1. A method of non-invasive assessment coronary flow reserve (CFR) using medical image data, comprising: receiving a first sequence of medical image data acquired during a resting state using a computed tomography (CT) scanner or an X-ray image acquisition device and a second sequence of medical image data acquired during hyperemia using a computed tomography (CT) scanner or an X-ray image acquisition device; generating a first anatomical model of a coronary artery from the first sequence of medical image data and a second anatomical model of the coronary artery from the second sequence of medical image data; estimating a maximum velocity of blood on a cross-section of the coronary artery during the resting state based on a spatio-temporal representation of contrast agent propagation over a length of the coronary artery in the first sequence of medical image data and estimating a maximum velocity of blood on the cross-section of the coronary artery during hyperemia based on a spatio-temporal representation of contrast agent propagation over the length of the coronary artery in the second sequence of medical image data; mapping the maximum velocity of the blood on the cross-section of the coronary artery during the resting state to an average rest velocity representing a spatial average of a velocity profile over the cross-section of the coronary artery during the resting state using patient-specific mapping parameters, and mapping the maximum velocity of the blood on the cross-section of the coronary artery during hyperemia to an average hyperemia velocity representing a spatial average of a velocity profile over the cross-section of the coronary artery during hyperemia using patient-specific mapping parameters; and calculating the coronary flow reserve for the coronary artery based on the average rest velocity and the average hyperemia velocity.