Dear AFNI experts,
I used align_epi_anat.py to align a T1 to a b0 image. Now I get 2 mat files - T1_al_mat_aff12.1D and T1_al_e2a_only_mat.aff12.1D.
My first question is, is the second one the inverse matrix?
I tried to find this out by supplying it to 3dallineate and aligning the b0 to the T1(inverse of what was done before). However the result is confusing because of obliquity.
So my second question is, how do you deal with obliquity when applying an inverse matrix obtained from align_epi_anat?
Thank you!