A motion compensation system includes a plurality of RF transmitters, a plurality of direction of arrival sensors, and a positioning table which together are usable to compensate for intrafraction motion of a patient during a medical procedure. The positioning table may be a secondary table arranged next to or above a primary table such as a radiotherapy couch, allowing for repositioning of part of patient such as the head and neck relative to a remainder of the body. The motion compensation system employs a direction of arrival sensor that includes rotating antenna elements in a configuration that improves the ease and accuracy of signal processing and analysis to identify the position of an RF transmitter affixed to a patient. The repositioning table has six degrees of freedom and is safe for use in imaging and radiation intensive environments.