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…
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
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.