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In this paper, we propose a fully automatic method to segment bone compartments in magnetic resonance (MR) images of knee joints gathered from a public database for research on knee osteoarthritis (OA), the osteoarthritis initiative (OAI). Considering the fixed scanning parameters which include position and flexion of the knee joint, the proposed method efficiently utilizes both shape and intensity priors obtained from pre-segmented data, and iteratively applies branch-and-mincut to a local subset of configurations of shape templates. More specifically, at each iteration, the optimal among a subset of the whole range in translation, rotation, and scale parameters are decomposed and separately computed, and motion is greedily selected by the lowest energy. Experimental results demonstrate the increased accuracy and efficiency compared to when only shape priors are applied and when branch-and-mincut is applied to the whole range of parameters at once, respectively.