How to run subjects in parallel using fmriprep-docker wrapper?

1

Hi all, I’m currently trying to run a few subjects in parallel, and used the guidelines as laid out in this post (mentioned in the FAQ): Fmriprep: Workaround for running subjects in parallel. I tried this command:

sleep 1m && fmriprep-docker [source] [dest] participant --participant-label 01 --anat-only --fs-license-file licenses/freesurfer/license.txt --fs-no-reconall
sleep 2m && fmriprep-docker [source] [dest] participant --participant-label 02 --anat-only --fs-license-file licenses/freesurfer/license.txt --fs-no-reconall
sleep 3m && fmriprep-docker [source] [dest] participant --participant-label 03 --anat-only --fs-license-file licenses/freesurfer/license.txt --fs-no-reconall
sleep 4m && fmriprep-docker [source] [dest] participant --participant-label 04 --anat-only --fs-license-file licenses/freesurfer/license.txt --fs-no-reconall

This didn’t work. It only ran the first subject. I assume you cannot use the same parallel strategy when running fmriprep via docker? Does anyone have any tips on how I could get this to work?

2

Hi, I updated that post here to make it a bit more clear: Updated: Fmriprep: Workaround for running subjects in parallel

Essentially, I tried to make clear that each line needs to be run as a separate job. Sorry if that was obvious to you already.

3

No problem, I realized later I just misunderstood your post. I figured to just open several terminal windows and run each line separately which did the trick.