Hi-

A couple things might be happening here.

First, while your EPIs might new newly recentered, the anatomical dataset might not be, and that can cause issues. You can check this in the GUI, but underlaying/overlaying the datasets.

Second, your EPI dset has pretty low tissue contrast (e.g., it is hard to see GM-WM boundaries and distinctions), as well as large bright patches around the edge. It is often the GM-WM-CSF patterns that drive alignment between volumes, and here those patterns are hard to pick up on. This might present a problem with *any* alignment. To deal with this, it might be possible to check changing a cost function (e.g., to nmi), but would you be able to upload a dataset if I share a Box drive with you (the input EPI and anatomical volumes), and I can take a look?

--pt