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Detection of atherosclerosis in its early stages with MRI could lead to more effective treatment of the disease. However, the changes that occur in the vessels of animals given a high cholesterol diet to induce atherosclerosis are not visually apparent with conventional MRI techniques. This paper describes a semi-automated algorithm designed to quantify enhancement of the aortic wall after administration of targeted and non-targeted contrast agents in rabbits given a high cholesterol diet. The performance of the program was evaluated on multiple slices taken from eight rabbits. No lumenal narrowing or overall non-specific contrast enhancement was detected in cholesterol-fed animals. Enhancement after administration of a nanoparticle contrast agent specifically targeted to molecules associated with the initial development of atherosclerosis was higher in the cholesterol fed rabbits, providing an early indicator of disease.