1. A method for fusion of multi-modal images, comprising: receiving a first image acquired using a first imaging modality; receiving a second image acquired using a second imaging modality; and jointly estimating a model of a target anatomical structure and a transformation between the first and second images from the first and second images, wherein both the model of the target anatomical structure and the transformation between the first and second images are estimated together as a function of both of the first and second images.