Thanks for the response. I am sorry that I was not clear about the AFNI side. I understand that people use the 3dAnatNudge to basically eyeball the matching of the structural volume to the functional mask. My request is steps for successfully AIR-co-registering anatmical and bringing back the registered anatomical into AFNI. So, I still appreciate any advice on that from people that have done such a thing. I am trying to see if we can minimze the subjectivity of the person who does the nudging. Thanks again!
RM