Hi Colm,
The afni_restproc.py program was written by Rayus in
Tulsa, and we do not maintain it. Maybe he will reply.
And unfortunately, afni_proc.py has not yet been
updated to accept masks outside of the 3dSeg result.
So if you use that, it probably means starting with
the 3dSeg ROIs and modifying it to use your own.
While allowing this is pretty high on my todo list,
it is surely months away, sorry.
- rick