Problems with brain extraction in fMRIprep ants

Hi All

I’m running fmriprep on an old dataset and brainextraction is failing in 48/49 subjects, giving outputs like this:

Im running fmriprep through docker using the following command

fmriprep-docker /mnt/RAIDSTORAGE/MONTEVIDEOREST/Nifti /mnt/RAIDSTORAGE/MONTEVIDEOREST/derivatives --participant-label c01 --fs-license-file /home/irebollo/freesurfer/license.txt --fs-subjects-dir /mnt/RAIDSTORAGE/MONTEVIDEOREST/freesurferdata --omp-nthreads 16 --output-spaces fsaverage MNI152NLin2009cAsym:res-3 --anat-only

Im using a linux mint PC, 64gb of ram, 32 cpus
fmriprep version 20.0.4

The problem seems related to this issue

, although I understand that there is no working directory issue since im running it through docker?

Please find here the report of the subject

And here the defaced anatomy

I am now running fmriprep with freesurfer (instead of providing the path to freesurfer files) to see if it solves the issue

Thank you very much for your help!

Strangely, recomputing freesurfer segmentation with fmriprep has solved the issue.
For info, I had the images processed with freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c