afni.nimh.nih.gov

I would probably do it with the first approach I mentioned - @Align_Centers for the central location (maybe with -cm) and then 3dresample to get the grid the same. Both those steps and in that order are needed. Computing an alignment with a shift only affine transformation will probably work too, but it's a little different. That seems more likely to fail if alignment is thrown off, but it might be okay for your acquisition types.