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]