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We created an automatic three-dimensional registration algorithm for magnetic resonance images of carotid vessels. Potential applications include atherosclerotic plaque characterization and plaque burden quantification vector-based segmentation using dark blood MR images having multiple contrast weightings (proton density (PD), T1, and T2). Another application is measurement of disease progression and regression with drug trials. We used mutual information registration algorithm to compensate movements between image acquisitions. PD, T1, and T2 images were acquired from patients and volunteers and then matched for image analysis. Visualization methods such as contour overlap showed that vessels well aligned after registration. Distance measurements from the landmarks indicated that the registration method worked well with an error of 1.09 ± 0.42 mm.