afni.nimh.nih.gov

Yes, you could do it like this or let auto_warp do the affine transformation too. That would combine interpolations to just a single one in that direction. That's not too critical for you because you want it the other direction anyway. The 3dNwarpApply command can be used to transform the atlas regions that are in alignment with the template back to the original native space. For ROIs, use the NN (nearest neighbor) method of interpolation.