Hi, Mike-
OK, I see. I guess I was wondering what your afni_proc.py command was, so I could see what options you were putting in there.
But, using @SSwarper would really be the best way to go; that will do a much better/more reliable skullstripping, as well as nonlinear warp estimation to standard space, if desired, and its results are passed directly into afni_proc.py as options. Are you warping your data to a template space? If so, which one?
--pt
