afni.nimh.nih.gov

Noticed that you said you aren't normalizing the data to MNI or standard space. You can still use this approach by taking those atlas regions back to subject space using the inverse transform out of auto_warp.py or @SSWarper.

If you use the Freesurfer segmentation, those are already in your subject space after you run @SUMA_Make_Spec_FS - though the principle is pretty similar and the results depending on the regions will be close.

-Pete