Hey Rick,
I just loaded the aparc+aseg and aparc.a2009s+aseg separately in freeview yesterday and verified the list of numbers in the example commands. In both cases the numbers referred to the same structures.
What caused me confusion yesterday was the mention of both atlases in the freesurfer note coupled with my experience of other atlases almost never overlapping in their choice of ROI numbers.
On an unrelated note, do you have any plans to integrate the Power et al motion scrubbing technique from afni_rest_proc.py into afni_proc.py? That would be a great addition to afni_proc.py.
--
Colm.