Current MRI technologies require subjects to remain largely motionless for achieving high quality magnetic resonance (MR) scans, typically for 5-10 minutes at a time. However, lying absolutely still inside the tight MR imager (MRI) tunnel is a difficult task, especially for children, very sick patients, or the mentally ill. Even motion ranging less than 1 mm or 1 degree can corrupt a scan. This invention involves a system that adaptively compensates for subject motion in real-time. An object orientation marker, preferably a retro-grate reflector (RGR), is placed on a patients' head or other body organ of interest during MRI. The RGR makes it possible to measure the six degrees of freedom (x, y, and z-translations, and pitch, yaw, and roll), or “pose”, required to track the organ of interest. A camera-based tracking system observes the marker and continuously extracts its pose. The pose from the tracking system is sent to the MR scanner via an interface, allowing for continuous correction of scan planes and position in real-time. The RGR-based motion correction system has significant advantages over other approaches, including faster tracking speed, better stability, automatic calibration, lack of interference with the MR measurement process, improved ease of use, and long-term stability. RGR-based motion tracking can also be used to correct for motion from awake animals, or in conjunction with other in vivo imaging techniques, such as computer tomography, positron emission tomography (PET), etc.