Percutaneous cochlear implantation (PCI) is a minimally-invasive image-guided cochlear implant approach, where access to the cochlea is achieved by drilling a linear channel from the skull surface to the cochlea. The PCI approach requires pre- and intra-operative planning. Computation of a safe linear drilling trajectory is performed in a preoperative CT. This trajectory is mapped to intraoperative space using the transformation matrix that registers the pre- and intra-operative CTs. However, the difference in orientation between the pre- and intra-operative CTs is too extreme to be recovered by standard, gradient descent-based registration methods. Thus far, the registration has been initialized manually by an expert. In this paper, we present a method that aligns the scans completely automatically. We compared the performance of the automatic approach to the registration approach when an expert does the manual initialization on 11 pairs of scans. There is a maximum difference of 0.18 mm between the entry and target points of the trajectory mapped with expert initialization and the automatic registration method. This suggests that the automatic registration method is accurate enough to be used in a PCI surgery.