Hmmm, I see. This does seem to be a notable difference between monkey EPIs and human EPIs: in the human case, typically the skullstripping/automasking isn't very important, because the skull often doesn't show up much. But for monkeys, it is a much bigger feature within the FOV.
I can imagine that lpc (or lpc+ZZ) might not work here---that is when the tissue contrast in the EPI is essentially opposite from that in the anatomical. For example, T1w anatomicals have dark ventricles, and EPIs have bright ones. So you will have to explore what works... Sometimes the EPIs have contrast agents included (e.g., MION for monkeys), and that can change the relative contrast, too, so a different cost function would be necessary.
--pt
