The system and method of the present application includes an image guided radiation therapy (IGRT) system, combined with a medical ventilator, to form a closed-loop system to optimize treatment of a tumor for patients who cannot comply with a normal respiratory management procedure. The ventilator may be used to generate respiratory maneuvers to facilitate clean images for dose planning, so that clinicians can more clearly visualize a target with fewer of the image artifacts associated with respiratory motion. The combined IGRT and ventilation systems approach facilitates treatment of specific organs most susceptible to respiratory motion artifact, and helps minimize the doses to the heart in left-breast treatments. Improved positioning of the anatomical target structures for exposure to external beam radiation may be accomplished through combinations of respiratory-gating, respiratory pause, and selective right or left lung mechanical ventilator techniques.