Recent advances in CT technology have made possible the acquisition of high resolution images of the heart in which important anatomical features such as the coronary vessels are visible. The state of the art in MR Imaging techniques, on the other hand, typically provides lower resolution but can facilitate the differentiation of viable (healthy) cardiac tissue from infarcted (injured) tissue. The registration of CT and MR images of the same heart permit the association of anatomy with function. As an example, given an infarcted region, the coronary vessels responsible for irrigating that region may be isolated and targeted for treatment (e.g., coronary bypass). We demonstrate a software package, PROTEUS, which is capable of registering CT and MR images. Since the manifestation of cardiac tissue in the two modalities differs so greatly we rely on features to perform the matching. Specifically, we employ a model-based approach that relies on segmented contours delineating the inner and outer borders of the left ventricle (LV). Given these contours, our technique is completely automatic.