Excuse my naiveness. The alignment looks like to works fairly well as far as the translation and rotation is concerned (by visual inspection), but is the fact that the bottom (inferior) part of the brain not covering the anatomical due to alignment error, or due to not having been acquired with the functionals in the first place? (on the same train of thought - is the squishy red blob in the medial inferior-posterior part supposed to be a distorted cerebellum on the functionals?)
Also, would it be possible to please send the screenshots with the realigned functional's opacity adjusted so that we could see the underlay and overlay at the same time?