afni.nimh.nih.gov

The auto_warp.py result has 2 transformations, an affine and a non-linear one, and they need to be concatenated. In your case, expect to do something like:

3dNwarpApply ... -nwarp "anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D"  ...

You can also see how this is handled in the context of an afni_proc.py script, in AFNI_data6/FT_analysis/s17.proc.FT.rest.11.

- rick