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 continuously generating external positional data about external motion of the patients body using an external sensor and generating a correlation model between the position of the internal target region and the external sensor 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.
