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homework 3 submission #12

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74cbffb
add timing script and files
monicaycli Aug 4, 2017
0b0150f
add experiment 1 script
monicaycli Aug 4, 2017
c4efe30
add afni auto-generated scripts for exp-1
monicaycli Aug 4, 2017
8226a54
add more file extensions to .gitignore
monicaycli Aug 4, 2017
389a393
update Exp-1 scripts
monicaycli Aug 4, 2017
18be69d
add Exp-2 scripts
monicaycli Aug 4, 2017
8efdaa9
rm tmp file
monicaycli Aug 4, 2017
3340122
fix regression contrast
monicaycli Aug 4, 2017
200610b
add homework response
monicaycli Aug 4, 2017
16d687b
discard the first TR (2.5 sec) from timing files
monicaycli Aug 5, 2017
2102ceb
drop first TR; add -tpattern alt+z; fix GLM typo
monicaycli Aug 5, 2017
a46d729
move homework 2 to subdirectory
monicaycli Aug 19, 2017
1fc8dfa
add homework 3 script and output files
monicaycli Aug 19, 2017
74f000d
select the REML acf blur estimates
monicaycli Aug 20, 2017
328b053
change 3dClustSim iterations to 10000
monicaycli Aug 20, 2017
de9f533
mask uncorrected z-map with FDR threshold
monicaycli Aug 20, 2017
831cf7d
add cluster size unit
monicaycli Aug 20, 2017
aa13570
update output
monicaycli Aug 20, 2017
97bfa05
merge with origin master
monicaycli Jan 31, 2018
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5 changes: 4 additions & 1 deletion .gitignore
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@@ -1,2 +1,5 @@
*.BRIK
*.HEAD
@*
*.jpg
.DS_Store

21 changes: 21 additions & 0 deletions hw2/Exp-1.sh
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#!/bin/bash

# 1. Threshold the stats at p <.05
3dmerge -1zscore -1thresh 1.96 -1noneg \
-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 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 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 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 Exp-1/mask+tlrc -dodice Exp-1/stats.test.bin+tlrc Exp-1/stats.retest.bin+tlrc
48 changes: 48 additions & 0 deletions hw2/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.ap.sub_03
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#!/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

29 changes: 29 additions & 0 deletions hw2/Exp-1/subject_results/group.retest/subj.sub_03/.orig.cmd.usubj.sub_03
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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
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