Summary of what happened: We are trying to run fMRIPrep and having some difficulty with field maps (direction: PA) being read by our fMRI Prep script (see below). We have 5 different runs of the task (rest, task 1, rest, task 2, rest), so we also have a bids_filtering script for each run. Ideally, we would like to have one script running fMRIPrep with all of these 5 runs with their specific field map, but first we are trying to just start with the field maps working for 1 run.

Any help with what could be wrong would be greatly appreciated. Thank you! 

Command used:

fMRIPrep Command:
for s in (cat{ROOTDIR}/MRI/subject_list.txt) ; do if [[ ! -d OUTDIR/derivatives/fmripreprestrun1/{s} ]] ; then echo "let "rnd = RANDOM{s}.out ${TMPDIR}/s.wrk; fmriprep{ROOTDIR}/MRI/rawdata ${TMPDIR}/s.outparticipant−−participantlabel{s} -w ${TMPDIR}/s.wrk−−output−spaceMNI152NLin6Asym:res−2T1wfsnativefsaveragefsaverage5−−nthreads1−−omp−nthreads1−−bids−filter−file{ROOTDIR}/code/bids_filter_rest_run1.json --skip_bids_validation --notrack --dummy-scan 4; \ mkdir -p OUTDIR/derivatives/fmripreprestrun1; rsync−a$TMPDIR/{s}.out/ OUTDIR/derivatives/fmripreprestrun1; rm−rf$TMPDIR/{s}.out ${TMPDIR}/s.wrk">>{SWARMFILE} fi done

Bids_Filter_Rest_1:
{
“bold”: {
“datatype”: “func”,
“task”: [“movie”],
“session”: [“1”],
“run”: [“1”],
“suffix”: “bold”
},
“fmap”: {
“datatype”: “fmap”,
“direction”: [“PA”],
“run”: [“1”]
}
}

Sample fmap file name:

sub-12345_ses-1_dir-opposite_run-1_epi.nii.gz

Version: fMRIPrep 25.1.3