Provided is a method for compensating for tissue motion during magnetic resonance (MR) imaging, and an apparatus for use thereof. The method includes acquiring a plurality of short-time MR scan images; selecting a reference scan image from the acquired plurality of short-time MR scan images; defining a set of transformation images based on the acquired plurality of short-time MR scan images other than the selected reference scan image; registering the reference scan image and the defined set of transformation images; calculating an average of aligned, registered images of the defined set of transformation images; and generating a motion-corrected image based on the calculated average.