Quantitative Susceptibility Mapping (QSM) can reveal the pathophysiological changes such as myelin, iron deposition, and tissue oxygenation. Diffusion Tensor Imaging (DTI) is an effective tool to assess the integrity of white matter. In our study, we performed whole-brain analysis of rat QSM and DTI using the recently reported SIGMA rat brain template (Nature Communication, 2019). The whole-brain segmentation demonstrated excellent performance. The derived parameters show high repeatability and are sensitive to age-related changes.