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I had already a conversation on this list in Jan-Feb 2002 on this topic, but I cannot reconstruct the whole thing, so I wonder if someone could jog my memory. I am trying to register a single slice T1 weighted image to a single slice T2 weighted image. I am using FSL v3.1 with FLIRT v5.0 (2D rigid body) on a linux redhat 8 system. I think I am not running the latest version of FLIRT because of a problem of incompatibility with my operating system. When I try running the registration I get a very odd image as the output (something that looks like 3 blobs rather than the axial brain image I started from) regardless of the cost function I use. Any idea as to why I get these strange results? Stefano Marenco, MD GCAP, Clinical Brain Disorders Branch, NIMH 10 Center Drive, room 4S235 Bethesda, MD 20892 tel. (301) 435-8964 fax. (301) 480-7795 email: <mailto:[log in to unmask]> [log in to unmask]