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A segmentation framework is proposed to determine the wall thickness, carotid artery plaque volume as morphological markers. MRI features, NMR peaks, oxidative stress markers as MRI-clinical correlates were compared in carotid and coronary plaques. The objective is to distinguish plaque components by their different MR image intensities at different image contrasts using in vivo and ex-vivo images; to segment and quantify plaque components (area and volume) using plaque contour; to compare NMR peaks, MRI features, relaxation times and oxidative stress markers in coronary and carotid endarterectomy samples to implicate plaque as lipid disorder. Fourteen pairs of coronary and ten pairs of carotid arteries after FSE T1 weighted MRI examination from post-surgery donors (aged 42 to 68 years) were analyzed for lipid proton NMR peaks and tissue oxidative stress markers. Ten pairs met the criteria for rigorous analysis. Carotid artery wall thickness and plaque volumes were measured from the MRI images. In vitro NMR peaks and oxidative stress markers were computed in both coronary and carotid artery samples. The carotid artery bifurcation is a site at which MRI can monitor plaque progression reproducibly. Total wall volumes of carotid arteries in vivo and in vitro were moderately correlated (concordance correlation coefficient r/sub c/=0.71). Correlation was measured for atheroma scores (r/sub c/=0.954); and plaque volume scores (r/sub c/=0.942). The observation of comparable NMR lipid peaks and oxidative stress suggested that diagnostic information about atherosclerosis progression in both coronary and carotid arteries may be similar. Carotid artery plaque features were MRI visible and predictive of plaque rupture and stability. Oxidative stress markers were significant in carotid artery tissues and comparable to coronary tissues. Lipid NMR peaks were significant suggestive of lipid accumulation in atherosclerosis of the human carotid arteries as a lipid disorder.