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Hello, I read the recommendations for Using FLIRT to register a few FMRI slices (http://www.fmrib.ox.ac.uk/fsl/flirt/ztrans.html): I have EPI data with 17 (5mm) slices that cover most of the brain (cutting off some parietal cortex and the occipital lobe). The idea was to maximize frontal and temporal cortex with the slice angle perpendicular to the long axis of the hippocampus. I also have a whole brain SPGR image for each subject. My problem is that I do not have the "whole_func" image (whole brain coverage). I would appreciate any advice on how best to co-register these partial EPI images given the missing intermediate "whole_func" images. Thanks, Matt -- Matthias H. Tabert, Ph.D. Assistant Professor of Clinical Psychology in Psychiatry Department of Biological Psychiatry Columbia University/NYSPI 1051 Riverside Drive, Unit 126 New York, NY 10032 Phone: 212-543-5046 Fax: 212-543-5854