OK, thanks for sharing that. I guess that is internal anatomical edges overlaid on the EPI?

A lot of the internal structures look well aligned. Has the EPI been skullstripped or something, though? It looks like some parts have been removed? Or is that just the presence of EPI distortions? Without seeing the set of anatomical lines that represents the pial surface ("outer" GM boundary), as well as the boundary of the anatomical, it is a little hard to see if that might be responsible for some alignment issues. (see the attach APQC HTML image for EPI-anatomical alignmnet for what I mean: the EPI is underlayed beneath edges of the anatomical volume; NB that here the EPI FOV did not include cerebellum---you can see distortion in the lowest slices from acquisition, but not how well the cortical structures align; you can also see how well the GM as a whole fits in, because there is both gray-white boundary and pial lines.)

EPI-anatomical alignment is also made trickier by the presence of EPI distortion. Do you have a sense of how much such distortion there is in this EPI? I can't tell from this image (I'm not sure if it is a raw EPI). Various EPI distortions can really be strong in the subcortical volume, esp. around sinuses and inferior frontal cortex.

--pt