Magnetic resonance imaging (MRI) has shown great potential in early detection and characterization of stroke injury. MRI methodologies such as diffusion and perfusion MRI have been successfully applied to both experimental stroke and clinical studies, covering a broad range of questions raised in the early treatment of stroke. However, potential MRI methodologies related to critical issues in the treatment of stroke have not been well reviewed. In the current review, we present an overview of possible MRI methodologies addressing the critical issues related to treatment of stroke, including MRI measurements for predicting and detecting hemorrhagic transformation, as well as staging ischemic tissue.