Methods and apparatuses for performing patient registration. 3D scan data from a 3D scanner, preoperative image data, first tracking data from a first tracking system, and second tracking data from a second tracking system are mapped to a common coordinate space. The 3D scan data and the first tracking data are mapped to each other using a transformation that is determined based on a calibration relating the 3D scan coordinate space and the tracking coordinate space. The 3D scan data and the preoperative image data are mapped to each other using a surface matching algorithm. The first tracking data and the second tracking data are mapped to each other based on tracking of the patient reference device.