A method for reconstructing a motion-compensated image depicting a subject with a magnetic resonance imaging (MRI) system is provided. An MRI system is used to acquire a time series of k-space data from the subject by sampling k-space along non-Cartesian trajectories, such as radial, spiral, or other trajectories at a plurality of time frames. Those time frames at which motion occurred are identified and this information used to segment the time series into a plurality of k-space data subsets. For example, the k-space data subsets contain k-space data acquired at temporally adjacent time frames that occur between those identified time frames at which motion occurred. Motion correction parameters are determined from the k-space data subsets. Using the determined motion correction parameters, the k-space data subsets are corrected for motion. The corrected data subsets are combined to form a corrected k-space data set, from which a motion-compensated image is reconstructed.