Fmriprep stucking during processing data with lesion mask

Hi everyone,

I used fmriprep to process data with lesion mask, but it had been struck at a certain step for long time (at least 5 days) without error report and also I’m not sure if it’s still running.

fmriprep was struck at this step:

Here is some information that may be helpful in solving the problem

  • fmriprep-docker version: 20.2.1

  • The command I used to run fmriprep:
    fmriprep-docker /data/disk1/test/ /data/disk1/test_output --participant-label sub-FCS029 --cifti-output 91k --fs-license-file /opt/software/freesurfer/license.txt --use-aroma --user $(id -u):$(id -g)

  • And I also placed the lesion mask data and the .ignore file:

  • This is the image of T1w and lesion mask:

Many thanks for your help!


I doubt the lesion mask has anything to do with it; fmriprep should ignore it. I would upgrade to 20.2.3, as 20.2.1 has been flagged. How much memory/cpus are you devoting to the job?

The computer runing fmriprep had 24 cpus and 94GB memory, I think it’s enough.
I will update to 20.2.3 and try it again, thanks!