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A novel 4D level set framework was developed to segment dynamic MR images into the cortex, medulla and collecting system. The novelty of the method is that it combines information from spatial anatomical structures and temporal dynamics. The accuracy of the fully automatic 4D level set algorithm was found to be comparable to manual segmentation performed by experts on renal anatomy. The algorithm requires less than one minute to automatically segment a single kidney 4D patient data set with more than 40 time points.