response_Control.1D (100%) rename timing_sub-03_ses-test_No_Response_Task.1D => hw2/timing_sub-03_ses-test_No_Response_Task.1D (100%) rename timing_sub-03_ses-test_Response_Control.1D => hw2/timing_sub-03_ses-test_Response_Control.1D (100%) diff --git a/.gitignore b/.gitignore index a4dadab..9ac6f2d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,4 @@ -*.tsv -*.1D *.BRIK *.HEAD @* -*.txt *.jpg diff --git a/Exp-1.sh b/hw2/Exp-1.sh similarity index 100% rename from Exp-1.sh rename to hw2/Exp-1.sh diff --git a/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 b/hw2/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 similarity index 100% rename from Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 rename to hw2/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 diff --git 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a/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 b/hw2/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 similarity index 100% rename from Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 rename to hw2/Exp-1/subject_results/group.test/subj.sub_03/proc.sub_03 diff --git a/Exp-2.sh b/hw2/Exp-2.sh similarity index 100% rename from Exp-2.sh rename to hw2/Exp-2.sh diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 b/hw2/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 similarity index 100% rename from Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 rename to hw2/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 b/hw2/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 similarity index 100% rename from Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 rename to hw2/Exp-2/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 b/hw2/Exp-2/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 similarity index 100% rename from Exp-2/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 rename to hw2/Exp-2/subject_results/group.retest/subj.sub_03/.orig.proc.sub_03 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 b/hw2/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 similarity index 100% rename from Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 rename to hw2/Exp-2/subject_results/group.retest/subj.sub_03/cmd.ap.sub_03 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 b/hw2/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 similarity index 100% rename from Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 rename to hw2/Exp-2/subject_results/group.retest/subj.sub_03/output.cmd.ap.sub_03 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 b/hw2/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 similarity index 100% rename from Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 rename to hw2/Exp-2/subject_results/group.retest/subj.sub_03/output.proc.sub_03 diff --git a/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 b/hw2/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 similarity index 100% rename from Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 rename to hw2/Exp-2/subject_results/group.retest/subj.sub_03/proc.sub_03 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 b/hw2/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 similarity index 100% rename from Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 rename to hw2/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.ap.sub_03 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 b/hw2/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 similarity index 100% rename from Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 rename to hw2/Exp-2/subject_results/group.test/subj.sub_03/.orig.cmd.usubj.sub_03 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 b/hw2/Exp-2/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 similarity index 100% rename from Exp-2/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 rename to hw2/Exp-2/subject_results/group.test/subj.sub_03/.orig.proc.sub_03 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 b/hw2/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 similarity index 100% rename from Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 rename to hw2/Exp-2/subject_results/group.test/subj.sub_03/cmd.ap.sub_03 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 b/hw2/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 similarity index 100% rename from Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 rename to hw2/Exp-2/subject_results/group.test/subj.sub_03/output.cmd.ap.sub_03 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 b/hw2/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 similarity index 100% rename from Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 rename to hw2/Exp-2/subject_results/group.test/subj.sub_03/output.proc.sub_03 diff --git a/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 b/hw2/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 similarity index 100% rename from Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 rename to hw2/Exp-2/subject_results/group.test/subj.sub_03/proc.sub_03 diff --git a/HomeworkAnswers.md b/hw2/HomeworkAnswers.md similarity index 100% rename from HomeworkAnswers.md rename to hw2/HomeworkAnswers.md diff --git a/hw2/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_events.tsv b/hw2/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_events.tsv new file mode 100755 index 0000000..fe96fb0 --- /dev/null +++ b/hw2/sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_events.tsv @@ -0,0 +1,161 @@ +onset duration weight trial_type +24.3064 1 1.0 Correct_Task +25.9464 1 1.0 Incorrect_Task +27.5864 1 1.0 Correct_Task +29.2264 1 1.0 Correct_Task +30.8664 1 1.0 Correct_Task +32.5064 1 1.0 Correct_Task +34.1464 1 1.0 Incorrect_Task +35.7863 1 1.0 Correct_Task +37.4263 1 1.0 Correct_Task +39.0663 1 1.0 Correct_Task +56.9728 1 1.0 Response_Control +58.6128 1 1.0 Response_Control +60.2528 1 1.0 Response_Control +61.8928 1 1.0 No_Response_Control +63.5328 1 1.0 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+529.059 1 1.0 No_Response_Control diff --git a/timing.py b/hw2/timing.py similarity index 100% rename from timing.py rename to hw2/timing.py diff --git a/timing_sub-03_ses-retest_Correct_Task.1D b/hw2/timing_sub-03_ses-retest_Correct_Task.1D similarity index 100% rename from timing_sub-03_ses-retest_Correct_Task.1D rename to hw2/timing_sub-03_ses-retest_Correct_Task.1D diff --git a/timing_sub-03_ses-retest_Incorrect_Task.1D b/hw2/timing_sub-03_ses-retest_Incorrect_Task.1D similarity index 100% rename from timing_sub-03_ses-retest_Incorrect_Task.1D rename to hw2/timing_sub-03_ses-retest_Incorrect_Task.1D diff --git a/timing_sub-03_ses-retest_No_Response_Control.1D b/hw2/timing_sub-03_ses-retest_No_Response_Control.1D similarity index 100% rename from timing_sub-03_ses-retest_No_Response_Control.1D rename to hw2/timing_sub-03_ses-retest_No_Response_Control.1D diff --git a/timing_sub-03_ses-retest_No_Response_Task.1D b/hw2/timing_sub-03_ses-retest_No_Response_Task.1D similarity index 100% rename from timing_sub-03_ses-retest_No_Response_Task.1D rename to hw2/timing_sub-03_ses-retest_No_Response_Task.1D diff --git a/timing_sub-03_ses-retest_Response_Control.1D b/hw2/timing_sub-03_ses-retest_Response_Control.1D similarity index 100% rename from timing_sub-03_ses-retest_Response_Control.1D rename to hw2/timing_sub-03_ses-retest_Response_Control.1D diff --git a/timing_sub-03_ses-test_Correct_Task.1D b/hw2/timing_sub-03_ses-test_Correct_Task.1D similarity index 100% rename from timing_sub-03_ses-test_Correct_Task.1D rename to hw2/timing_sub-03_ses-test_Correct_Task.1D diff --git a/timing_sub-03_ses-test_Incorrect_Task.1D b/hw2/timing_sub-03_ses-test_Incorrect_Task.1D similarity index 100% rename from timing_sub-03_ses-test_Incorrect_Task.1D rename to hw2/timing_sub-03_ses-test_Incorrect_Task.1D diff --git a/timing_sub-03_ses-test_No_Response_Control.1D b/hw2/timing_sub-03_ses-test_No_Response_Control.1D similarity index 100% rename from timing_sub-03_ses-test_No_Response_Control.1D rename to hw2/timing_sub-03_ses-test_No_Response_Control.1D diff --git a/timing_sub-03_ses-test_No_Response_Task.1D b/hw2/timing_sub-03_ses-test_No_Response_Task.1D similarity index 100% rename from timing_sub-03_ses-test_No_Response_Task.1D rename to hw2/timing_sub-03_ses-test_No_Response_Task.1D diff --git a/timing_sub-03_ses-test_Response_Control.1D b/hw2/timing_sub-03_ses-test_Response_Control.1D similarity index 100% rename from timing_sub-03_ses-test_Response_Control.1D rename to hw2/timing_sub-03_ses-test_Response_Control.1D From 1fc8dfa034cd24c82d87b99f6d879e03618e7a4e Mon Sep 17 00:00:00 2001 From: Monica Li Date: Fri, 18 Aug 2017 21:39:25 -0400 Subject: [PATCH 13/18] add homework 3 script and output files --- hw3/output/Words.group_FDR.md | 142 +++++++++++++ hw3/output/Words.group_attr.1D | 241 +++++++++++++++++++++++ hw3/output/Words.group_clusters.md | 17 ++ hw3/scripts/Homework-3_Group-Analysis.sh | 91 +++++++++ 4 files changed, 491 insertions(+) create mode 100644 hw3/output/Words.group_FDR.md create mode 100644 hw3/output/Words.group_attr.1D create mode 100644 hw3/output/Words.group_clusters.md create mode 100644 hw3/scripts/Homework-3_Group-Analysis.sh diff --git a/hw3/output/Words.group_FDR.md b/hw3/output/Words.group_FDR.md new file mode 100644 index 0000000..ccd0fbb --- /dev/null +++ b/hw3/output/Words.group_FDR.md @@ -0,0 +1,142 @@ +# Words-Fixation Activation Map (FDR Correction) +* q = .05 +* coordinates are center of mass of each cluster in MNI space + +| Cluster Size | Peak Value (Z) | x (mm) | y (mm) | z (mm) | +| ------------ | -------------- | ------:| ------:| ------:| +| 3554 | 3.2815 | 3.7 | 57.3 | 33.9 | +| 1133 | 3.1054 | 12.5 | -44 | 11.5 | +| 693 | 3.113 | 39.8 | 67.8 | -10.2 | +| 528 | 3.0362 | -36.9 | 71.7 | -11.4 | +| 443 | 3.0362 | -54.9 | 14.8 | 10 | +| 260 | 3.113 | 0.5 | -9.2 | 54.6 | +| 183 | 3.113 | 48 | 0.8 | 43 | +| 160 | 3.1054 | -25.9 | -35.3 | 45.2 | +| 123 | 2.8517 | -43.5 | -0.2 | 44.2 | +| 109 | 2.832 | -27.6 | -60.6 | 16.2 | +| 101 | 3.0695 | -3.7 | 70.4 | -19.3 | +| 74 | 2.8091 | -30.2 | 57.4 | 47.4 | +| 66 | 2.9463 | 25.2 | 54.3 | 46.3 | +| 63 | 2.8595 | 33.1 | -24.8 | 7.1 | +| 52 | 2.9323 | -29.2 | 45.3 | -7.8 | +| 48 | 2.8194 | 60.9 | 28.1 | 26.3 | +| 36 | 2.899 | -22.8 | 12.4 | 59.5 | +| 25 | 2.6046 | 57.8 | -1.2 | -23.6 | +| 20 | 2.4962 | 40.9 | 22.2 | 58 | +| 16 | 2.9598 | -60.1 | 44.8 | 42.4 | +| 15 | 2.6225 | -32.6 | 52.9 | 6.4 | +| 15 | 2.9951 | 19 | 26.8 | 8.3 | +| 13 | 2.7898 | 25.1 | 39.9 | 58.1 | +| 12 | 2.8196 | 37.5 | 14.3 | 34.3 | +| 11 | 2.661 | -19.6 | -35.9 | -1.9 | +| 11 | 2.3227 | -41.4 | -33.2 | 23.4 | +| 11 | 2.2315 | 48.6 | -31.4 | 35.7 | +| 10 | 2.3986 | -37.8 | -15.1 | -12.9 | +| 10 | 2.6816 | -19.8 | 19.4 | -3.5 | +| 10 | 2.3236 | -57 | 47.4 | 7.2 | +| 9 | 2.5982 | 7.9 | 20.5 | -8.4 | +| 9 | 2.2699 | 5.7 | 99.4 | 9.7 | +| 9 | 2.4501 | 7.3 | -3 | 24 | +| 9 | 2.1847 | -3 | -23.3 | 26.7 | +| 8 | 2.5729 | 32.7 | 30 | 32.3 | +| 8 | 2.2952 | -1.5 | -61.9 | 32.3 | +| 8 | 2.2893 | -46.9 | 53.6 | 46.1 | +| 7 | 2.3202 | 62.2 | 57.8 | -8.5 | +| 7 | 2.4284 | 36.4 | 19.7 | 1.7 | +| 7 | 2.1129 | 11.1 | 21.4 | 25.3 | +| 7 | 2.6014 | -24 | -18 | 60.8 | +| 6 | 2.4779 | -54.5 | -30 | -5 | +| 6 | 2.491 | 22 | -2.5 | -5.1 | +| 6 | 2.0826 | -33.5 | -25 | 2 | +| 6 | 2.1962 | 41 | 29.6 | 8.5 | +| 6 | 2.5684 | 19.5 | -21 | 32 | +| 5 | 2.427 | -64.8 | 6.6 | -24 | +| 5 | 2.2239 | 19.2 | 37.8 | -18.1 | +| 5 | 2.3669 | -32.4 | 70.2 | 3.1 | +| 5 | 2.2723 | 67.2 | 22.8 | 0.6 | +| 5 | 2.2281 | 54.7 | 22.9 | 10.8 | +| 5 | 2.5274 | 22.8 | -28.8 | 21.1 | +| 5 | 2.3311 | 9.6 | 8.5 | 32.4 | +| 4 | 2.2094 | 45.7 | -14.2 | -20.3 | +| 4 | 2.4703 | 46.4 | 12 | 3 | +| 4 | 2.1785 | -47.9 | -40.5 | 5.3 | +| 4 | 2.5742 | -68.3 | 39.7 | 14.3 | +| 4 | 2.2167 | -18.1 | -27 | 16.5 | +| 4 | 2.4073 | 15.7 | -33 | 23.9 | +| 4 | 2.244 | 42 | 35.3 | 26.4 | +| 4 | 2.318 | 61.5 | -7.5 | 27 | +| 4 | 2.2286 | 65.3 | 27.8 | 41.3 | +| 4 | 2.5143 | -9 | 22.7 | 64.4 | +| 3 | 2.2226 | -43 | -1 | -30 | +| 3 | 2.3435 | -32 | -21 | -27.9 | +| 3 | 2.1955 | 30 | -37 | -11 | +| 3 | 2.0953 | 21 | 1 | 8 | +| 3 | 2.1552 | -4 | -49 | 27 | +| 3 | 2.161 | -34 | 28 | 41 | +| 2 | 2.3001 | 37.4 | -18 | -36 | +| 2 | 2.2888 | 54 | -10.4 | -33 | +| 2 | 2.7347 | -31.4 | -28.4 | -19.6 | +| 2 | 2.1885 | 30 | 25.5 | -15 | +| 2 | 2.4731 | 21 | -52.5 | -15 | +| 2 | 2.0509 | -61.5 | 51 | -3 | +| 2 | 2.0055 | 66 | 40.5 | 0 | +| 2 | 2.2403 | 33 | 34.5 | 0 | +| 2 | 2.2426 | -42 | 37.5 | 3 | +| 2 | 2.2026 | -15 | -1.5 | 3 | +| 2 | 2.1128 | 36 | 39 | 13.5 | +| 2 | 2.3705 | -34.4 | -21 | 12 | +| 2 | 2.5353 | 3 | -24 | 13.6 | +| 2 | 2.013 | 39 | -43.5 | 13.5 | +| 2 | 2.0589 | -46.5 | -15 | 18 | +| 2 | 2.0849 | -10.5 | 21 | 21 | +| 2 | 2.1302 | 10.6 | 93 | 24 | +| 2 | 2.2077 | 31.6 | 15 | 27 | +| 2 | 1.9941 | -49.5 | 10.5 | 27 | +| 2 | 2.4466 | -34.4 | 13.4 | 31.6 | +| 2 | 2.0714 | 60 | 39 | 43.5 | +| 2 | 2.0942 | -33 | 13.5 | 42 | +| 2 | 2.2862 | 45 | 36 | 46.6 | +| 2 | 2.1863 | -31.5 | -13.5 | 51 | +| 2 | 2.1169 | -12 | -19.5 | 60 | +| 2 | 2.0433 | -6 | -34.5 | 60 | +| 1 | 2.0258 | 45 | 3 | -36 | +| 1 | 1.972 | -15 | 75 | -30 | +| 1 | 2.0618 | -24 | 69 | -30 | +| 1 | 2.3999 | -48 | 51 | -30 | +| 1 | 1.9779 | -9 | 24 | -30 | +| 1 | 2.1306 | 27 | 18 | -27 | +| 1 | 2.2248 | -21 | 18 | -24 | +| 1 | 1.9715 | 18 | 15 | -24 | +| 1 | 1.967 | 36 | -6 | -21 | +| 1 | 2.0179 | 6 | 48 | -18 | +| 1 | 1.9682 | -42 | 15 | -18 | +| 1 | 2.0902 | 45 | 15 | -15 | +| 1 | 1.9687 | 18 | -33 | -15 | +| 1 | 2.2552 | -21 | -33 | -15 | +| 1 | 2.0172 | 30 | 12 | -12 | +| 1 | 2.0593 | 54 | -42 | -12 | +| 1 | 2.0448 | 69 | 27 | -9 | +| 1 | 2.0782 | -72 | 18 | -9 | +| 1 | 1.9645 | 42 | 3 | -9 | +| 1 | 2.4857 | -60 | 39 | -3 | +| 1 | 2.0686 | -48 | 30 | 0 | +| 1 | 2.0539 | -21 | -27 | 0 | +| 1 | 1.9644 | -48 | -48 | 0 | +| 1 | 2.0113 | -42 | -9 | 3 | +| 1 | 2.2464 | -18 | 33 | 6 | +| 1 | 2.0685 | -15 | -15 | 9 | +| 1 | 2.1577 | 51 | 12 | 12 | +| 1 | 1.9692 | 33 | 30 | 15 | +| 1 | 2.0126 | 24 | 18 | 18 | +| 1 | 2.1026 | -24 | 36 | 21 | +| 1 | 2.0082 | 27 | 21 | 30 | +| 1 | 1.961 | -24 | 0 | 30 | +| 1 | 2.1906 | -24 | -12 | 30 | +| 1 | 2.2538 | -12 | 6 | 33 | +| 1 | 2.0314 | 27 | -24 | 36 | +| 1 | 1.9676 | 15 | 12 | 39 | +| 1 | 1.9659 | 12 | -54 | 45 | +| 1 | 2.2616 | -12 | -24 | 54 | +| 1 | 2.125 | 12 | 15 | 57 | +| 1 | 1.9813 | -30 | -30 | 57 | +| 1 | 2.0621 | 39 | 6 | 66 | diff --git a/hw3/output/Words.group_attr.1D b/hw3/output/Words.group_attr.1D new file mode 100644 index 0000000..2718f66 --- /dev/null +++ b/hw3/output/Words.group_attr.1D @@ -0,0 +1,241 @@ +HISTORY_NOTE = [mli@Ringo-Lite.frontier.com: Fri Aug 18 19:14:42 2017] {AFNI_17.2.06:macosx_10.7_local} 3dttest++ -mask full_mask.group+tlrc -prefix Words.group -setA 'betas/stats*+tlrc.HEAD[Words#0_Coef]'\n[mli@Ringo-Lite.frontier.com: Fri Aug 18 19:29:06 2017] {AFNI_17.2.06:macosx_10.7_local} 3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:cluster.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:cluster.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:cluster.NN2_1sided.niml -atrstring AFNI_CLUSTSIM_NN3_1sided file:cluster.NN3_1sided.niml -atrstring AFNI_CLUSTSIM_NN1_2sided file:cluster.NN1_2sided.niml -atrstring AFNI_CLUSTSIM_NN2_2sided file:cluster.NN2_2sided.niml -atrstring AFNI_CLUSTSIM_NN3_2sided file:cluster.NN3_2sided.niml -atrstring AFNI_CLUSTSIM_NN1_bisided file:cluster.NN1_bisided.niml -atrstring AFNI_CLUSTSIM_NN2_bisided file:cluster.NN2_bisided.niml -atrstring AFNI_CLUSTSIM_NN3_bisided file:cluster.NN3_bisided.niml Words.group+tlrc~ +TYPESTRING = 3DIM_HEAD_FUNC~ +IDCODE_STRING = AFN_RRkQT1ONZHTBuc06DvAv0g~ +IDCODE_DATE = Fri Aug 18 19:14:42 2017~ +SCENE_DATA = 2 11 1 -999 -999 -999 -999 -999 +LABEL_1 = zyxt~ +LABEL_2 = zyxt~ +DATASET_NAME = zyxt~ +ORIENT_SPECIFIC = 1 2 4 +ORIGIN = 90 126 -72 +DELTA = -3 -3 3 +IJK_TO_DICOM = -3 0 0 90 0 -3 0 126 0 0 3 -72 +IJK_TO_DICOM_REAL = -3 0 0 90 0 -3 0 126 0 0 3 -72 +BRICK_STATS = -0.248389 0.225726 -9.351179 8.191493 +DATASET_RANK = 3 2 0 0 0 0 0 0 +DATASET_DIMENSIONS = 61 73 61 0 0 +BRICK_TYPES = 3 3 +BRICK_FLOAT_FACS = 0 0 +BRICK_LABS = SetA_mean~SetA_Tstat~ +BRICK_STATAUX = 1 3 1 16 +BRICK_STATSYM = none;Ttest(16)~ +FDRCURVE_000001 = 0.000129 0.092062 0.443462 0.472502 0.506242 0.539848 0.577305 0.616368 0.659138 0.700843 0.744295 0.791323 0.839838 0.888438 0.939331 0.989339 1.040367 1.092791 1.146421 1.20042 1.254131 1.308733 1.362172 1.41752 1.470654 1.524289 1.577432 1.633076 1.686124 1.737868 1.791292 1.842088 1.892841 1.943333 1.991563 2.041249 2.089485 2.136528 2.181833 2.226235 2.270943 2.313704 2.355185 2.396872 2.437348 2.47631 2.514298 2.547712 2.580618 2.609116 2.646286 2.675714 2.706881 2.735897 2.763161 2.78445 2.811696 2.830003 2.851635 2.876096 2.899488 2.919909 2.942753 2.959107 2.974747 2.989804 2.997524 3.014758 3.014771 3.024873 3.036207 3.036207 3.03701 3.055237 3.065696 3.070787 3.082001 3.090105 3.10342 3.105447 3.105447 3.105447 3.105447 3.105447 3.105447 3.106586 3.10774 3.110595 3.113038 3.113038 3.113038 3.11365 3.113867 3.134915 3.159632 3.18435 3.209066 3.233783 3.258501 3.269092 3.279443 3.281517 3.281517 +MDFCURVE_000001 = -6.123312 0.200753 0.999066 0.998484 0.997668 0.996029 0.994475 0.992022 0.987634 0.981551 0.973525 0.963736 0.951574 0.935694 0.914703 0.889466 0.861413 0.824368 0.783225 0.736574 0.683813 0.622429 0.551571 0.473139 0.3865 0.293849 0.201926 0.109237 0.03316 0 +TEMPLATE_SPACE = MNI~ +INT_CMAP = 0 +BYTEORDER_STRING = LSB_FIRST~ +AFNI_CLUSTSIM_NN1_1sided = <3dClustSim_NN1 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="1-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 390 502 613 760 + 65.1627 77.853 91.49506 111 + 16.83356 20.72851 24.05696 28 +~ +AFNI_CLUSTSIM_MASK = eNrtXEuS47gRBYMO04uO5iy9cBhX6GUvJkwfZY4xC4cBx1wME30R+AZccoEgDCATROJDiarq +tqpqkIuSSIEURTxkvpeZLMa6devWrVu3bt26devWrVu3bt26devWrVu3bt26detGbISXdQgv +0sLmNsOrhd16gU0Do6XAg3DUNvT7+Dz7J77GOeLhRVmYHG1hztY4szhs5zjhcdiQfWwmHB4G +TewnnOfd7V/d9O9DOIUS/hQj2zjstu5jN0QLfwHuLHOAUkCVO2J1o5T7AuMO1iOTcAnslz6H +TdO4rHDmLKy6DV6ltQtsWg6bYSZX9+qnbnevg58EG4a7UWH4DsP8aBtmHY7aYJMZOJjhJoNP +/VkQQwAWg2CBK3Bnm/D1m//Dtb+izY4Beu7rjfXfNIXhmw1v2T77t+7MAwujeXjr/Y1HoPc3 +uzt4mwJe2L/dd6Oj+rnjIrP9PyNMTVjnEmdug+n2mxznd0rTvuJuj4YRQGJxlIDZ9xMddg9p +tIFNhpsKDvYfBxjsgB2VroAjlEZE2ojnnuDUFk7phrnr+uY/Xu2i/BXsdtisdxuLf+tdmH/L +jAjezMPNvQ1Oxn+lAX/jl4n3Wspdut/UwW91C3Pz+4wgmREVY1r1En3Dhs6ATLtILiNM2ViB +RONo6mAQaQKRNiN2Ci81wOgFMTOlK5gBJBpBsgNIADNjGOR3u6F72C0k7J61P9lu3dvJuyG2 +C/9NQwhxLlZp6y9gCEFJcwhK28i0v6B/uEv8w4OETcD1zEQW7pqDZCUgGXOQcETDhOsa/Q0B +icGT4CiNfsfAwRJ3r7ibnnPEcw7wqYDB7txh0+0OIFkQJBMBSTiJRuwYK0L4dO+NO9g7Gz/K +ASbQJQcYh5dAnTw9cpQpBCUfqxYgwz4oOewo79ocg/ma3cC/wkv0OkipPbay3Tj607sEiWHh +V6llG9HpD4AKgZhZahKic0+STSg6Fg6LPxAGGK0QOxtiB+YXDp4PNEjcvSJ2djhJBhKOIBkB +DQLRMMM5vH+Ak6yIHZMjzI3+r/+q4GC4vxAXnDxInIMJhGZQ/rLd+y1c9hiC0rpAUHJk2Gsp +z5ODm5x/Dlpq/52HWOXWWnBD2n4LHtqIjJWvImfjO87Cn982SBDiUmxIFy1IDADJDsxAI0hs +AsmCzqAAiShAMuHc4LQvOO2JVmw4GqddIaQ2xA66DIwvESQbBYnFTzmCZJSInRVRsecHRzdk +4IJkcDA+hLngFL55DqwXybCykwRsgyxzzsb7G4cdBSF22RohlrrJIa25Pxmg3xL1gUY2bqJs +mDNl/+Zs+UpljUI2aSDMqNqTLIUnGa6CxOa0Ik1V2L3eYBviVSAZVOGGdnrO8M0KLogD67Uj +wHMJ/sZNrwG/KMEB8hUWBt9FCrEr3oodfqtCf7hhLMU743f/Bmxt+QJ3eQTMLDgJE5WazL4V +Ao2hVSOYUVtsAI7IZ5FkqtyTqBwkksaVMQcJr0CSoaGgFQuOwohhmXo9SJbjYASJavGcBM/C +AUr0dGuDh3HcPcLoOyG2YPpTSiV4vfcJbv4IK3VBf4MK/e/PBguC1kRswytKjg1+RUsZJxmT +rSrkJCVIxvsChXDPAyRNTyIugiSnKhVItjZI0Ic1o+SMu2sedhsk6w2mT7Qk+m2ZcgYoRCPP +GZ+dY0OqghkuAxemMQoRuRqTF7hJZAx1vQJvAT+oqM5THScgidxzv+FJxIOeJDtnDRJLFVMC +CY5qUqkBdi9HiI0L4worL9xQIjRRS+pCPZgjscTpFDnG8yywYO5xPS5oJklTnXIaguTYqNZN +8Tm7YYmhmvbCLVTsFZDMD4WbAngVSHQujViSRon1Fn4x/pqpCrE7ibwxVtVuqCA0koBEYHCf +0pKMiaWoMVYMSofa/r+bzKPQCuCQeH0mJb7mlIilCRFC4uiqSjJG2kzr5nMyxqnKJ/SaBD4F +iW0BbzhhQ7IFkoJvx6AUf83QVHS1dGvFKnLDVgKSotoRY/4AH3Na7dDi6VFIMEKpGunaIaVW +NyIHx4PpS+qg0w0r7nY2JynVkU3o3TzJbZA0Y1WRZLmln89F2QBfdUf2o74vYpWopREtiRXV +jjGltBRiRiNmtH2anv5LpoUk0ts6E8dJLC1y+tTHTtUN2ykFOO72Scb1EkjYIyAR5cHyln6e +7yj3UtFtjVi1HLGqJDRbnoumJbElgSQmx3VaqTGJMRIGw/72NOayoYc7asecJFniZe/JTS51 +uraIz4auvbQks4VbpeWvgIQ/BJK5PHh9SD9vNwmNvE1oNI1CQ5ZkiR55ScGdlsSQ3saVOhFm +oGJK5renaaJPnzAKTeeVZUXc5NROsvCHkixV7eYHgORekuWE0NwCyVLxMEMJTQKJyfVzWU7d +qyRLq24ai+vIDGLSlP3607NzLod+jsyFE2yvaQVYdjPJIiqZ0NTP00v088tAMl0EyWOs1zRY +Lz/koKSZuKmZibPnINEp08VJ+cX9DpAkn59dPZIHc5nw+pBZWZZ6AvS5fhYpPu9N/SxvZeJ+ +jH621/WzrajUy0Ei2iCZ2yAhmThdaCCkjzGzHpUIU892LEowkjGUiVlxUh4yqdvtdfqZt/Uz +/676WV/Qz+ISSGxbP597EkPqQY0Wr/02SOyRxOC0LVDZN9ZnlTMXkvlvtDud6OeWNBKVNDqZ 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+zAexzxgT8AWFSUEnRBYju3Xr1q1bt27dunXr1q1bt27dunXr1q1bt27dunXr1u3D2v8AoPzl +7A=====271633~ +AFNI_CLUSTSIM_NN2_1sided = <3dClustSim_NN2 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="1-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 583.4988 750 853.4951 1076 + 72.85513 86.13865 100.7426 121 + 17.5391 21.34667 24.36394 28.29945 +~ +AFNI_CLUSTSIM_NN3_1sided = <3dClustSim_NN3 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="1-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 669 822 1019 1229 + 75.49529 90 105.7426 126 + 17.68944 21.51895 24.66536 28.63393 +~ +AFNI_CLUSTSIM_NN1_2sided = <3dClustSim_NN1 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="2-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 184 213.7464 251 312 + 46.86891 54.2897 63.15832 70.48756 + 14.42016 17 19.763 23.73162 +~ +AFNI_CLUSTSIM_NN2_2sided = <3dClustSim_NN2 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="2-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 225.1981 275 323 402 + 50.71377 58.70737 67.49013 79.47508 + 14.74798 17.44949 19.85834 24.1451 +~ +AFNI_CLUSTSIM_NN3_2sided = <3dClustSim_NN3 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="2-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 247.1981 297.3301 350 435 + 51.58872 60 69.32673 81 + 14.83897 17.5301 19.92863 24.29945 +~ +AFNI_CLUSTSIM_NN1_bisided = <3dClustSim_NN1 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="bi-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 184 213.7464 251 312 + 46.86891 54.2897 63.15832 70.48756 + 14.42016 17 19.763 23.73162 +~ +AFNI_CLUSTSIM_NN2_bisided = <3dClustSim_NN2 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="bi-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 225.1981 275 323 402 + 50.71377 58.70737 67.49013 79.47508 + 14.74798 17.44949 19.85834 24.1451 +~ +AFNI_CLUSTSIM_NN3_bisided = <3dClustSim_NN3 + ni_type="4*float" + ni_dimen="3" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + thresholding="bi-sided" + nxyz="61,73,61" + dxyz="3.000,3.000,3.000" + fwhmxyz="0.00,0.00,0.00" + iter="2000" + pthr="0.05,0.01,0.001" + athr="0.1,0.05,0.025,0.01" + mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_name="./full_mask.group+tlrc.HEAD" + mask_count="57300" > + 245 295 347.4951 433 + 51.58872 60 69.32673 81 + 14.83897 17.5301 19.92863 24.29945 +~ +BRICK_KEYWORDS = (null) diff --git a/hw3/output/Words.group_clusters.md b/hw3/output/Words.group_clusters.md new file mode 100644 index 0000000..73e50af --- /dev/null +++ b/hw3/output/Words.group_clusters.md @@ -0,0 +1,17 @@ +# Words-Fixation Activation Map (Cluster Correction) +* voxel-wise threshold = .001, cluster-wise threshold = .05 +* coordinates are peak voxel of each cluster in MNI space + +| Cluster Size | Peak Value (Z) | x (mm) | y (mm) | z (mm) | +| ------------ | -------------- | ------:| ------:| ------:| +| 413 | 5.0654 | 33 | 87 | -6 | +| 287 | 4.3925 | -42 | 57 | -18 | +| 175 | 4.9605 | 6 | -12 | 51 | +| 105 | 4.9438 | 48 | -6 | 36 | +| 44 | 3.8046 | -33 | 60 | 45 | +| 39 | 4.0637 | 51 | 48 | 0 | +| 38 | 3.9016 | -45 | 0 | 51 | +| 37 | 4.5484 | -9 | 66 | -18 | +| 31 | 4.083 | 24 | 51 | 45 | +| 30 | 3.917 | 33 | -21 | 9 | +| 22 | 3.9008 | 3 | 72 | -24 | diff --git a/hw3/scripts/Homework-3_Group-Analysis.sh b/hw3/scripts/Homework-3_Group-Analysis.sh new file mode 100644 index 0000000..28add78 --- /dev/null +++ b/hw3/scripts/Homework-3_Group-Analysis.sh @@ -0,0 +1,91 @@ +#!/bin/bash + +# Part 0: Prep +3dmask_tool \ +-input masks/full_mask.sub-*+tlrc.HEAD \ +-frac 1.0 \ +-prefix full_mask.group + + +# Part 1: Group statistics +3dttest++ -mask full_mask.group+tlrc -prefix Words.group -setA 'betas/stats*+tlrc.HEAD[Words#0_Coef]' + + +# Part 2: Cluster correction +## Estimate Data Smoothness +for f in blurs/blur_est.*.1D; do + 1d_tool.py -infile $f -select_rows 3 -write - >> blurs.acf.1D +done + +1dsum -mean blurs.acf.1D > blurs.acf.avg.1D + +3dClustSim \ +-mask full_mask.group+tlrc \ +-acf `1dcat blurs.acf.avg.1D'[0:2]'` \ +-both \ +-pthr .05 .01 .001 \ +-athr .1 .05 .025 .01 \ +-iter 2000 \ +-prefix cluster \ +-cmd refit.cmd + +## attach ClustSim tables to dataset +`cat refit.cmd` Words.group+tlrc + +## convert t-values to z-values +3dmerge -1zscore -prefix statz_Words.group 'Words.group+tlrc[1]' + +## find clusters that survive threshold (pthr = .001, athr = .05) +### NN3 = 1.74 = (2*sqrt(.5^2+.5)) +### NN2 = 1.42 = (2*sqrt(.5^2+.5^2)) +### NN1 = 1.01 +### p = .05; z = 1.96 (one sided) +### p = .01; z = 2.3 (one sided) +### p = .001; z= 3 (one sided) +cluster_size=`1dcat cluster.NN3_1sided.1D'[2]{2}'` +3dclust -1Dformat -nosum \ + -inmask \ + -1noneg \ + -1clip 3 \ + -dxyz=1 \ + 1.74 $cluster_size \ + statz_Words.group+tlrc > Words.group_clusters.1D + +## create table +echo "# Words-Fixation Activation Map (Cluster Correction)" > Words.group_clusters.md +echo "* voxel-wise threshold = .001, cluster-wise threshold = .05 " >> Words.group_clusters.md +echo "* coordinates are peak voxel of each cluster in MNI space " >> Words.group_clusters.md +echo " " >> Words.group_clusters.md +echo "| Cluster Size | Peak Value (Z) | x (mm) | y (mm) | z (mm) |" >> Words.group_clusters.md +echo "| ------------ | -------------- | ------:| ------:| ------:|" >> Words.group_clusters.md +1d_tool.py -infile Words.group_clusters.1D \ + -select_cols '[0,12,13,14,15]' \ + -write stdout \ + | awk '{print "| " $1 " | " $2 " | " $3 " | " $4 " | " $5 " |"}' >> Words.group_clusters.md + + +# Part 3. FDR correction +3dFDR -input 'Words.group+tlrc[1]' -prefix FDRz_Words.group +3dclust -1Dformat -nosum \ + -inmask \ + -1noneg \ + -1clip 1.96 \ + -dxyz=1 \ + 1.74 1 \ + FDRz_Words.group+tlrc > Words.group_FDR.1D + +## create table +echo "# Words-Fixation Activation Map (FDR Correction)" > Words.group_FDR.md +echo "* q = .05 " >> Words.group_FDR.md +echo "* coordinates are center of mass of each cluster in MNI space " >> Words.group_FDR.md +echo " " >> Words.group_FDR.md +echo "| Cluster Size | Peak Value (Z) | x (mm) | y (mm) | z (mm) |" >> Words.group_FDR.md +echo "| ------------ | -------------- | ------:| ------:| ------:|" >> Words.group_FDR.md +1d_tool.py -infile Words.group_FDR.1D \ + -select_cols '[0,12,1,2,3]' \ + -write stdout \ + | awk '{print "| " $1 " | " $2 " | " $3 " | " $4 " | " $5 " |"}' >> Words.group_FDR.md + + +# Part 4. Output attributes +3dAttribute -all Words.group+tlrc > Words.group_attr.1D From 74f000d490155fe3f71c503e469dfb9489039b89 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Sat, 19 Aug 2017 20:33:49 -0400 Subject: [PATCH 14/18] select the REML acf blur estimates --- hw3/scripts/Homework-3_Group-Analysis.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) mode change 100644 => 100755 hw3/scripts/Homework-3_Group-Analysis.sh diff --git a/hw3/scripts/Homework-3_Group-Analysis.sh b/hw3/scripts/Homework-3_Group-Analysis.sh old mode 100644 new mode 100755 index 28add78..39ebfb5 --- a/hw3/scripts/Homework-3_Group-Analysis.sh +++ b/hw3/scripts/Homework-3_Group-Analysis.sh @@ -14,7 +14,7 @@ # Part 2: Cluster correction ## Estimate Data Smoothness for f in blurs/blur_est.*.1D; do - 1d_tool.py -infile $f -select_rows 3 -write - >> blurs.acf.1D + 1d_tool.py -infile $f -select_rows 5 -write - >> blurs.acf.1D done 1dsum -mean blurs.acf.1D > blurs.acf.avg.1D From 328b05312f7121bbd5cf79a9025dc07268754fa4 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Sat, 19 Aug 2017 20:36:10 -0400 Subject: [PATCH 15/18] change 3dClustSim iterations to 10000 --- hw3/scripts/Homework-3_Group-Analysis.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hw3/scripts/Homework-3_Group-Analysis.sh b/hw3/scripts/Homework-3_Group-Analysis.sh index 39ebfb5..526c4eb 100755 --- a/hw3/scripts/Homework-3_Group-Analysis.sh +++ b/hw3/scripts/Homework-3_Group-Analysis.sh @@ -25,7 +25,7 @@ done -both \ -pthr .05 .01 .001 \ -athr .1 .05 .025 .01 \ --iter 2000 \ +-iter 10000 \ -prefix cluster \ -cmd refit.cmd From de9f5332d0441119028327affd0dbd766a183980 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Sat, 19 Aug 2017 20:39:06 -0400 Subject: [PATCH 16/18] mask uncorrected z-map with FDR threshold --- hw3/scripts/Homework-3_Group-Analysis.sh | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/hw3/scripts/Homework-3_Group-Analysis.sh b/hw3/scripts/Homework-3_Group-Analysis.sh index 526c4eb..feadc5e 100755 --- a/hw3/scripts/Homework-3_Group-Analysis.sh +++ b/hw3/scripts/Homework-3_Group-Analysis.sh @@ -65,14 +65,20 @@ echo "| ------------ | -------------- | ------:| ------:| ------:|" >> Words.gr # Part 3. FDR correction +## apply FDR correction and convert t-values into z-values 3dFDR -input 'Words.group+tlrc[1]' -prefix FDRz_Words.group + +## use FDR corrected z-values > 1.96 (q = .05) to mask the uncorrected z-map +3dcalc -a 'Words.group+tlrc[1]' -b FDRz_Words.group+tlrc \ + -expr 'a*ispositive(b-1.96)' -prefix FDR-masked_Words.group + +## run 3dclust on FDR correction masked z-map 3dclust -1Dformat -nosum \ - -inmask \ + -inmask \ -1noneg \ - -1clip 1.96 \ -dxyz=1 \ 1.74 1 \ - FDRz_Words.group+tlrc > Words.group_FDR.1D + FDR-masked_Words.group+tlrc > Words.group_FDR.1D ## create table echo "# Words-Fixation Activation Map (FDR Correction)" > Words.group_FDR.md From 831cf7d5bedd733b5e6f2d8faf272caa97dd5df4 Mon Sep 17 00:00:00 2001 From: Monica Li Date: Sat, 19 Aug 2017 20:44:51 -0400 Subject: [PATCH 17/18] add cluster size unit --- hw3/scripts/Homework-3_Group-Analysis.sh | 26 +++++++++++++----------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/hw3/scripts/Homework-3_Group-Analysis.sh b/hw3/scripts/Homework-3_Group-Analysis.sh index feadc5e..b7fdda1 100755 --- a/hw3/scripts/Homework-3_Group-Analysis.sh +++ b/hw3/scripts/Homework-3_Group-Analysis.sh @@ -52,12 +52,13 @@ cluster_size=`1dcat cluster.NN3_1sided.1D'[2]{2}'` statz_Words.group+tlrc > Words.group_clusters.1D ## create table -echo "# Words-Fixation Activation Map (Cluster Correction)" > Words.group_clusters.md -echo "* voxel-wise threshold = .001, cluster-wise threshold = .05 " >> Words.group_clusters.md -echo "* coordinates are peak voxel of each cluster in MNI space " >> Words.group_clusters.md -echo " " >> Words.group_clusters.md -echo "| Cluster Size | Peak Value (Z) | x (mm) | y (mm) | z (mm) |" >> Words.group_clusters.md -echo "| ------------ | -------------- | ------:| ------:| ------:|" >> Words.group_clusters.md +echo "# Words-Fixation Activation Map (Cluster Correction)" > Words.group_clusters.md +echo "* voxel-wise threshold = .001, cluster-wise threshold = .05 " >> Words.group_clusters.md +echo "* coordinates are peak voxel of each cluster in MNI space " >> Words.group_clusters.md +echo "* voxel size is 3 mm x 3 mm x 3 mm " >> Words.group_clusters.md +echo " " >> Words.group_clusters.md +echo "| Cluster Size (# of Voxel) | Peak Value (Z) | x (mm) | y (mm) | z (mm) |" >> Words.group_clusters.md +echo "| ------------------------- | -------------- | ------:| ------:| ------:|" >> Words.group_clusters.md 1d_tool.py -infile Words.group_clusters.1D \ -select_cols '[0,12,13,14,15]' \ -write stdout \ @@ -81,12 +82,13 @@ echo "| ------------ | -------------- | ------:| ------:| ------:|" >> Words.gr FDR-masked_Words.group+tlrc > Words.group_FDR.1D ## create table -echo "# Words-Fixation Activation Map (FDR Correction)" > Words.group_FDR.md -echo "* q = .05 " >> Words.group_FDR.md -echo "* coordinates are center of mass of each cluster in MNI space " >> Words.group_FDR.md -echo " " >> Words.group_FDR.md -echo "| Cluster Size | Peak Value (Z) | x (mm) | y (mm) | z (mm) |" >> Words.group_FDR.md -echo "| ------------ | -------------- | ------:| ------:| ------:|" >> Words.group_FDR.md +echo "# Words-Fixation Activation Map (FDR Correction)" > Words.group_FDR.md +echo "* q = .05 " >> Words.group_FDR.md +echo "* coordinates are center of mass of each cluster in MNI space " >> Words.group_FDR.md +echo "* voxel size is 3 mm x 3 mm x 3 mm " >> Words.group_FDR.md +echo " " >> Words.group_FDR.md +echo "| Cluster Size (# of Voxel) | Peak Value (Z) | x (mm) | y (mm) | z (mm) |" >> Words.group_FDR.md +echo "| ------------------------- | -------------- | ------:| ------:| ------:|" >> Words.group_FDR.md 1d_tool.py -infile Words.group_FDR.1D \ -select_cols '[0,12,1,2,3]' \ -write stdout \ From aa135705f56cc16f820f8358a906f7e1cd0fb66f Mon Sep 17 00:00:00 2001 From: Monica Li Date: Sat, 19 Aug 2017 20:45:18 -0400 Subject: [PATCH 18/18] update output --- hw3/output/Words.group_FDR.md | 190 ++++++++--------------------- hw3/output/Words.group_attr.1D | 114 ++++++++--------- hw3/output/Words.group_clusters.md | 5 +- 3 files changed, 112 insertions(+), 197 deletions(-) diff --git a/hw3/output/Words.group_FDR.md b/hw3/output/Words.group_FDR.md index ccd0fbb..96f5fe4 100644 --- a/hw3/output/Words.group_FDR.md +++ b/hw3/output/Words.group_FDR.md @@ -1,142 +1,56 @@ # Words-Fixation Activation Map (FDR Correction) * q = .05 * coordinates are center of mass of each cluster in MNI space +* voxel size is 3 mm x 3 mm x 3 mm -| Cluster Size | Peak Value (Z) | x (mm) | y (mm) | z (mm) | -| ------------ | -------------- | ------:| ------:| ------:| -| 3554 | 3.2815 | 3.7 | 57.3 | 33.9 | -| 1133 | 3.1054 | 12.5 | -44 | 11.5 | -| 693 | 3.113 | 39.8 | 67.8 | -10.2 | -| 528 | 3.0362 | -36.9 | 71.7 | -11.4 | -| 443 | 3.0362 | -54.9 | 14.8 | 10 | -| 260 | 3.113 | 0.5 | -9.2 | 54.6 | -| 183 | 3.113 | 48 | 0.8 | 43 | -| 160 | 3.1054 | -25.9 | -35.3 | 45.2 | -| 123 | 2.8517 | -43.5 | -0.2 | 44.2 | -| 109 | 2.832 | -27.6 | -60.6 | 16.2 | -| 101 | 3.0695 | -3.7 | 70.4 | -19.3 | -| 74 | 2.8091 | -30.2 | 57.4 | 47.4 | -| 66 | 2.9463 | 25.2 | 54.3 | 46.3 | -| 63 | 2.8595 | 33.1 | -24.8 | 7.1 | -| 52 | 2.9323 | -29.2 | 45.3 | -7.8 | -| 48 | 2.8194 | 60.9 | 28.1 | 26.3 | -| 36 | 2.899 | -22.8 | 12.4 | 59.5 | -| 25 | 2.6046 | 57.8 | -1.2 | -23.6 | -| 20 | 2.4962 | 40.9 | 22.2 | 58 | -| 16 | 2.9598 | -60.1 | 44.8 | 42.4 | -| 15 | 2.6225 | -32.6 | 52.9 | 6.4 | -| 15 | 2.9951 | 19 | 26.8 | 8.3 | -| 13 | 2.7898 | 25.1 | 39.9 | 58.1 | -| 12 | 2.8196 | 37.5 | 14.3 | 34.3 | -| 11 | 2.661 | -19.6 | -35.9 | -1.9 | -| 11 | 2.3227 | -41.4 | -33.2 | 23.4 | -| 11 | 2.2315 | 48.6 | -31.4 | 35.7 | -| 10 | 2.3986 | -37.8 | -15.1 | -12.9 | -| 10 | 2.6816 | -19.8 | 19.4 | -3.5 | -| 10 | 2.3236 | -57 | 47.4 | 7.2 | -| 9 | 2.5982 | 7.9 | 20.5 | -8.4 | -| 9 | 2.2699 | 5.7 | 99.4 | 9.7 | -| 9 | 2.4501 | 7.3 | -3 | 24 | -| 9 | 2.1847 | -3 | -23.3 | 26.7 | -| 8 | 2.5729 | 32.7 | 30 | 32.3 | -| 8 | 2.2952 | -1.5 | -61.9 | 32.3 | -| 8 | 2.2893 | -46.9 | 53.6 | 46.1 | -| 7 | 2.3202 | 62.2 | 57.8 | -8.5 | -| 7 | 2.4284 | 36.4 | 19.7 | 1.7 | -| 7 | 2.1129 | 11.1 | 21.4 | 25.3 | -| 7 | 2.6014 | -24 | -18 | 60.8 | -| 6 | 2.4779 | -54.5 | -30 | -5 | -| 6 | 2.491 | 22 | -2.5 | -5.1 | -| 6 | 2.0826 | -33.5 | -25 | 2 | -| 6 | 2.1962 | 41 | 29.6 | 8.5 | -| 6 | 2.5684 | 19.5 | -21 | 32 | -| 5 | 2.427 | -64.8 | 6.6 | -24 | -| 5 | 2.2239 | 19.2 | 37.8 | -18.1 | -| 5 | 2.3669 | -32.4 | 70.2 | 3.1 | -| 5 | 2.2723 | 67.2 | 22.8 | 0.6 | -| 5 | 2.2281 | 54.7 | 22.9 | 10.8 | -| 5 | 2.5274 | 22.8 | -28.8 | 21.1 | -| 5 | 2.3311 | 9.6 | 8.5 | 32.4 | -| 4 | 2.2094 | 45.7 | -14.2 | -20.3 | -| 4 | 2.4703 | 46.4 | 12 | 3 | -| 4 | 2.1785 | -47.9 | -40.5 | 5.3 | -| 4 | 2.5742 | -68.3 | 39.7 | 14.3 | -| 4 | 2.2167 | -18.1 | -27 | 16.5 | -| 4 | 2.4073 | 15.7 | -33 | 23.9 | -| 4 | 2.244 | 42 | 35.3 | 26.4 | -| 4 | 2.318 | 61.5 | -7.5 | 27 | -| 4 | 2.2286 | 65.3 | 27.8 | 41.3 | -| 4 | 2.5143 | -9 | 22.7 | 64.4 | -| 3 | 2.2226 | -43 | -1 | -30 | -| 3 | 2.3435 | -32 | -21 | -27.9 | -| 3 | 2.1955 | 30 | -37 | -11 | -| 3 | 2.0953 | 21 | 1 | 8 | -| 3 | 2.1552 | -4 | -49 | 27 | -| 3 | 2.161 | -34 | 28 | 41 | -| 2 | 2.3001 | 37.4 | -18 | -36 | -| 2 | 2.2888 | 54 | -10.4 | -33 | -| 2 | 2.7347 | -31.4 | -28.4 | -19.6 | -| 2 | 2.1885 | 30 | 25.5 | -15 | -| 2 | 2.4731 | 21 | -52.5 | -15 | -| 2 | 2.0509 | -61.5 | 51 | -3 | -| 2 | 2.0055 | 66 | 40.5 | 0 | -| 2 | 2.2403 | 33 | 34.5 | 0 | -| 2 | 2.2426 | -42 | 37.5 | 3 | -| 2 | 2.2026 | -15 | -1.5 | 3 | -| 2 | 2.1128 | 36 | 39 | 13.5 | -| 2 | 2.3705 | -34.4 | -21 | 12 | -| 2 | 2.5353 | 3 | -24 | 13.6 | -| 2 | 2.013 | 39 | -43.5 | 13.5 | -| 2 | 2.0589 | -46.5 | -15 | 18 | -| 2 | 2.0849 | -10.5 | 21 | 21 | -| 2 | 2.1302 | 10.6 | 93 | 24 | -| 2 | 2.2077 | 31.6 | 15 | 27 | -| 2 | 1.9941 | -49.5 | 10.5 | 27 | -| 2 | 2.4466 | -34.4 | 13.4 | 31.6 | -| 2 | 2.0714 | 60 | 39 | 43.5 | -| 2 | 2.0942 | -33 | 13.5 | 42 | -| 2 | 2.2862 | 45 | 36 | 46.6 | -| 2 | 2.1863 | -31.5 | -13.5 | 51 | -| 2 | 2.1169 | -12 | -19.5 | 60 | -| 2 | 2.0433 | -6 | -34.5 | 60 | -| 1 | 2.0258 | 45 | 3 | -36 | -| 1 | 1.972 | -15 | 75 | -30 | -| 1 | 2.0618 | -24 | 69 | -30 | -| 1 | 2.3999 | -48 | 51 | -30 | -| 1 | 1.9779 | -9 | 24 | -30 | -| 1 | 2.1306 | 27 | 18 | -27 | -| 1 | 2.2248 | -21 | 18 | -24 | -| 1 | 1.9715 | 18 | 15 | -24 | -| 1 | 1.967 | 36 | -6 | -21 | -| 1 | 2.0179 | 6 | 48 | -18 | -| 1 | 1.9682 | -42 | 15 | -18 | -| 1 | 2.0902 | 45 | 15 | -15 | -| 1 | 1.9687 | 18 | -33 | -15 | -| 1 | 2.2552 | -21 | -33 | -15 | -| 1 | 2.0172 | 30 | 12 | -12 | -| 1 | 2.0593 | 54 | -42 | -12 | -| 1 | 2.0448 | 69 | 27 | -9 | -| 1 | 2.0782 | -72 | 18 | -9 | -| 1 | 1.9645 | 42 | 3 | -9 | -| 1 | 2.4857 | -60 | 39 | -3 | -| 1 | 2.0686 | -48 | 30 | 0 | -| 1 | 2.0539 | -21 | -27 | 0 | -| 1 | 1.9644 | -48 | -48 | 0 | -| 1 | 2.0113 | -42 | -9 | 3 | -| 1 | 2.2464 | -18 | 33 | 6 | -| 1 | 2.0685 | -15 | -15 | 9 | -| 1 | 2.1577 | 51 | 12 | 12 | -| 1 | 1.9692 | 33 | 30 | 15 | -| 1 | 2.0126 | 24 | 18 | 18 | -| 1 | 2.1026 | -24 | 36 | 21 | -| 1 | 2.0082 | 27 | 21 | 30 | -| 1 | 1.961 | -24 | 0 | 30 | -| 1 | 2.1906 | -24 | -12 | 30 | -| 1 | 2.2538 | -12 | 6 | 33 | -| 1 | 2.0314 | 27 | -24 | 36 | -| 1 | 1.9676 | 15 | 12 | 39 | -| 1 | 1.9659 | 12 | -54 | 45 | -| 1 | 2.2616 | -12 | -24 | 54 | -| 1 | 2.125 | 12 | 15 | 57 | -| 1 | 1.9813 | -30 | -30 | 57 | -| 1 | 2.0621 | 39 | 6 | 66 | +| Cluster Size (# of Voxel) | Peak Value (Z) | x (mm) | y (mm) | z (mm) | +| ------------------------- | -------------- | ------:| ------:| ------:| +| 693 | 8.1915 | 39.7 | 68 | -10.2 | +| 528 | 6.2685 | -36.9 | 71.7 | -11.4 | +| 260 | 7.8546 | 0.5 | -9.1 | 54.6 | +| 183 | 7.8021 | 48.1 | 0.7 | 42.9 | +| 123 | 5.1566 | -43.5 | -0.2 | 44.4 | +| 101 | 6.6676 | -3.9 | 70.4 | -19.3 | +| 74 | 4.9594 | -30.2 | 57.4 | 47.3 | +| 66 | 5.544 | 25.2 | 54.2 | 46.2 | +| 63 | 5.1885 | 33.1 | -24.8 | 7.1 | +| 20 | 4.0048 | 40.9 | 22.2 | 58 | +| 15 | 4.3598 | -32.6 | 52.8 | 6.4 | +| 11 | 4.4665 | -19.6 | -35.9 | -2 | +| 11 | 3.6103 | -41.4 | -33.2 | 23.4 | +| 10 | 3.613 | -57 | 47.4 | 7.1 | +| 9 | 4.2831 | 7.9 | 20.6 | -8.4 | +| 9 | 3.8999 | 7.3 | -2.9 | 24 | +| 7 | 3.1746 | 11.1 | 21.4 | 25.3 | +| 6 | 3.9917 | 22 | -2.5 | -5.1 | +| 6 | 3.1176 | -33.5 | -25 | 2 | +| 6 | 4.1992 | 19.5 | -21 | 32.1 | +| 5 | 3.7067 | -32.4 | 70.2 | 3.1 | +| 5 | 4.0892 | 22.9 | -28.9 | 21.1 | +| 4 | 3.3746 | 45.7 | -14.2 | -20.3 | +| 4 | 3.442 | 42 | 35.3 | 26.4 | +| 4 | 3.6003 | 61.5 | -7.5 | 27 | +| 4 | 4.0509 | -9 | 22.8 | 64.3 | +| 3 | 3.1409 | 21 | 1 | 8 | +| 2 | 3.434 | 33 | 34.5 | 0 | +| 2 | 3.7155 | -34.3 | -21 | 12 | +| 2 | 3.0717 | -46.5 | -15 | 18 | +| 2 | 3.1221 | -10.5 | 21 | 21 | +| 2 | 3.3709 | 31.6 | 15 | 27 | +| 2 | 3.1388 | -33 | 13.4 | 42 | +| 2 | 3.5294 | 45 | 36 | 46.6 | +| 1 | 3.7813 | -48 | 51 | -30 | +| 1 | 2.8986 | 36 | -6 | -21 | +| 1 | 2.9016 | -42 | 15 | -18 | +| 1 | 2.993 | 30 | 12 | -12 | +| 1 | 2.8944 | 42 | 3 | -9 | +| 1 | 3.9799 | -60 | 39 | -3 | +| 1 | 3.0912 | -48 | 30 | 0 | +| 1 | 3.0622 | -21 | -27 | 0 | +| 1 | 2.9816 | -42 | -9 | 3 | +| 1 | 2.9838 | 24 | 18 | 18 | +| 1 | 3.1536 | -24 | 36 | 21 | +| 1 | 2.9768 | 27 | 21 | 30 | +| 1 | 2.8872 | -24 | 0 | 30 | +| 1 | 3.3345 | -24 | -12 | 30 | +| 1 | 3.0793 | 39 | 6 | 66 | diff --git a/hw3/output/Words.group_attr.1D b/hw3/output/Words.group_attr.1D index 2718f66..f14ddaf 100644 --- a/hw3/output/Words.group_attr.1D +++ b/hw3/output/Words.group_attr.1D @@ -1,7 +1,7 @@ -HISTORY_NOTE = [mli@Ringo-Lite.frontier.com: Fri Aug 18 19:14:42 2017] {AFNI_17.2.06:macosx_10.7_local} 3dttest++ -mask full_mask.group+tlrc -prefix Words.group -setA 'betas/stats*+tlrc.HEAD[Words#0_Coef]'\n[mli@Ringo-Lite.frontier.com: Fri Aug 18 19:29:06 2017] {AFNI_17.2.06:macosx_10.7_local} 3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:cluster.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:cluster.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:cluster.NN2_1sided.niml -atrstring AFNI_CLUSTSIM_NN3_1sided file:cluster.NN3_1sided.niml -atrstring AFNI_CLUSTSIM_NN1_2sided file:cluster.NN1_2sided.niml -atrstring AFNI_CLUSTSIM_NN2_2sided file:cluster.NN2_2sided.niml -atrstring AFNI_CLUSTSIM_NN3_2sided file:cluster.NN3_2sided.niml -atrstring AFNI_CLUSTSIM_NN1_bisided file:cluster.NN1_bisided.niml -atrstring AFNI_CLUSTSIM_NN2_bisided file:cluster.NN2_bisided.niml -atrstring AFNI_CLUSTSIM_NN3_bisided file:cluster.NN3_bisided.niml Words.group+tlrc~ +HISTORY_NOTE = [mli@Ringo-Lite.frontier.com: Sat Aug 19 20:23:01 2017] {AFNI_17.2.06:macosx_10.7_local} 3dttest++ -mask full_mask.group+tlrc -prefix Words.group -setA 'betas/stats*+tlrc.HEAD[Words#0_Coef]'\n[mli@Ringo-Lite.frontier.com: Sat Aug 19 20:28:10 2017] {AFNI_17.2.06:macosx_10.7_local} 3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:cluster.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:cluster.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:cluster.NN2_1sided.niml -atrstring AFNI_CLUSTSIM_NN3_1sided file:cluster.NN3_1sided.niml -atrstring AFNI_CLUSTSIM_NN1_2sided file:cluster.NN1_2sided.niml -atrstring AFNI_CLUSTSIM_NN2_2sided file:cluster.NN2_2sided.niml -atrstring AFNI_CLUSTSIM_NN3_2sided file:cluster.NN3_2sided.niml -atrstring AFNI_CLUSTSIM_NN1_bisided file:cluster.NN1_bisided.niml -atrstring AFNI_CLUSTSIM_NN2_bisided file:cluster.NN2_bisided.niml -atrstring AFNI_CLUSTSIM_NN3_bisided file:cluster.NN3_bisided.niml Words.group+tlrc~ TYPESTRING = 3DIM_HEAD_FUNC~ -IDCODE_STRING = AFN_RRkQT1ONZHTBuc06DvAv0g~ -IDCODE_DATE = Fri Aug 18 19:14:42 2017~ +IDCODE_STRING = AFN_hJ3bSZ43iN_GUzzAgWe4VA~ +IDCODE_DATE = Sat Aug 19 20:23:01 2017~ SCENE_DATA = 2 11 1 -999 -999 -999 -999 -999 LABEL_1 = zyxt~ LABEL_2 = zyxt~ @@ -27,20 +27,20 @@ BYTEORDER_STRING = LSB_FIRST~ AFNI_CLUSTSIM_NN1_1sided = <3dClustSim_NN1 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="1-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 390 502 613 760 - 65.1627 77.853 91.49506 111 - 16.83356 20.72851 24.05696 28 + 400.5706 488.666 592 741 + 65.59692 77.91489 90.91487 108.5629 + 16.53977 19.69049 23.4056 28.62756 ~ AFNI_CLUSTSIM_MASK = eNrtXEuS47gRBYMO04uO5iy9cBhX6GUvJkwfZY4xC4cBx1wME30R+AZccoEgDCATROJDiarq tqpqkIuSSIEURTxkvpeZLMa6devWrVu3bt26devWrVu3bt26devWrVu3bt26detGbISXdQgv @@ -97,145 +97,145 @@ zAexzxgT8AWFSUEnRBYju3Xr1q1bt27dunXr1q1bt27dunXr1q1bt27dunXr1u3D2v8AoPzl AFNI_CLUSTSIM_NN2_1sided = <3dClustSim_NN2 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="1-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 583.4988 750 853.4951 1076 - 72.85513 86.13865 100.7426 121 - 17.5391 21.34667 24.36394 28.29945 + 571.4532 699.2493 857.1984 1044 + 73.46697 88.2702 103.2608 124.4334 + 17.11004 20.23859 23.90208 29.14529 ~ AFNI_CLUSTSIM_NN3_1sided = <3dClustSim_NN3 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="1-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 669 822 1019 1229 - 75.49529 90 105.7426 126 - 17.68944 21.51895 24.66536 28.63393 + 652 809.499 983 1204 + 75.5631 92.11592 108 130 + 17.24232 20.45582 24.07778 29.44805 ~ AFNI_CLUSTSIM_NN1_2sided = <3dClustSim_NN1 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="2-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 184 213.7464 251 312 - 46.86891 54.2897 63.15832 70.48756 - 14.42016 17 19.763 23.73162 + 185.5571 217.9158 253.5976 309 + 47.13444 54.52903 62.91642 74.59404 + 14.25741 16.73355 19.50444 23.75385 ~ AFNI_CLUSTSIM_NN2_2sided = <3dClustSim_NN2 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="2-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 225.1981 275 323 402 - 50.71377 58.70737 67.49013 79.47508 - 14.74798 17.44949 19.85834 24.1451 + 228.2717 271.2706 320 391 + 50.79831 60.02682 68.73059 81 + 14.61249 17.11479 19.84442 24.04511 ~ AFNI_CLUSTSIM_NN3_2sided = <3dClustSim_NN3 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="2-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 247.1981 297.3301 350 435 - 51.58872 60 69.32673 81 - 14.83897 17.5301 19.92863 24.29945 + 247.691 293.4423 348.499 430 + 51.93026 61.23649 70.14133 82.62376 + 14.70088 17.19333 19.93298 24.1651 ~ AFNI_CLUSTSIM_NN1_bisided = <3dClustSim_NN1 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="bi-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 184 213.7464 251 312 - 46.86891 54.2897 63.15832 70.48756 - 14.42016 17 19.763 23.73162 + 185.5571 217.9158 253.5976 309 + 47.13444 54.52903 62.91642 74.59404 + 14.25741 16.73355 19.50444 23.75385 ~ AFNI_CLUSTSIM_NN2_bisided = <3dClustSim_NN2 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="bi-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 225.1981 275 323 402 - 50.71377 58.70737 67.49013 79.47508 - 14.74798 17.44949 19.85834 24.1451 + 228.2717 271 319.6653 389 + 50.79831 60.02682 68.73059 81 + 14.61249 17.11479 19.84442 24.04511 ~ AFNI_CLUSTSIM_NN3_bisided = <3dClustSim_NN3 ni_type="4*float" ni_dimen="3" - commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823343 4.20372 14.3254 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 2000 -prefix cluster -cmd refit.cmd" + commandline="3dClustSim -mask full_mask.group+tlrc -acf 0.823891 4.19962 14.369 -both -pthr .05 .01 .001 -athr .1 .05 .025 .01 -iter 10000 -prefix cluster -cmd refit.cmd" thresholding="bi-sided" nxyz="61,73,61" dxyz="3.000,3.000,3.000" fwhmxyz="0.00,0.00,0.00" - iter="2000" + iter="10000" pthr="0.05,0.01,0.001" athr="0.1,0.05,0.025,0.01" - mask_dset_idcode="AFN_ZeM47MLgCcNqPlGKIEXhRg" + mask_dset_idcode="AFN_Xz48B9nBZElhaRoI4RZt3Q" mask_dset_name="./full_mask.group+tlrc.HEAD" mask_count="57300" > - 245 295 347.4951 433 - 51.58872 60 69.32673 81 - 14.83897 17.5301 19.92863 24.29945 + 246 291.4584 346.499 427 + 51.93026 61.23649 70.14133 82.62376 + 14.70088 17.19333 19.93298 24.1651 ~ BRICK_KEYWORDS = (null) diff --git a/hw3/output/Words.group_clusters.md b/hw3/output/Words.group_clusters.md index 73e50af..b08a352 100644 --- a/hw3/output/Words.group_clusters.md +++ b/hw3/output/Words.group_clusters.md @@ -1,9 +1,10 @@ # Words-Fixation Activation Map (Cluster Correction) * voxel-wise threshold = .001, cluster-wise threshold = .05 * coordinates are peak voxel of each cluster in MNI space +* voxel size is 3 mm x 3 mm x 3 mm -| Cluster Size | Peak Value (Z) | x (mm) | y (mm) | z (mm) | -| ------------ | -------------- | ------:| ------:| ------:| +| Cluster Size (# of Voxel) | Peak Value (Z) | x (mm) | y (mm) | z (mm) | +| ------------------------- | -------------- | ------:| ------:| ------:| | 413 | 5.0654 | 33 | 87 | -6 | | 287 | 4.3925 | -42 | 57 | -18 | | 175 | 4.9605 | 6 | -12 | 51 |