Embodiments disclose a method and system for segmenting medical images. In certain embodiments, the system comprises a database configured to store a plurality of medical images acquired by an image acquisition device. The plurality of images include at least one first medical image of an object, and a second medical image of the object, each first medical image associated with a first structure label map. The system further comprises a processor that is configured to register the at least one first medical image to the second medical image, determine a classifier model using the registered first medical image and the corresponding first structure label map, and determine a second structure label map associated with the second medical image using the classifier model.