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Hi, We have a couple of brains that do not register correctly using tbss_2, but that do register correctly in flirt if you use the full search (-180 to 180 degrees). The matrices that come out of flirt and tbss also seem very different. I see that flirt is called by tbss_2_reg and then fsl_reg, but am not sure what I could do to change the flirt parameters that are implemented. Is there a way to do that so at least for the difficult cases they can still go through tbss? (there isn't anything very obvious wrong with the raw images other than 1 or 2 slices cut off the top of a few, and quite large ventricles in some). Any advice would be appreciated! thanks! Katie _________________________________________ Katie Karlsgodt, Ph.D. Post Doctoral Fellow, Neurogenetics Affinity Group Semel Institute University of California, Los Angeles phone: 310-794-9673 fax: 310-794-9740