A radiation therapy system comprises: a radiation therapy subsystem (20, 22, 32) configured to perform radiation therapy by applying radiation pulses to a region of a subject at pulse intervals (Tpi) a magnetic resonance (MR) imaging subsystem (10, 16, 30, 36) configured to acquire a dataset of MR imaging data samples from the region of the subject over one or more MR sampling intervals (TAQ) that are longer than the pulse intervals, the one or more MR sampling intervals overlapping at least some of the pulse intervals a synchronizer (40) configured to identify MR imaging data samples of the dataset whose acquisition times overlap pulse intervals and a reconstruction processor (44) configured to reconstruct the dataset without the measured values for the MR imaging data samples identified as having acquisition times overlapping pulse intervals to generate a reconstructed MR image.
