A method of compensating for breathing and other motions of a patient during treatment includes periodically generating internal positional data about an internal target region. The method further includes generating external positional data about external motion of the patients body using an external sensor and generating a correlation between one or more positions of the internal target region and one or more positions of an external region using the external positional data of the external sensor and the internal positional data of the internal target region. The method further includes predicting the position of the internal target region at some later time based on the correlation model.
