afni.nimh.nih.gov

I believe the -fraction option of 3dToutcount will give you what you need.

3dToutcount -automask -fraction epi+orig.

Automask should reduce to the number of voxels in the EPI. But you could also supply your own mask. If you run 3dToutcount without a mask, then you will be asking for outliers both in the brain and outside of the brain. You can get the total number of voxels by running 3dBrickStat:

3dBrickStat -count epi+orig.[0]