1. A method of treating a cyclically varying target region in a patient, the method comprising: acquiring a first plurality of projection images of the patient interior; acquiring a signal from the patient, the signal being one capable of acting as a surrogate for a location of the target region in the patient; using the first plurality of projection images, establishing a relationship between location of the target region and the surrogate signal by the substeps of reconstructing a plurality of volumetric images of the patient from the first plurality of projection images, each volumetric image being reconstructed from projection images having a like breathing phase; identifying a position of the target region in each volumetric image; associating the surrogate signal with the projection images; and determining a relationship between the surrogate signal and the position of the target region in the volumetric images; 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 projection images of the patient, and updating the volumetric images using the second plurality of projection, images and updating the relationship on the basis the updated volumetric images; and continuing said treatment on the basis of the surrogate signal and said updated relationship.