afni.nimh.nih.gov

If you are interested in a dataset with only a single value (only one ROI in the dataset), then one easy way to get the number of voxels is by using 3dBrickStat.

3dBrickStat -count -non-zero dset+orig
or
3dBrickStat -count -mask mask+orig dset+orig

Otherwise, 3dROIstats has an nzvoxels option for multiple ROIs to count the number of non-zero voxels for each mask value.

3dROIstats -nzvoxels -mask mask+orig dset+orig