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Multimodality MR image processing and analysis aims to determine to what extent information from various imaging modalities is redundant or complementary and how changes in various regions of the brain, detected by various modalities, interact with each other to produce cognitive and functional changes. Here, we presented a multimodality image processing framework to integrate unique and complementary observations on anatomical and physiological brain changes measured by structural and perfusion MR imaging modalities. A unique aspect to this study is that we performed a test on mediation hypothesis that requires a model based on measurements from both MR imaging modalities. Our findings from these integrated multi-modality analysis were congruent with previously published results on neuropathology of AD patients and supplied a comprehensive explanation on the integration between structural atrophy and physiological deterioration due to AD.