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Radiation therapy is one of the most commonly used modalities for cancer treatment. However, if unaccounted for, internal organ motion during radiation delivery may lead to under-dosing of cancer cells or overdosing of normal tissue, potentially causing treatment failure or normal-tissue toxicity. A recent development in the field of external beam radiation therapy is the advent of radiation therapy devices with an on-board MRI scanner, capable of providing a real-time view of the patient anatomy with a high temporal resolution during radiation delivery. The anatomy visualization offers the opportunity to devise a fundamentally new organ-motion management approach in which the radiation therapy plan actively adapts to anatomical variation in real time during irradiation. This research proposes a control-theoretic framework that uses the real-time MRI information available on MRI guided radiation therapy platforms to monitor the delivery of radiation dose and to dynamically adjust the treatment plan in response to dose discrepancies due to organ motion.