Fmriprep no freesurfer output for some participants

I’ve run fMRIPrep on a singularity container for a bunch of participants. All participants have a derivatives/fmriprep output folder, and the majority also have a derivatives/freesurfer subject folder, but some do not. I’ve used the same command line for all participants. Any idea why one subject would have freesurfer output folder and others wouldnt?


Was FreeSurfer run as part of fMRIPrep? It is by default, unless you add the --fs-no-reconall flag. Did the subjects who do not have freesurfer outputs have fMRIPrep processes that crashed? If so, what kind of error logs are there?


Hi Steven,

I did not include the --fs-no-reconall flag in my fmriprep command. Some subjects had errors (e.g., BIDS formatting errors mostly), but those were all fixed and I reran fmriprep without any additional errors. However, the freesurfer folder is still not created. Is there a way to rerun freesurfer for these participants?

Thank you!

As a note, fMRIPrep 21+ by default puts FreeSurfer directory in sourcedata instead of derivatives. Did you look there?