afni.nimh.nih.gov

I would think the T1w volume that is at/near its acquired resolution would have more details left in it, for better alignment.

If you are aligning the data to another (undistorted) dset from the same subject, it might not make too much difference in practice. Using the lower-res T1w would be faster... but I would still go for the likely "security" of using the more detailed, normal-res T1w volume.

--pt