Systems and methods for virtual reality or augmented reality (VR/AR) visualization of 3D medical images using a VR/AR visualization system are disclosed that includes a computing device operatively coupled to a VR/AR device, which includes a holographic display and at least one sensor. The holographic display is configured to display a holographic image to an operator. The computing device is configured to receive at least one stored 3D image of a subject's anatomy and at least one real-time 3D position of at least one surgical instrument, to register the at least one real-time 3D position of the at least one surgical instrument to correspond to the at least one 3D image of the subject's anatomy, and to generate the holographic image comprising the at least one real-time position of the at least one surgical instrument overlaid on the at least one 3D image of the subject's anatomy.