Correlations between the MRI data and histology is required to elucidate the nature of the MRI contrast. Histologically validated high-resolution MRI may enable a more precise definition of the boundaries and substructures of the SN. In previous studies, the overall correlation was calculated either based on a visual comparison between MRI and histological sections or with atlases obtained from different subjects25. However, visual comparison is prone to misalignment error. Recently, more precise postmortem high-resolution MRI and histological correlations from the same sections were performed using semi-automatic co-registration methods based on manually placed landmarks or block-face images1121. In this study, we used a fully automated MI-based image registration method to align the MRI and histology images with a new transformation model (2D rigid transformation + 1D translation) rather than a fully 3D rigid transformation model, to account for possible transformations that happen during slice preparation. In addition, our image registration used thresholded binary histology images such that a localized registration-induced bias would not be introduced in the correlation studies between T2*-related MR images and histology images (except for the T1WI to KB-stained image registration).