afni.nimh.nih.gov

That sounds fine to me. Changing the actual coordinates would change the reference system, but if you were creating a new atlas, that might be a better way. For the zeropad idea, you can do this a bit more automatically with 3dAutobox using a brain mask and then 3dZeropad with the autoboxed brain mask as the master. Add a few slices around to allow for alignment of other datasets.