The output is empty because there are no atlases in MNI space in the current AFNI distribution. While the whereami coordinate look-up functions go across spaces, the overlap functions currently require the atlas to be in the same space as the dataset. So datasets in Talairach or MNI_ANAT space would get the overlap mask computed with the atlas datasets already included with AFNI. It is not difficult to shift the atlas to MNI space, so I've created a downloadable tgz file with the MNI space atlases here:

http://afni.nimh.nih.gov/pub/dist/atlases/MNIatlases.tgz

Untar the atlases and then let AFNI know about these new atlases with these commands:

cd
tar xzvf MNIatlases.tgz
@AfniEnv -set AFNI_SUPP_ATLAS_DIR ~/MNI_atlases

Thanks for posting this issue.