Hello Christopher,

I don't quite understand what your question is.
I am guessing you want to use something like 3dTagalign followed by 3dWarp to perform the alignment. This allows for stretching and compression in addition to shifting and rotation. For 3dTagalign, you do not need to worry about voxel coordinates; this is taken care of internally by AFNI. I wrote some documentation on using 3dTagalign for SUMA which you might find useful. Search for the section titled: "Aligning SurfVol to ExpVol using 3dTagalign" at [afni.nimh.nih.gov] .

cheers,
Ziad