Methods and systems utilizing the data provided by a non-contrast-enhanced CAC scan that is left unused by the “whole-heart” Agatston or volume scores. Agatston and volume scores summarize overall coronary calcium burden, but do not show the number of vessels involved, the geographic distribution of the lesions, the size and shape of the individual lesions and the distance of the lesions from the coronary ostium. The methods and systems described herein extract and use the enhanced information provided by 3-D CAC scan data and significantly increases its clinical predictive value by providing vessel and lesion specific CAC scores which are superior to the whole-heart Agatston and volume scores in predicting obstructive Coronary artery disease (CAD).