afni.nimh.nih.gov

I should also mention that I have tried to de-oblique the data both at the beginning and mid-stream (to determine if this is actually the issue), but there was no change.

I have also tried adjusting the alignment using the following:

1) 3dresample -orient RAI -prefix reorient_mprage -inset mprage_ss+orig
2) align_epi_anat.py -anat reorient_mprage -epi func+orig -epi_base 0 -cost LPC

But, they don't seem to help anything in this case...