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 and a second sequence of medical image data acquired during hyperemia; 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 in the coronary artery during the resting state based on a spatio-temporal representation of contrast agent propagation in the first sequence of medical image data and a maximum velocity of blood in the coronary artery during hyperemia based on a spatio-temporal representation of contrast agent propagation in the first sequence of medical image data; mapping the maximum velocity at rest to an average velocity at rest and the maximum velocity at hyperemia to an average velocity at hyperemia; and calculating the coronary flow reserve for the coronary artery based on the average rest velocity and the average hyperemia velocity.