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Measuring energy metabolism in patients with acute and chronic heart failure is an important research tool for understanding the pathophysiology of the disease and developing new treatments. Measuring energy metabolism of the lower extremities using 31P NMR imaging, may establish an alternate method of studying the pathophysiology of heart failure. The 31P NMR imaging technique yields extremely low spatial resolution, making image registration with this modality problematic. In previous studies, 31P NMR images were registered manually with 1H MR images to correlate the image information with physical space. This process takes a great deal of time for the physician. Therefore, a MATLAB-based image registration system has been designed to automate this process for the physician to improve both time and registration efficacy.