Local hemodynamic forces, such as wall shear stress (WSS), are thought to trigger cellular and molecular mechanisms that determine atherosclerotic plaque vulnerability to rupture. Magnetic resonance imaging has emerged as a powerful tool to characterize human carotid atherosclerotic plaque composition and morphology, and to identify plaque features shown to be key determinants of plaque vulnerability. Image-based computational fluid dynamics has allowed researchers to obtain time-resolved WSS information of atherosclerotic carotid arteries. A deeper understanding of the mechanisms of initiation and progression of atherosclerosis can be obtained through the comparison of WSS and plaque composition and morphology. To date, however, advance in knowledge has been limited greatly due to the lack of a reliable infrastructure to perform such analysis. The aim of this study is to establish a framework that will allow for the co-registration and analysis of the three-dimensional distribution of WSS and plaque components and morphology. The use of this framework will lead to future studies targeted to determining the role of WSS in atherosclerotic plaque progression and vulnerability.