WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI

Lechanoine, François; Jacquesson, Timothée; Beaujoin, Justine; Serres, Barthélemy; Mohammadi, Mohammad; Andersson, Frédéric; Poupon, Fabrice; Poupon, Cyril; Destrieux, Christophe

doi:10.1016/j.neuroimage.2021.118080

Cited by 16 publications

(14 citation statements)

References 30 publications

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“…From Klingler's seminal papers 11,43 , dozens of dissection papers were published 1,6,47,48 , and the tissue modi cations induced by the freezing-thawing process were elucidated 12 . More recently, diffusion-weighted imaging became an effective tool for exploring the white matter anatomy in 16 and ex vivo 49,50 , at a spatial resolution as small as 0.1 mm, and to access white matter microstructure and connectivity 51,52 . Others methods, based on the optical properties of the white matter, such as polarized light imaging 53,54 and optical coherence tomography 55,56 , provide information on its anatomy at the micrometer scale.…”

Section: Discussionmentioning

confidence: 99%

Fibravasc: a method to assess the vascularization of main white matter fiber tracts

Smirnov

Maldonado

Destrieux

2022

Preprint

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Advances in the techniques for assessing human cerebral white matter have recently contributed to greater attention to structural connectivity. Yet, little is known about the vascularization of most white matter fasciculi and the fascicular composition of the vascular territories. This paper presents an original method to label the arterial supply of macroscopic white matter fasciculi based on a standardized protocol for post-mortem injection of colored material combined with a novel fiber dissection technique. A detailed description of every step, from obtaining the specimen to image acquisition of its dissection, is provided. Injection and dissection results show the reproducibility and feasibility of the protocol. In addition, we discuss the challenges we faced and overcame during the development of the presented method, highlight its originality, and briefly review the white matter's place in modern clinical practice and research.

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Section: Discussionmentioning

confidence: 99%

Fibravasc: a method to assess the vascularization of main white matter fiber tracts

Smirnov

Maldonado

Destrieux

2022

Preprint

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“…Thus, the masks of the solitary nucleus (NTS), the nucleus ambiguus (NA), the motor nucleus of the vagus nerve (Xmn), the rostral ventrolateral medulla (RVLM), the caudal ventrolateral medulla (CVLM), the spinal nucleus of the trigeminal nerve (SpV), the parabrachial complex (PBC), the locus coeruleus (LC) and the periaqueductal grey (PAG) were created manually. These ROI masks are based on the localization relative to neuroanatomical landmarks and distinct contrast differences as indicated by different neuroanatomical atlases (Mai & Paxinos, 2012; Naidich et al, 2009; Nieuwenhuys et al, 2008; Paxinos & Huang, 2013) as well as the Brainstem wiki (http://fibratlas.univ-tours.fr/mediawiki/index.php), which is part of the Fibratlas Project that provides detailed descriptions on how to identify regions (Lechanoine et al, 2021). For the PBC, LC and PAG regions, additional masks in MNI space, provided by Edlow et al (Edlow et al, 2012), were used to allocate the corresponding region for each subject.…”

Section: Methodsmentioning

confidence: 99%

“…In terms of spatial resolution, the HARDI data acquired via the HPC project, account for a resolution of 1.25 mm. The NTS diameter ranges from 1 to 2 mm in the human (Lechanoine et al, 2021); thus, the spatial resolution certainly needs to be taken into account as it may diminish accuracy of structure location. Although, the identification of structures within the brainstem proves difficult several other attempts to identify brainstem structures at corresponding field strength (3 tesla) and similar spatial resolution were successfully conducted in the past, suggesting feasibility of the applied method (Habas & Cabanis, 2007; Mueller, 2020; Straub et al, 2019).…”

Section: Limitationsmentioning

confidence: 99%

The solitary nucleus connectivity to key autonomic regions in humans

Forstenpointner

Maallo

Elman

et al. 2022

Eur J of Neuroscience

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The nucleus tractus solitarius (NTS) is a key brainstem structure relaying interoceptive peripheral information to the interrelated brain centres for eliciting rapid autonomic responses and for shaping longer‐term neuroendocrine and motor patterns. Structural and functional NTS' connectivity has been extensively investigated in laboratory animals. But there is limited information about NTS' connectome in humans. Using MRI, we examined diffusion and resting state data from 20 healthy participants in the Human Connectome Project. The regions within the brainstem (n = 8), subcortical (n = 6), cerebellar (n = 2) and cortical (n = 5) parts of the brain were selected via a systematic review of the literature and their white matter NTS connections were evaluated via probabilistic tractography along with functional and directional (i.e. Granger causality) analyses. The underlying study confirms previous results from animal models and provides novel aspects on NTS integration in humans. Two key findings can be summarized: (1) the NTS predominantly processes afferent input and (2) a lateralization towards a predominantly left‐sided NTS processing. Our results lay the foundations for future investigations into the NTS' tripartite role composed of interoreceptors' input integration, the resultant neurochemical outflow and cognitive/affective processing. The implications of these data add to the understanding of NTS' role in specific aspects of autonomic functions.

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“…The THOMAS atlas is a template of thalamic nuclei derived from the manual segmentation of 20 White-Matter-Nulled Magnetization Prepared Rapid Gradient Echo (MP-RAGE) 7T datasets warped to the MNI space(Su et al 2019). We used the WIKIBrainStem atlas to identify the brainstem nuclei(Lechanoine et al 2021). This template is based on mesoscopic T2-weighted and diffusion-weighted images obtained from the ultra-high-eld scanning (11.7T) of an ex vivo human specimen.…”

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confidence: 99%

“…This template is based on mesoscopic T2-weighted and diffusion-weighted images obtained from the ultra-high-eld scanning (11.7T) of an ex vivo human specimen. It provides detailed segmentations of 99 brainstem structures(Lechanoine et al 2021).…”

mentioning

confidence: 99%

The subcortical and neurochemical organization of the ventral and dorsal attention networks

Schotten

Alves²,

Corbetta

et al. 2022

Preprint

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Attention is a core cognitive function that filters and selects behaviourally relevant information in the environment. The cortical mapping of attentional systems identified two segregated networks that mediate stimulus-driven and goal-driven processes, the Ventral and the Dorsal Attention Networks (VAN, DAN). Deep brain electrophysiological recordings, behavioural data from phylogenetic distant species and observations from human brain pathologies challenge purely corticocentric models. Here, we used advanced methods of functional alignment applied to resting-state functional connectivity analyses to map the subcortical architecture of the Ventral and the Dorsal Attention Networks. Our investigations revealed the involvement of the pulvinar, the superior colliculi, the head of caudate nuclei, and a cluster of brainstem nuclei relevant for both networks. These nuclei are densely connected structural network hubs as revealed by diffusion-weighted imaging tractography and establish interrelations with the acetylcholine nicotinic receptor as well as dopamine and serotonin transporters systems. This convergence of functional, structural, and neurochemical evidence provides a novel framework to comprehensively understand the neural basis of attention across different species and brain diseases.

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WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI

Cited by 16 publications

References 30 publications

Fibravasc: a method to assess the vascularization of main white matter fiber tracts

Fibravasc: a method to assess the vascularization of main white matter fiber tracts

The solitary nucleus connectivity to key autonomic regions in humans

The subcortical and neurochemical organization of the ventral and dorsal attention networks

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