1. A radiation therapy system, comprising: a real-time 3D imaging means for generating a baseline and a plurality of real-time 3D images of at least a portion of a subject body region including a target region and one or more Organs At Risk (OARs), the baseline image including an array of voxels with each voxel having a value indicative of radiation absorption properties of tissue in the voxel; a registration means for deformably registering a planning image of the subject body region and the baseline image, and mapping radiation absorptive properties of tissue in the planning image to the baseline image; a motion means for measuring motion of the target region and OARs during radiation therapy treatment based on the real-time 3D images; and a real-time dose computation means for computing a real-time radiation dose accumulated for each voxel of the real time 3D images based on an initial intensity of radiation beam, attenuation along a trajectory leading to and intersecting each voxel, and how much radiation is deposited in the voxel in a time which the trajectory is intersecting the voxel; wherein the radiation deposited is integrated or summed over all of trajectories intersecting each intersected voxel during the radiation therapy treatment as the radiation beams, the target region, and the OARs move relative to a nominal position in the planning image.