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
–fs-license-file /home/oad4/freesurferLicense/license.txt
-w /home/oad4/scratch60/work
–nthreads 8
–ignore slicetiming
–participant_label 1468

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.

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

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