An example method includes acquiring a first image using a medical imaging modality that includes a two-dimensional field of view to include a patient and a multi-modal marker. A second image is acquired using the medical image modality. The second image includes the patient and the multimodal marker and is along a non-coincident angle with respect to the first image. Predetermined portions of the multi-modal marker are visible in the first and second images and have a known location and orientation with respect to at least one sensor detectable by a tracking system. The method also includes estimating a three-dimensional position for predetermined portions of the multi-modal marker. The method also includes determining an affine transformation for registering a three-dimensional coordinate system of the tracking system with a three-dimensional coordinate system of the medical imaging modality.
