Hi, Yang-
OK, thanks for explaining those points. I guess we had covered the cost function item in a different thread.
The EPI-anatomical alignment does look pretty reasonable to me, actually, as much as I can tell. It is more challenging both to align and to verify because of the low contrast, but I think that is doing a reasonable job. In the VMPFC part of the brain (frontal+inferior region, above the eyes and sinuses), I think there is probably signal dropout, and that is why the EPI looks effectively missing there. That is a common thing in FMRI, that most people will observe when looking at their data in detail like this. If you need data in that region for your study, you would have to do additional work to get an acquisition to get more data there (and likely in the subcortical regions).
I wouldn't worry about the left-right flip things here---I don't think there is enough signal to differentiate by cost function, nor is nmi the best cost function to use for it. But the visual comparison looks better for standard EPI-anatomical alignment.
The variance line warnings can happen as false positives at times, which is why we include the visual check. Edges of high variance can trigger a warning, but indeed I don't see any here.
--pt