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Background: The pedunculopontine nucleus (PPN) has been studied as a possible target for deep brain stimulation (DBS) for Parkinson's disease (PD). However, identifying the PPN can be challenging as the PPN is poorly visualized on conventional or even high-resolution MR scans. From histological studies it is known that the PPN is surrounded by major white matter tracts, which could function as possible anatomical landmarks.Methods: This study aimed to localize the PPN using 7T magnetic resonance (MR) imaging and diffusion tensor imaging (DTI) of its white matter borders in one post-mortem brain. Histological validation of the same specimen was performed. The PPN was segmented in both spaces, after which the two masks were compared using the Dice Similarity Index (DSI). The DSI compared the similarity of two samples on an inter-individual level and validated the MR findings. The error in distance between the center of the two 3D segmentations was measured by use of the Euclidean distance.Results: The PPN can be found in between the superior cerebellar peduncle and the medial lemniscus on both the FA-maps of the DTI images and the histological sections. The histological transverse sections showed to be superior to recognize the PPN (DSI: 1.0). The DTI images have a DSI of 0.82. The overlap-masks of both spaces showed a DSI of 0.32, whereas the concatenation-masks of both spaces showed a remarkable overlap, a DSI of 0.94. Euclidean distance of the overlap- and concatenation-mask in the two spaces showed to be 1.29 mm and 1.59 mm, respectively.Conclusion: This study supports previous findings that the PPN can be identified using FA-maps of DTI images. For possible clinical application in DBS localization, in vivo validation of the findings of our study is needed. [ABSTRACT FROM AUTHOR]