Brain images cropped during brain extraction and segmentation with fMRIprep

Summary of what happened:

The results of the brain extraction and segmentation for two T1 images of my subjects appear unusual. The brain appears to be cropped, which, of course, affects the subsequent functional images. The raw data seems to be intact. Has anyone else encountered this issue? Any insights would be greatly appreciated. Thank you all in advance!

P.S. In consideration of data protection, I uploaded an image of the functional images .:wink:

Command used (and if a helper script was used, a link to the helper script or the command generated):


fMRI prep version 20.2.1

Environment (Docker, Singularity, custom installation):

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

Hi @Jella_V,

Looks like an issue with skull stripping. Can you please provide the rest of the information in the post template so we can best help? Also, you can try upgrading to the most recent version (23.1.4 at this time).


Hi Steven,

thank you for response! The issue is solved. It seems to be a problem with the freesurfer version my version of fMRIprep is using. If I process the data outside with e.g. fastsurfer and feed that into the fMRIprep preprocessing pipeline the data looks fine.