Adil SM, Calabrese E, Charalambous LT, Cook JJ, Rahimpour S, Atik AF, Cofer GP, Parente BA, Johnson GA, Lad SP, White LE (2021) A high-resolution interactive atlas of the human brainstem using magnetic resonance imaging. Neuroimage 237:118135. https://doi.org/10.1016/j.neuroimage.2021.118135

Article  PubMed  Google Scholar 

Afshar F, Watkins S, Yap JC (1978) Stereotaxic atlas of the human brainstem and cerebellar nuclei: a variability study. Raven Press, New York

Google Scholar 

Aggarwal M, Zhang J, Pletnikova O, Crain B, Troncoso J, Mori S (2013) Feasibility of creating a high-resolution 3D diffusion tensor imaging based atlas of the human brainstem : a case study at 11.7T. Neuroimage 74:117–127. https://doi.org/10.1016/j.neuroimage.2013.01.061

Article  PubMed  Google Scholar 

Anaclet C, Fuller PM (2017) Brainstem regulation of slow-wave-sleep. Curr Opin Neurobiol 44:139–143. https://doi.org/10.1016/j.conb.2017.04.004

Article  CAS  PubMed  PubMed Central  Google Scholar 

Augustinack JC, Helmer K, Huber KE, Kakunoori S, Zöllei L, Fischl B (2010) Direct visualization of the perforant pathway in the human brain with ex vivo diffusion tensor imaging. Front Hum Neurosci. https://doi.org/10.3389/FNHUM.2010.00042

Article  PubMed  PubMed Central  Google Scholar 

Avants B, Epstein C, Grossman M, Gee J (2008) Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal 12(1):26–41. https://doi.org/10.1016/j.media.2007.06.004

Article  CAS  PubMed  Google Scholar 

Avants BB, Tustison NJ, Song G, Cook PA, Klein A, Gee JC (2011) A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage 54(3):2033–2044. https://doi.org/10.1016/j.neuroimage.2010.09.025

Article  PubMed  Google Scholar 

Birkl C, Langkammer C, Golob-Schwarzl N, Leoni M, Haybaeck J, Goessler W, Fazekas F, Ropele S (2016) Effects of formalin fixation and temperature on MR relaxation times in the human brain. NMR Biomed 29(4):458–465. https://doi.org/10.1002/nbm.3477

Article  CAS  PubMed  Google Scholar 

Brodal P (2010) The central nervous system: structure and function. Oxford University Press, Oxford

Google Scholar 

Calabrese E, Hickey P, Hulette C, Zhang J, Parente B, Lad SP, Johnson GA (2015) Postmortem diffusion MRI of the human brainstem and thalamus for deep brain stimulator electrode localization. Hum Brain Mapp 36(8):3167–3178. https://doi.org/10.1002/hbm.22836

Article  PubMed  PubMed Central  Google Scholar 

Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K (2013) Structural and molecular interrogation of intact biological systems. Nature 497(7449):332–337. https://doi.org/10.1038/nature12107

Article  CAS  PubMed  PubMed Central  Google Scholar 

Coulombe V, Saikali S, Goetz L, Takech MA, Philippe É, Parent A, Parent M (2021) A topographic atlas of the human brainstem in the Ponto-mesencephalic junction plane. Front Neuroanat 15(August):1–62. https://doi.org/10.3389/fnana.2021.627656

Article  Google Scholar 

D’Arceuil HE, Westmoreland S, de Crespigny AJ (2007) An approach to high resolution diffusion tensor imaging in fixed primate brain. Neuroimage 35(2):553–565. https://doi.org/10.1016/j.neuroimage.2006.12.028

Article  PubMed  Google Scholar 

Eapen M, Zald DH, Gatenby JC, Ding Z, Gore JC (2011) Using high-resolution MR imaging at 7T to evaluate the anatomy of the midbrain dopaminergic system. Am J Neuroradiol 32(4):688–694. https://doi.org/10.3174/ajnr.A2355

Article  CAS  PubMed  PubMed Central  Google Scholar 

Edlow BL, Takahashi E, Wu O, Benner T, Dai G, Bu L, Grant PE, Greer DM, Greenberg SM, Kinney HC, Folkerth RD (2012) Neuroanatomic connectivity of the human ascending arousal system critical to consciousness and its disorders. J Neuropathol Exp Neurol 71(6):531–546. https://doi.org/10.1097/NEN.0B013E3182588293

Article  PubMed  Google Scholar 

Elias GJB, Loh A, Gwun D, Pancholi A, Boutet A, Neudorfer C, Germann J, Namasivayam A, Gramer R, Paff M, Lozano AM (2021) Deep brain stimulation of the brainstem. Brain 144(3):712–723. https://doi.org/10.1093/brain/awaa374

Article  PubMed  Google Scholar 

Hammers A, Allom R, Koepp MJ, Free SL, Myers R, Lemieux L, Mitchell TN, Brooks DJ, Duncan JS (2003) Three-dimensional maximum probability atlas of the human brain, with particular reference to the temporal lobe. Hum Brain Mapp 19(4):224–247. https://doi.org/10.1002/hbm.10123

Article  PubMed  PubMed Central  Google Scholar 

Henssen DJHA, Kuppens D, Meijer FJA, van Walsum AMC, Temel Y, Kurt E (2019) Identification of the pedunculopontine nucleus and surrounding white matter tracts on 7T diffusion tensor imaging, combined with histological validation. Surg Radiol Anat 41(2):187–196. https://doi.org/10.1007/S00276-018-2120-3/FIGURES/5

Article  CAS  PubMed  Google Scholar 

Hosobuchi Y (1983) Combined electrical stimulation of the periaqueductal gray matter and sensory thalamus. Stereotact Funct Neurosurg 46(1–4):112–115. https://doi.org/10.1159/000101249

Article  CAS  Google Scholar 

Jones DK, Alexander DC, Bowtell R, Cercignani M, Dell’Acqua F, McHugh DJ, Miller KL, Palombo M, Parker GJM, Rudrapatna US, Tax CMW (2018) Microstructural imaging of the human brain with a ‘super-scanner’: 10 key advantages of ultra-strong gradients for diffusion MRI. Neuroimage 182:8–38. https://doi.org/10.1016/j.neuroimage.2018.05.047

Article  CAS  PubMed  Google Scholar 

Keuken MC, Bazin PL, Schäfer A, Neumann J, Turner R, Forstmann BU (2013) Ultra-high 7T MRI of structural age-related changes of the subthalamic nucleus. J Neurosci 33(11):4896–4900. https://doi.org/10.1523/JNEUROSCI.3241-12.2013

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keuken MC, Bazin P-L, Crown L, Hootsmans J, Laufer A, Müller-Axt C, Sier R, van der Putten EJ, Schäfer A, Turner R, Forstmann BU (2014) Quantifying inter-individual anatomical variability in the subcortex using 7 T structural MRI. Neuroimage 94:40–46. https://doi.org/10.1016/j.neuroimage.2014.03.032

Article  CAS  PubMed  Google Scholar 

Keuken MC, Bazin P-L, Backhouse K, Beekhuizen S, Himmer L, Kandola A, Lafeber JJ, Prochazkova L, Trutti A, Schäfer A, Turner R, Forstmann BU (2017) Effects of aging on T1, T2∗, and QSM MRI values in the subcortex. Brain Struct Funct 222(6):2487–2505. https://doi.org/10.1007/s00429-016-1352-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kwon D-H, Kim J-M, Oh S-H, Jeong H-J, Park S-Y, Oh E-S, Chi J-G, Kim Y-B, Jeon BS, Cho Z-H (2012) Seven-tesla magnetic resonance images of the substantia nigra in Parkinson disease. Ann Neurol 71(2):267–277. https://doi.org/10.1002/ana.22592

Article  PubMed  Google Scholar 

Lechanoine F, Jacquesson T, Beaujoin J, Serres B, Mohammadi M, Planty-Bonjour A, Andersson F, Poupon F, Poupon C, Destrieux C (2021) WIKIBrainStem: an online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI. Neuroimage. https://doi.org/10.1016/j.neuroimage.2021.118080

Article  PubMed  Google Scholar 

Leprince Y, Schmitt B, Destrieux C, Barantin L, Vignaud A, Rivière D, Poupon C (2015) Optimization of sample preparation for MRI of formaldehyde-fixed brains. International Society for Magnetic Resonance in Medicine

Liu KY, Acosta-Cabronero J, Cardenas-Blanco A, Loane C, Berry AJ, Betts MJ, Kievit RA, Henson RN, Düzel E, Howard R, Hämmerer D (2019) In vivo visualization of age-related differences in the locus coeruleus. Neurobiol Aging 74:101–111. https://doi.org/10.1016/j.neurobiolaging.2018.10.014

Article  PubMed  PubMed Central  Google Scholar 

Lozano AM, Lipsman N (2013) Probing and regulating dysfunctional circuits using deep brain stimulation. Neuron 77(3):406–424. https://doi.org/10.1016/j.neuron.2013.01.020

Article  CAS  PubMed  Google Scholar 

Lu L, Xu K, Shi L, Dou W, Liu K, Ma H, Xie L, Zhang C, Lu C (2021) Measuring subthalamic nucleus volume of Parkinson’s patients and evaluating its relationship with clinical scales at pre- and postdeep brain stimulation treatment : a magnetic resonance imaging study. BioMed Res Int. https://doi.org/10.1155/2021/6646416

Article  PubMed  PubMed Central  Google Scholar 

Margoni M, Poggiali D, Zywicki S, Rubin M, Lazzarotto A, Franciotta S, Anglani MG, Causin F, Rinaldi F, Perini P, Filippi M, Gallo P (2021) Early red nucleus atrophy in relapse-onset multiple sclerosis. Hum Brain Mapp 42(1):154–160. https://doi.org/10.1002/hbm.25213

Article  PubMed  Google Scholar 

Mavridis I, Boviatsis E, Anagnostopoulou S (2014) Stereotactic anatomy of the human subthalamic nucleus: providing coordinates for accurate electrode placement. J Neurol Surg Part a: Cent Eur Neurosurg 75(04):289–298. https://doi.org/10.1055/s-0034-1368093

Article  Google Scholar 

McNab JA, Jbabdi S, Deoni SCL, Douaud G, Behrens TEJ, Miller KL (2009) High resolution diffusion-weighted imaging in fixed human brain using diffusion-weighted steady state free precession. Neuroimage 46(3):775–785. https://doi.org/10.1016/j.neuroimage.2009.01.008

Article  PubMed  Google Scholar 

Mills EP, Di Pietro F, Alshelh Z, Peck CC, Murray GM, Vickers ER, Henderson LA (2018) Brainstem pain-control circuitry connectivity in chronic neuropathic pain. J Neurosci 38(2):465–473. https://doi.org/10.1523/JNEUROSCI.1647-17.2017

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mueller SG, Nei M, Bateman LM, Knowlton R, Laxer KD, Friedman D, Devinsky O, Goldman AM (2018) Brainstem network disruption: a pathway to sudden unexplained death in epilepsy? Hum Brain Mapp 39(12):4820. https://doi.org/10.1002/HBM.24325

Article  PubMed  PubMed Central