All MRI researchers and medical doctors interested in investigating neurodegenerative diseases, in particular Parkinson’s disease.In recent years, quantitative susceptibility mapping (QSM) has been introduced¹, which allows for in vivo imaging of iron in brain tissue². Furthermore, the imaging technique can provide quantitative measurements of brain structures³. However, the spatial iron difference in deep grey matter of Parkinson's disease (PD) patients has not been investigated in a clinical setting using QSM. The aim of this study was to determine whether QSM is appropriate to define geometries of basal nuclei of PD patients on a clinical 3T MR scanner.This study utilizes QSM maps and histological stains of three different post-mortem specimens containing deep grey matter nuclei, which were obtained from the Rocky Mountains MS Center (RMMSC). The brain slabs (66 y, f / 53 y, m / 60 y, m) were embedded in agar, scanned on a 3 T SIEMENS scanner using a GRE sequence (resolution: 0.6 mm3/TE1=7ms/ΔTE=4.1ms/10 echos/TR=49 ms). QSM maps were calculated using a multiple orientation reconstruction from tissue fields applying COSMOS, which allows exact calculation of susceptibility⁴. Adjacent to scanning, brain blocks were cut, sliced and stained employing Perls’ Prussian blue for trivalent ferric iron (Fe³⁺), which reflects the iron distribution in post-mortem brain tissue. Additionally, Sudan Black B lipid stain was done on one specimen to aid delineating the nuclei from adjacent structures. The dimensions of the basal nuclei in QSM were measured using ImageJ (NIH, Bethesda, MD), whereas the dimensions in histology were measured using Leica LAS X (Leica Microsystems, Wetzlar, Germany). Both, histology images and QSM maps were registered applying the thin plate spline approach in MIPAV (NIH, Bethesda, MD).Coronally oriented QSM maps and coronally sliced histological stains of brain samples were acquired, which contain the substantia nigra (SN), subthalamic nucleus (STN) and red nucleus (RN) (Fig. 1-3). The major and minor axis of these ellipsoid-shaped basal ganglia nuclei were measured in both modalities, QSM maps and histological stains. The basal ganglia contain a high iron concentration in comparison to adjacent regions and thus can be easily delineated in both image modalities. The dimensions of the nuclei vary depending on the spatial location within the human brain. Nevertheless, the dimensions measured in QSM and histology at different spatial location are in concordance with each other in all three samples (Fig. 4). The slope is slightly smaller than 1 indicating a slightly larger appearance of these nuclei in QSM images.We could show that the dimensions of SN, STN and RN are almost identical in QSM and histology, confirming that QSM can be used as a reliable measure for deep grey matter nuclei dimensions and geometries. The larger dimensions measured in QSM can be attributed to the voxels at the boundary of the measured structure. These voxels appear paramagnetic and thus being part of the nucleus, although a voxel might not fully cover the object of interest.This data suggests that the STN geometries defined on QSM can be used in pre-surgical mapping for deep brain stimulation targeting STN. Additionally, further improvements in QSM imaging alleviate the detection of iron accumulations in Parkinson’s disease brains. We believe that this research will very likely lead to an impactful outcome, establishing QSM based nigral iron mapping as a biomarker for PD progression.