A method for tracking a contour in cardiac phase contrast flow magnetic resonance (MR) images includes estimating a global translation of a contour in a reference image in a time sequence of cardiac phase contrast flow MR images to a contour in a current image in the time sequence of images by finding a 2-dimensional translation vector that maximizes a similarity function of the contour in the reference image and the current image calculated over a bounding rectangle containing the contour in the reference image, estimating an affine transformation of the contour in the reference image to the contour in the current image, and performing a constrained local deformation of the contour in the current image.