Hi afni experts,
I have a pair of T1 and EPI which I manually coregistered (for some reason) in FreeSurfer, using the following command:
tkregister2 --s subj_id --mov epi.nii --surf orig --reg register.dat --regheader
Now with the affine transform matrix at hand (in the register.dat file), I would like to apply it to the T1 volume in AFNI, using 3dAllineate.
However, due to the incompatible coordinates conventions between FS and AFNI (e.g., RAS vs RAI) I guess, or difference in volume orientations, or some other reasons, the matrix in register.dat doesn’t work in its raw form.
So how to apply affine transform matrix generate by FreeSurfer using 3dAllineate?