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The use of a contrast medium allows the high-resolution anatomical information provided by standard magnetic resonance to be combined with functional information obtained by means of diffusion of contrast agent in tissues or in the vascular net. To effectively use this kind of image for medical diagnosis, quantitative analysis should be performed. We propose an automatic registration procedure based on maximization of the mutual information that address the requirement of fast and automatic tools for quantitative analysis of contrast medium enhanced MR images. Two optimization algorithms for maximization of the mutual information are discussed, taking into account both time performance and registration quality. We present also preliminary results on cardiac and wrist MR images showing that misalignments and artifacts introduced by patient movement during the examination are greatly reduced by our application.