Hello!
My lab is currently comparing pipelines for fmri analysis. Right now I am working on setting up our fsl pipeline. I’ve set up all of the appropriate inputs (BET’d anatomicals, events txt files, confounds txt files, slice timing files…) and have used the FSL gui to run FEAT on one subject. Following the instructions at this guide I saved the parameters as and FSF, then went through and replaced subject-specific data with variables.
e.g. this:
4D AVW data or FEAT directory (1)
set feat_files(1) “/oak/stanford/groups/russpold/data/uh2/aim1/BIDS_scans/sub-s999/ses-1/func/sub-s999_ses-1_task-DPX_run-1_bold”
and this:
Total volumes
set fmri(npts) 1100
became:
4D AVW data or FEAT directory (1)
set feat_files(1) “/oak/stanford/groups/russpold/data/uh2/aim1/BIDS_scans/{RELATIVE_BOLD}”
Total volumes
set fmri(npts) {NTP}
because the ntp varies based on how long the subject was comfortable in the scanner, I have a python script that looks at each nii.gz 's header and then writes a string like this to my sbatch file:
sed -e “s|{RELATIVE_BOLD}|/sub-s999/ses-1/func/sub-s999_ses1_task-DPX_run-1_bold|g” -e “s|{SUBJECT}|s999|g” -e “s|{NTP}|1100|g” template_DPX_fsl.fsf | feat
So my sbatch file will just be a long list of these strings (I’m sure there is a better way but am struggling to happen upon one).
Unfortunately, this is not working. the slurm .err file is blank, and the .out file is simply
Usage: feat <design.fsf>
Nothing else seems to be generated. My hope is that one of you knowledgeable readers will quickly (and with minimal judgement) catch my error, or know where to look for more information.
Best,
Henry