1. A method for registering 3D image data, the method comprising: a) receiving a first 3D image and a second 3D image; b) determining at least one rendering transform for applying to each of the first 3D image and the second 3D image; c) applying the at least one rendering transform to i) the first 3D image to provide at least one 2D projection corresponding to the first 3D image and ii) the second 3D image to provide at least one 2D projection corresponding to the second 3D image; d) marking one or more locations in the at least one 2D projection corresponding to the second 3D image such that the one or more locations in the at least one 2D projection correspond to one or more locations in the second 3D image; e) determining at least one elastic registration for mapping the one or more locations in the at least one 2D projection corresponding to the second 3D image to homologous one or more locations in the at least one 2D projection corresponding to the first 3D image, wherein determining each of the at least one elastic registration comprises: i) generating a plurality of candidate mappings wherein each candidate mapping in the plurality of candidate mappings defines a mapping of the one or more locations in the at least one 2D projection corresponding to the second 3D image to the homologous one or more locations in the at least one 2D projection corresponding to the first 3D image; ii) determining a plurality of similarity values, wherein for each candidate mapping in the plurality of candidate mappings the plurality of similarity values includes an associated similarity value corresponding with the quality of the registration under that candidate mapping; iii) selecting from the plurality of candidate mappings a candidate mapping with a highest associated similarity value; and iv) initializing the elastic registration based on the candidate mapping with the highest associated similarity value; f) mapping the one or more locations in the at least one 2D projection corresponding to the second 3D image to the homologous one or more locations in the at least one 2D projection corresponding to the first 3D image based on the at least one elastic registration; and g) mapping the one or more locations in the at least one 2D projection corresponding to the first 3D image to homologous one or more locations in the first 3D image.