Hi AFNI team,
I had trouble aligning anatomy with vr_base. The following is my code:
align_epi_anat.py -anat2epi -anat FreqAP05_MPRAGE_c1234_U+orig
-save_skullstrip -suffix _al_junk
-epi vr_base+orig -epi_base 0
-volreg off -tshift off
The alignment result (*al_junk) is usually that the brain is rotated off by some angles and mismatch the anatomy brain (see attached).
I’m using Unifized data. I’ve tried different ways including: skull-stripping before aligning, different cost functions (lpa, lpc/+zz and others), other skull-strip method, various movement level (big_move, ginormous_move etc.) and none of these could align well (some was able to improve it to some extent).
I never had this problem before with other subjects, so not sure why this one would happen.
Can you please help with this? Thanks!