It is possible to calculate voxelwise quantities across the whole brain, and then view them or make calculations with them within specific ROIs or masks.

I will just guess that you are overlaying an anatomical on a background of ALFF values? (It wasn't clear from the description which dset was the overlay and which the underlay). Again, I don't see a problem with that-- ALFF values are calculated everywhere, but you can use the very same anatomical you are using here as a mask for calculational purposes. That is a very common step in FMRI processing-- we mask as little possible and calculate within the whole FOV if possible, and you can restrict to regions of interest later. That helps you see possible errors, artifacts, or other issues.

--pt