Hi Derek,
Look at the help from the command line program 'whereami'. You can get any of the ROIs available in any of the atlases distributed in AFNI. Perhaps one of these would do the trick.
Alternately, you can use FreeSurfer to automatically generate ROIs on a per-subject basis. The process may take a day or two but it is fully automated. Once you create the segemented volumes, AFNI's @SUMA_Make_Spec_FS script will port the segmented volumes for use in AFNI.
Regarding your other question. Afni can read Analyze but that format from hell is incomplete so there is no way to know for sure how it should be displayed. You should be using NIFTI for volume transfer across applications.
Upload the volumes and explain how you expect them to overlap. Perhaps someone can help you out.
Lastly, check out the education material for the talk on volume registration and Talairach transformation. It contains examples on how to extract various atlas-based ROIs in AFNI: [
afni.nimh.nih.gov]
cheers,
ziad