For the given processing stream, there is no need to
de-oblique the data. You could just leave it as acquired.
To make those warnings go away, edit your .afnirc file
and set AFNI_NO_OBLIQUE_WARNING to YES.
However, you mention comparing groups of subjects.
How can that be done without aligning the data to a
template? And to get good alignment for each subject,
it would then also be important for their EPI data to be
well aligned with their anatomical.
It sounds like you want well registered data, not per
subject results in orig space.
- rick