I would try using @SSwarper ("skullstrip + warp") before running afni_proc.py:
[afni.nimh.nih.gov]

It will both skullstrip the anatomical *and* calculate a nonlinear warp to template space (using 3dQwarp).

Target data sets for it include things in the distribution that end with "_SSW.nii.gz", as described in the @SSwarper help file; if you are using one of those as target template space already, you should be good to go.

The outputs of @SSwarper can be put directly into your afni_proc.py command, so you don't have to do skullstripping there or calculate the nonlinear warp again. Examples for doing that are in the @SSwarper help file.

-pt