Hi Alex,

In theory, it should not really matter whether starting
with the anat aligned to the EPI or the EPI to the anat.

Our examples typically use EPI to anat to preserve
more of the anatomical shape, since there tends to be
little distortion in the anatomical volumes. But that
should not make much difference after then aligning
to a template. Still, it feels a little cleaner.

The important thing is to start with data that are aligned.
I particularly wanted to make sure that your stripped anat
was actually aligned with the EPI (or that you know the
transformation to apply).

- rick