Different functional mask beween sessions

Dear all

The functional mask in sess-01 include area that is non-brain in both hemispheres, and sess-02 only the left hemi.
Should I run the preprocessing again with different parameters?
It is important that sess-1 and sess-2 will be similar…



sess-02 functional

sess-01 functional

What parameters did you run fMRIPrep with, and what version?

The default parameters…only change the output-spaces so I can continue with FSL for higher analysis…
–fs-no-reconall --dummy-scans 2 --ignore {t2w,flair} --output-spaces MNI152NLin6Asym:res-2 --fd-spike-threshold 0.8 --dvars-spike-threshold 3


Now I see…
WARNING: Version 20.2.1 of fMRIPrep (current) has been FLAGGED
(reason: Functional outputs in standard space can be wrong depending on the original data’s orientation headers - see Failed resampling of BOLD into MNI space - starting with v20.1.1 · Issue #2307 · nipreps/fmriprep · GitHub).
That means some severe flaw was found in it and we strongly

I would recommend updating to the most current stable release, and enabling FS recon-all. Using Freesurfer outputs allows for surface boundary-based registration, which works better than volume based registration. Hopefully that could help orientations be more consistent.