A three-dimensional pose of the head of a subject is determined based on depth data captured in multiple images. The multiple images of the head are captured, e.g., by an RGBD camera. A rotation matrix and translation vector of the pose of the head relative to a reference pose is determined using the depth data. For example, arbitrary feature points on the head may be extracted in each of the multiple images and provided along with corresponding depth data to an Extended Kalman filter with states including a rotation matrix and a translation vector associated with the reference pose for the head and a current orientation and a current position. The three-dimensional pose of the head with respect to the reference pose is then determined based on the rotation matrix and the translation vector.