Radiation therapy of a lesion within a patient is guided to take into account movement of the lesion caused by respiration and/or cardiac effects by using MRI to image the patient while on the treatment support to obtain a series of images of a location of the lesion within the patient while obtaining data relating to respiration and/or cardiac function of the patient to generate lesion movement data as a function of respiration and/or cardiac function. After the magnet is removed from the bunker, during the radiation therapy, real time data relating to respiration and/or cardiac function of the patient is used to guide the radiation therapy using the lesion movement data obtained during the imaging.