A method for cardiac segmentation in magnetic resonance (MR) cine data, includes providing a time series of 3D cardiac MR images acquired at a plurality of phases over at least one cardiac cycle, in which each 3D image includes a plurality of 2D slices, and a heart and blood pool has been detected in each image. Gray scales of each image are analyzed to compute histograms of the blood pool and myocardium. Non-rigid registration deformation fields are calculated to register a selected image slice with corresponding slices in each phase. Endocardium and epicardium gradients are calculated for one phase of the selected image slice. Contours for the endocardium and epicardium are computed from the gradients in the one phase, and the endocardium and epicardium contours are recovered in all phases of the selected image slice. The recovered endocardium and epicardium contours segment the heart in the selected image slice.