This paper details a method for tracking 3D kinematics of the skull and brain deformation in post-mortem human subjects (PMHS) using 2D cineradiographic images during a high-rate loading event. Brain displacement and resulting strain due to blast loading is a metric for Traumatic Brain Injury (TBI), however physically measuring brain motion experimentally is a significant challenge. A shock tube, used to simulate blast exposure, created skull and brain motion tracked using implanted radio-opaque markers and high-speed X-ray images. These images were registered to a computed tomography (CT) scan using intensity-based 2D-3D registration techniques. To register the 2D images to the 3D scan, digitally reconstructed radiographs were generated from the CT scan, and then compared to the recorded x-ray frames by maximizing similarity metrics between the images using a Covariance Matrix Adaptation Evolution Strategy. As compared to pure 2D tracking, 2D-3D registration provides out-of-plane kinematics by fully leveraging information in the x-ray projection image and prior information from the 3D CT scan. Data generated with these techniques are critical for physically understanding the mechanisms associated with blast exposure that may lead to TBI, and can be used for human computational model validation.