The SVReg registration module performs full anatomical alignment of subject to atlas. This alignment is much more accurate than AC-PC alignment. Can you please explain some more about why you want to do AC-PC alignment? Is it for visualization purpose?
Yes that is correct, my goal is tractography. I’ve seen some process workflows use MIPAV for AC-PC alignment prior to diffusion weighted image preprocessing using TORTOISE, as part of the AFNI distribution.