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Registration of Magnetic Resonance (MR) and Positron Emission Tomographic (PET) images is a crucial step in multi-modality brain image analysis. We have developed a technique which we call iterative principal axes registration (IPAR). Using this method, partial volumes of PET images can be accurately registered with complete MR scans. We will present qualitative and quantitative results of the new method. These results show that IPAR is accurate and practical as a registration method for MR-PET correlation studies.