System lupus erythematosus (SLE) is an autoimmune disease that can lead to lupus nephritis and glomerulonephritis. Studies have evaluated kidneys from SLE patients using diffusion-weighted imaging. However, specific MRI metrics most related to the underlying disease has not been identified. In this study, we evaluate a lupus model with MRI and determine the physical properties that contribute to the MRI signal. This is achieved through structural analysis of glomeruli with whole kidney 3D micro-CT and pathological evaluation of glomeruli, tubules, interstitium, and arterioles. Finally, a comprehensive correlation analysis is performed to determine top MRI metrics most sensitive to the disease.