Hi Rick,
I'm working on the same dataset. All of the Afni_Proc.py (which is run on individual subjects) output is in participant space.
In parallel to afni_proc.py we use auto_warp.py to nonlinearly warp T1 images to MNI 2009c space. Subsequently, we use 3dNwarpApply (-iwarp) to bring the stats and anything else from patient space (which was epi2anat aligned) to MNI space. Ultimately, we're using the HMAT atlas to look at subject specific voxels within the given HMAT regions in MNI space.
Thanks for your help!