dcm2bidsscriptsBIDS1_to_2.sh: Merges attempts and saves them toBIDS2/, this is the working directory.fmriprepscripts
Relies on 3TME_XA30_ME4_NORDIC_16bit_maton_PA_Pha_part[12].json files.
Note that I copied my own nordic files for debugging so I could set the log
directory.
Takes dicom_dir, sub_label, and ses_label and writes to BIDS/. Takes up
to an hour or so depending on how many func files there are.
After this script is done, there will only be part-mag files in func/.
Loops over my dicoms dir, extracts sub and ses labels from directory name,
and runs conversion script if output directory does not exist in BIDS/.
Takes identical arguments to part1. Converts phase files and runs one
sbatch script per mag/phase pair to run NORDIC. They are submitted with
sbatch --wait, which means this script does not exit until all runs are done.
Takes 15-45 minutes (excluding queue time).
Loops over BIDS/ and identifies sessions that are ready to be converted.
If there are no part-mag files, it assumes it is converted and skips it.
Because I have few sessions (33) I just let it run in sequence, but would need
to be parallelized to handle many more sessions.
The BLFU sessions have two attempts: A1 and A2. This script combines those
and removes the A. label from all sessions and copies them to BIDS2.
It skips those that still have any part- files remaining. Relies on
combine_bids_sessions.