Not certain if this is what you're after, but at ISMRM in 2001 there was a poster (number 1199 on the CD) that compared several widely available methods of automated registration, including AFNI's registration algorithm and AIR, and found that AIR left by far the largest residuals, IIRC.
Sorry I haven't got any procedural specifics for you; hopefully someone else does.
--
Matthew Belmonte
Autism Research Centre
Section of Developmental Psychiatry
University of Cambridge
Douglas House
18b Trumpington Road
Cambridge CB2 2AH, UK