Paul points out I was somewhat terse in my reply last night. The outputs of this script are described when you type
@SSwarper -help
or when you follow this link:
https://afni.nimh.nih.gov/pub/dist/doc/program_help/@SSwarper.html
The output files include the skull-stripped dataset in original coordinates, and as warped to the MNI 2009 template dataset. The transformation files needed for afni_proc.py to avoid re-doing the nonlinear warping are also save. The "-help" output also describes how these files are named and how to input those files to afni_proc.py.
