Summary of what happened:
Hi. I have observed that preprocessing with fMRIPrep v25.2.3 results in CIFTI files with zero-valued time series in parcels 120 and 300 of the Glasser (and CAB-NP) atlases for some of the subjects. As a solution, pre-running the surface reconstruction using FreeSurfer 6 and providing those derivatives to fMRIPrep via the --fs-subjects-dir flag appears to resolve the issue. I am interested to know if others have encountered this specific zeroing of parcels in recent releases and whether this manual hand-off is considered a reliable and recommended solution, or if there are specific volume-to-surface mapping flags I should investigate instead. Do you recommend another or a better solution?
Command used (and if a helper script was used, a link to the helper script or the command generated):
PASTE CODE HERE
Version:
fMRIPrep v25.2.3, Freesurfer 6 and >7
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer/Singularity for both fMRIPrep and Freesurfer6
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE