Voxel-wise correlation analyses were performed between the MR images and the density maps derived from the histology images. No further comparisons between MR and histology images were performed when tissue damage or MRI boundary image artefacts were visually distinct or when the correlation values of neuronal density between KB, TH, and Perl stains were low from possible co-registration error. With these criteria, six sequential slides from each subject were studied. These included the caudal to rostral areas of the SN. Three different polygonal regions of interest (ROIs) were manually selected (Supplementary Figure S3): ROI-whole SN contains the whole SN based on KB staining corresponding to the bulk of SN hypointensity on the T2*WI; ROI-SNc contains the SNc based on TH staining within the ROI-whole SN including the A9 cell group, and ROI-SNr contains the SNr, which is obtained by subtracting ROI-SNc from ROI-whole SN. For voxels within ROIs, direct correlations between the T2* values and the density of neurons, NM, and iron pigments were evaluated.