Thanks Daniel, for your reply. I spent some time playing with -master_anat, but without much luck.

Option A seems to give about the same result as what I had - anatomical data cut-off in the same way EPI is (intentionally) cut off. Data definitely then needs to be shifted before running @auto_tlrc...that output suggests @Align_Centers, which works fine, but I'm guessing I'll need to apply that transformation to EPI datasets as well.

Option B looks great in theory (correct me if I've misinterpreted) - move anat into the oblique space of the EPI, preventing an extra EPI transformation. For the purposes of align_epi_anat.py, do I run "-anat anat+orig" or "-anat anat_ob2epi" along with "-master_anat anat_ob2epi+orig"? Either way, the output is way off for @auto_tlrc, requiring the same shift.

Not sure how to make option C work.

I'm starting to think "align_epi_anat.py -giant_move -deoblique off" (as you suggest in this post) might be the simplest approach - definitely easy to add to afni_proc.py. @Align_Centers on everything at the beginning might work as well, but that's got the transformation we're trying to avoid.

Thanks again.

JP