upadated README.md

Author: clarkenj

adni/README.md

@@ -5,7 +5,7 @@ Scripts for preprocessing ADNI data with fMRIPrep2.2.7lts.
 - Python
 ## Retrieving data
 Data not openly available. Used BIDS-ified dataset on Elm.
-## BIDS errors
+## BIDS validation fixes
 Ran the following scripts to fix errors:
 1. `1_create_dataset_description.py`
     -  creates `dataset_description.json` at the root directory with minimal information
@@ -25,6 +25,20 @@ Ran the following scripts to fix errors:
     - halves the slice timing for sub-109S4594 (ses-20160502), which appears to be doubled (see [discussion](https://neurostars.org/t/help-with-bids-errors-66-and-75-in-legacy-dataset/25625))
     - fixes BIDS validation error `code: 66 SLICETIMING_VALUES_GREATOR_THAN_REPETITION_TIME`
 
+## Run fMRIPrep
+- `5_generate_slurm_script.sh`
+- `6_archive_fmriprep.sh`
+
+## Run QC
+- `7_submit_qc_array.sh`
+    - run once with `--reindex-bids` flag on one participant to build the database layout (increase wall time)
+    - remove flag and run again with all participants.
+- `8_archive_qc.sh`
+
+## Generate connectomes
+- `9_connectome_slurm_array.bash` and `9_submit_connectome_array.sh`. As above run once with `--reindex-bids` flag and one atlas/strategy. I submitted each atlas/strategy pair individually because I hadn't yet figured out the optimal way to submit them (see e.g. HCP-EP)
+- `10_archive_connectome.sh`
+
 n.b. error `code: 75 - NIFTI_PIXDIM4` affected two subjects. Suggested fix to edit nifti header fields (see [discussion](https://neurostars.org/t/help-with-bids-errors-66-and-75-in-legacy-dataset/25625/2)). One subject would fail anyway, since `Time` field is `0`, so in interests of saving time I have left this for now.
 
 n.b.(b?) around 100 subjects processed without --use-aroma flag. Used detect_timeout.py script to remove.