Preparing a plan to synchronize radiation delivery to a target in a patient with patient breathing phase and amplitude as the independent variable comprising (a) obtaining simultaneous data on patient breathing and target shape and location, (b) correlating the data and optimizing the correlation, (c) establishing optimal parameters of radiation delivery for each breathing phase/amplitude or for each target shape/location； and (d) synchronizing radiation delivery to a target in a patient with patient breathing comprising (a) positioning the patient, (b) monitoring actual breathing or the shape/location of the target, and (c) while monitoring, delivering radiation to the target according to a plan； and a system for controlling radiation delivery by a device to a target in a patient comprising (i) a processor, which receives and processes data on breathing or the shape/location of the target, and (ii) a controller, which controls radiation delivery to the target according to a plan, which synchronizes radiation delivery to the target with breathing data or the shape/location of the target.
