Hello troubled souls,
What you want to do is register volumes of different contrast properties. That is known as cross-modality registration. This type of registration is not performed by AFNI at the moment. We plan to have a tool to do this in the future. For the moment, if you must register your EPI data to your high-res anatomical with affine transformations, you will have to use other tools. FSL's flirt and mcflirt would do the trick. I should get around to posting the necessary steps sometime next week.
cheers,
-ziad