1. A method of treating a cyclically varying target region in a patient, the method comprising: acquiring a first plurality of internal images of the patient; acquiring a signal from the patient, the signal being one capable of acting as a surrogate for the location of the target region in the patient; using the first plurality of internal images, establishing a relationship between the location of the target region and the surrogate signal; beginning treatment of the target region on the basis of the surrogate signal and the established relationship; during said treatment, acquiring a second plurality of internal images of the patient, and updating said relationship on the basis of a dataset that includes images from the second plurality; and continuing said treatment on the basis of the surrogate signal and said updated relationship.