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A hierarchical non-linear method for image registration was presented, which integrates image segmentation and registration under a variational framework. An improved deformable model is used to simultaneously segment and register feature from multiple images. The objects in the image pair are segmented by evolving a single contour and meanwhile the parameters of affine registration transformation are found out. After that, a contour-constrained elastic registration is applied to register the images correctly. The experimental results indicate that the proposed approach is effective to segment and register medical images.