afni.nimh.nih.gov

Not sure what you mean. The script aligns the EPI from each session to the mean in-between anatomical dataset, and not to the anatomical dataset acquired within the session. All EPI datasets within the session are treated equivalently in that motion correction (volume registration to a common base) and alignment to the in-between anatomical dataset are done for all sub-brick volumes of each EPI run in the same way.