afni.nimh.nih.gov

Hi Justin,

The fact that you are using -affter means your
software is a bit old.

We usually do a separate affine registration to
the template before the non-linear one, just to
be sure the volumes are on the same grid and
in basically the same box.

3dNwarpApply defaults to wsinc5 for interpolation.
If you end up mapping a mask or something, then
consider NN (nearest neighbor).

Thanks,

- rick