Visual comparison of rest/stress cardiac positron emission tomography indicates coronary flow reserve for diagnosing and assessing severity of coronary artery disease. An accurate, rapid, automated method for comparison and quantitation of paired cardiac PET studies has been developed to analyze size, intensity, statistical significance of and changes in perfusion or metabolism. The method utilizes polar coordinate maps derived from circumferential profiles of true short axis slices; from the short axis data algorithms determine mean and minimum activity levels in the anterior, septal, lateral, inferior and apical regions of the myocardium, percent of the cardiac image in specific ranges of activity levels or their changes and the percent of myocardium beyond 1.5, 2.0, and 2.5 standard deviations from the normal range with blackout display of the areas beyond these statistical limits for rest, stress, and stress/rest ratio polar maps. Additional applications include comparing stress-stress images to evaluate progression/regression of stenoses, early and late resting rubidium images for determining myocardial viability based on rubidium washout kinetics, and perfusion-metabolic comparisons for quantifying ischemia, viability and necrosis after acute myocardial infarction.