Hi @Steven,
I just wanted to report back that when using the LTS branch (20.2.7) I do not have the SDC issue I originally posted. As in the discussion with @themeo, it does seem to be an issue of improper skull stripping. Looking over the SDC workflow/code it does seem like fMRIprep does perform skull stripping of the magnitude images. Given this issue with multiple subjects, it looks like the current implementation of skull-stripping isn’t good enough such that it still is retaining some non-brain voxels which is what is causing the SDC to perform worse near the edges. Maybe recommending that they add an erosion step to the skull-strip mask would resolve this.
Best,
Jagan.