@michaelcohen This is a guess, but I’ve been exploring a possibly related issue that seems attributable to the poor coregistration that you’re noticing (as in, it’s not so much an issue with estimation or application of the fieldmap, but instead in the application of a fieldmap that has been taken out of register from the bold). The end is some pretty wild SDC exhibiting a range of artifacts (one example below).
For what it’s worth, a potential solution to the coregistration is in progress: Dilate fmap and epi masks before coregistration · Issue #461 · nipreps/sdcflows · GitHub (associated neurostars post Poor Fieldmap <-> Functional Registration in fMRIPrep (highly variable step)).
