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Acute rejection is the most common reason of graft failure after kidney transplantation, and early detection is crucial to survive the transplanted kidney function. Automatic classification of normal and acute rejection transplants from dynamic contrast enhanced magnetic resonance imaging (DCEMRI), is of great importance. Kidney segmentation is the first step for such classification. The image intensity inside the kidney is used as an indication of failure/success. Differentiating between different cases cases is implemented by comparing subsequential kidney scans signals. So, this process is mainly dependent on segmentation. This paper introduces a new shape-based segmentation approach based on level sets. Training shapes are collected from different real data sets to represent the shape variations. Signed distance functions are used to represent these shapes. The methodology incorporates image and shape prior information in a variational framework. The shape registration is considered the backbone of the approach where more general transformations can be used to handle the process. We introduce a novel shape dissimilarity measure that enables the use of different (inhomogeneous) scales. The approach gives successful results compared with other techniques restricted to transformations with homogeneous scales. Results for segmenting kidney images will be illustrated and compared with other approaches to show the efficiency of the proposed technique.