Ischemic stroke of the brain stem affects a considerable number of human patients. However, mechanisms of degeneration and recovery are not well understood and animal models of brain stem ischemia are rare compared to models of cortical stroke. Here we implemented a rat model of brain stem ischemia and applied diffusion tensor MR imaging as a noninvasive means to assess structural connectivity. Probabilistic mapping and histology indicate structural remodeling at the level of thalamus. These results add evidence for a potential compensatory mechanism for the observed partial recovery after brain stem stroke.