afni.nimh.nih.gov

The minor upsamplign to voxel size seems both appropriate and convenient.

To deal with the anatomical grid/FOV: What if you used 3dAutobox (maybe with -npad to repad it a little) or 3dZeropad to shrink the FOV of your anatomical volume?

I am assuming you are not using the "tlrc" block to go to standard space? If so, you could use either of the above to shrink a copy of your template volume, and use that as a final target?

--pt