Apply affine transform generated by freesurfer using afni

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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?

Thank you!