Breathing induces phase encoding directional artifact motion.

Raj, D., Anderson, A.W., Gore, J.C., 2001. Respiratory effects in human functional magnetic resonance imaging due to bulk susceptibility changes. Phys Med Biol 46, 3331-3340.

If your acquisition is A to P PE, each slice has the different amount of A to P directional motion, depending on the breathing cycle, even without the actual head motion. Since EPI volume image stacks up each different amount of A to P motion slices, each volume has different combination of A to P motion slices, from which 3dvolreg estimates the artificial volume motion. Postmortem or ex-vivo brain phantom would generate the actual motion free data. If TR is coherent to the breathing cycle under anesthesia, the slice wise A to P motion has less variation across volumes and the estimated 3d rigid motion is minimized.

Hope it helps
-Wanyong