afni.nimh.nih.gov

The @SSwarper alignment is a different alignment, so I don't want to confuse the two issues here. For the alignment between EPI and anatomical datasets, you can specify one of the partial coverage options to align_epi_anat.py if you have a very limited field of view.

This is just a guess, but the blurriness in the @SSwarper anatomical to template alignment may come from the regions becoming relatively larger in that part of the brain. It doesn't look too extreme here, and this may not be a problem.