Error running FreeSurfer via fMRIPrep

I encountered a similar issue (I think). With an error in the sampler - when I’ve looked, a didn’t find the files rh.cortex.label

I run this one using Singularity on a slurm based HPC

I attach the full log:

slurm-36299795.txt (1.7 MB)

Hi @orduek, your execution fails because of this:

mri_vol2surf: could not open label file /gpfs/ysm/scratch60/oad4/output/freesurfer/fsaverage5/label/rh.cortex.label
Invalid argument
mri_vol2surf: could not load label file /gpfs/ysm/scratch60/oad4/output/freesurfer/fsaverage5/label/rh.cortex.label

which is under the fsaverage5 directory (meaning, unrelated to the other thread you first posted).

This should be working out for you.

Can you check whether /gpfs/ysm/scratch60/oad4/output/freesurfer/fsaverage5/label/rh.cortex.label exists at all?

Thanks for the response.
I’ve checked, the file is not there - actually this specific folder is completely empty for some reason

Are you trying to reuse some existing freesurfer run?

Nope. I just ran a standard fmriPrep singularity with recon-all, on a new set of nifti files.
These are the commands I was using:

singularity run --cleanenv /project/ysm/levy_ifat/fmriPrep/fmriprep-1.4.1.simg
/home/oad4/scratch60/kpeBIDS/kpe_forFmriPrep /home/oad4/scratch60/kpeOutput
participant
–skip_bids_validation
–fs-license-file /home/oad4/freesurferLicense/license.txt
-w /home/oad4/scratch60/work
–nthreads 8
–ignore slicetiming
–participant_label 1468

Ok,
I cleaned the working directory and it seems to work better.
I have used the same working directory with previous versions and that might caused an issue.
Thanks,
Or.

Glad you found out the issue, and thanks for your patience given the slow response.

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