Besides 3dhistog, there are a few other simple ways to count voxels. See this previous posting:
http://afni.nimh.nih.gov/afni/community/board/read.php?1,77807,77820#msg-77820
From the AFNI GUI, you can use the interactive clusterize tool, maybe in combination with the instacalc feature, or the histogram plugin as other ways to count voxels.
You might also look at incorporating that probabilistic atlas into AFNI and then use whereami for finding locations and computing overlaps.
http://afni.nimh.nih.gov/sscc/dglen/Makinganatlas
