The present invention is a method and apparatus for semi-automatically registering low signal to noise ratio relaxation-time images, with particular application to tracking motion in moving organs and quantifying myocardial perfusion reserve. For each image acquired in a time series, a corresponding high signal to noise ratio image is extrapolated from the collected data. The high signal to noise ratio images are registered to track motion, and the resulting registration data is copied onto the corresponding relaxation time image.