Systems and methods for tracking head motion during medical imaging. In accordance to one aspect, a head holder for a medical scanner is provided. The head holder includes at least one movable component that moves with patient's head while the head is placed on the movable component during brain imaging. The head holder further includes one or more inertial measurement units (IMUs) attached to the movable component that measure motion data, wherein any change in orientation of the movable component indicated by the motion data represents movement of the head. The one or more IMUs may communicate with a computer system during brain imaging in substantially real time to record motion parameters.
