Hi Rick,
Thank you for your reply.
I did as you suggested: 3dcopy, @align_centers with anat and epi only, 3dWarp -deoblique both anat and epi, then for the align_epi_anat.py I ran the following:
align_epi_anat.py -anat $sub.anat_deob_ns+orig. \
-epi $sub.MID_shft_deob+orig. -epi2anat -epi_base 2 -anat_has_skull \
no -verb 1 -save_vr -giant_move
Although the alignment is now correct, the top part of the brain has been cut off. Could you please take a look at the transformed anat and epi in zipped folder "SarahJ.tgz" and please let me know if there are any other options I could use to correct for this issue?
Thank you very much for your advice.
Sarah
