A method of quantifying plaques imaged by cardiac computed tomography angiography (“CCTA”) scan data. Calcified and non-calcified component thresholds are determined based at least in part on attenuation values of a pool of blood in the CCTA scan data. An epicardial fat threshold is determined and used to classify epicardial fat in the CCTA scan data. A portion of CCTA scan data positioned between a detected outer boundary of the coronary artery and a portion classified as lumen is classified as arterial wall. NCP and CP seeds are identified in the arterial wall portion. Portions of the CCTA scan data continuous with a NCP seed and having attenuation values greater than an artery wall value and less than the NCP threshold are classified as NCP, and portions of the CCTA scan data continuous with the CP seed and having attenuation values greater than the CP threshold are classified as CP.
