Howdy-

Sooo, I think the issue is that whereami is being a little too clever for its own good. It is finding the ROI that matches the specified name, AND restricting it to one side of the x=0 line. I think this behavior was developed for atlases that didn't separate left and right with names, and so one could split a bilateral ROI with the centerline. Here, that behavior is inappropriate. This might be something we change...

In the meantime, the way i would do what you want (select several ROIs by label, and make a single mask out of them) would be as follows, via 3dcalc:

3dcalc \
    -a aparc.a2009s+aseg.nii.gz'<Brain-Stem,Left-Cerebellum-Cortex,Right-Cerebellum-Cortex,Left-Cerebellum-White-Matter,Right-Cerebellum-White-Matter,Left-VentralDC,Right-VentralDC>' \
    -expr 'step(a)' \
    -prefix NEW_MASK.nii

This is using the "AFNI selectors", in this case the angle-brackets to select ROI by label or by number (labels being preferred, if possible, for clarity). The quotes are necessary (either single or double here).

If you wanted the values+labels left in (so you still have a "map" of your selected ROIs), you could run:

3dcalc \
    -a aparc.a2009s+aseg.nii.gz'<Brain-Stem,Left-Cerebellum-Cortex,Right-Cerebellum-Cortex,Left-Cerebellum-White-Matter,Right-Cerebellum-White-Matter,Left-VentralDC,Right-VentralDC>' \
    -expr 'a' \
    -prefix NEW_MAP.nii

# reattach labeltable and put ROI-dset appropriate colorbar as default
3drefit -copytables aparc.a2009s+aseg.nii.gz  NEW_MAP.nii
3drefit -cmap INT_CMAP            NEW_MAP.nii

--pt