Thanks for your reply,
I didn't find much of use on this topic in the Skup paper, but I'll look again more closely. I guess I was looking for something EPI specific, but without anything, I can follow the examples in the sMRI literature. Interestingly, the script you mention creates an unbiased transform between the anatomicals between sessions, but doesn't worry about the same issue for the EPI data within session. Is this because it is expected that within session - between series head motion to be so small that it will have minimal bias?
Regards,
Cameron