This technology includes a fully automated computer aided diagnosis system to quantify myocardial blood flow (MBF) and myocardial perfusion reserve (MPR) pixel maps from the first-pass contrast-enhanced cardiac magnetic resonance (CMR) perfusion images. This system performs automated image registration, motion compensation, segmentation, and modeling to extract quantitative features from different myocardial regions of interest. It then performs automated classification to detect potential lesions in the myocardium and generates analysis reports to summarize global and regional myocardial perfusion, possible myocardial sectors/territories and coronary arteries that may be diseased to assist physicians in clinical decision making.