1. A method for aligning medical images, comprising: manually aligning a first pair of learning images acquired by first and second modalities to produce a first joint distribution, wherein the first and second modalities are different from each other; generating, by the processor, a learned joint distribution based on the first joint distribution; manually aligning a second pair of learning images acquired by the first and second modalities to produce a second joint distribution; updating, by the processor, the learned joint distribution with the second joint distribution; acquiring, using the first modality, a first image of a patient; acquiring, using the second modality, a second image of the patient; and aligning, by the processor, the first and second images based on the learned joint distribution.