1. A method of registering a first image of an object with data representative of a second image of the object, the object including one or more structures, the method comprising: reconstructing from the data at least one DRR (digitally reconstructed radiograph); enhancing the DRR and the first image so as to increase the visibility in the DRR and the first image of at least one structure; selecting an ROI (region of interest) within the DRR, wherein the ROI includes at least one structure in the object; estimating one or more 2D local motion fields within the ROI, and constructing a full 3D motion field from the local motion fields; and determining from the full 3D motion field a set of non-rigid transformation parameters that represent the difference in the position and orientation of at least one structure as shown in the first image, as compared to the position and orientation of the at least one structure as shown in the DRR.