Lead-DBS v3.0: Mapping Deep Brain Stimulation Effects to Local Anatomy and Global Networks.

Following its introduction in 2014 and with support of a broad international community, the open-source toolbox Lead-DBS has evolved into a comprehensive neuroimaging platform dedicated to localizing, reconstructing, and visualizing electrodes implanted in the human brain, in the context of deep brain stimulation (DBS) and epilepsy monitoring. Expanding clinical indications for DBS, increasing availability of related research tools, and a growing community of clinician-scientist researchers, however, have led to an ongoing need to maintain, update, and standardize the codebase of Lead-DBS. Major development efforts of the platform in recent years have now yielded an end-to-end solution for DBS-based neuroimaging analysis allowing comprehensive image preprocessing, lead localization, stimulation volume modeling, and statistical analysis within a single tool. The aim of the present manuscript is to introduce fundamental additions to the Lead-DBS pipeline including a deformation warpfield editor and novel algorithms for electrode localization. Furthermore, we introduce a total of three comprehensive tools to map DBS effects to local, tract- and brain network-levels. These updates are demonstrated using a single patient example (for subject-level analysis), as well as a retrospective cohort of 51 Parkinson's disease patients who underwent DBS of the subthalamic nucleus (for group-level analysis). Their applicability is further demonstrated by comparing the various methodological choices and the amount of explained variance in clinical outcomes across analysis streams. Finally, based on an increasing need to standardize folder and file naming specifications across research groups in neuroscience, we introduce the brain imaging data structure (BIDS) derivative standard for Lead-DBS. Thus, this multi-institutional collaborative effort represents an important stage in the evolution of a comprehensive, open-source pipeline for DBS imaging and connectomics

lEtude des mécanismes de la Stimulation Cérébrale Profonde pour la restauration de la conscience en neuro-imagerie fonctionnelle dans un modèle Primate Non-Humain

Les traumatismes crâniens les plus sévères peuvent altérer les communications entre des régions cérébrales distantes et conduire à des désordres chroniques de la conscience. Il a été rapporté que la Stimulation Cérébrale Profonde (SCP) du Thalamus module l'éveil et améliore le comportement des patients en état de conscience minimale. Cependant, il n'existe aucune démonstration évidente des mécanismes cérébraux pour la restauration spécifique et causale de l˅accès conscient, i.e. la prise de conscience, par la stimulation électrique. Dans cette étude, nous dressons l'hypothèse que la stimulation thalamique spécifique pourrait restaurer à la fois la vigilance et la prise de conscience à travers la restauration de l'activité thalamo-corticale et de la réorganisation des dynamiques corticales subséquentes.Nous avons créé une installation expérimentale qui combine la SCP et l'Imagerie par Résonance Magnétique fonctionnelle 'IRMf' chez le Primate Non-Humain (PNH) et appliqué une anesthésie finement contrôlée pour supprimer la conscience. Nous avons enregistré l'activité cérébrale du cerveau entier et développé un module de pré-traitement des images, Pypreclin, pour résoudre le problème d'artéfact lié à l'électrode. Sous sédation profonde, la stimulation électrique du noyau Centro-Median du Thalamus (CMT) a induit une forte vigilance de façon binaire. Lorsque la SCP du CMT a été déclenchée, le signal IRMf mesuré a augmenté dans les cortex préfrontal, pariétal et cingulaire, pour retourner progressivement à la valeur de référence quelques secondes après que le stimulateur a été éteint. De plus, la SCP du CMT a conduit à une reconfiguration des dynamiques corticales des états de repos en diminuant la similarité entre fonction et structure, précédemment décrite comme signature de la conscience. Enfin, la SCP du CMT a rétabli une vaste réponse hiérarchique à la régularité auditive globale qui était interrompuesous anesthésie générale. Ainsi, la SCP du CMT a restauré les deux dimensions principales de la conscience que sont l˅éveil et le contenu conscient, ouvrant la voie vers une application thérapeutique chez les patients atteint de désordres chroniques de la conscience.Severe brain injuries may lead to the disruption of long-range inter-region brain communications resulting in chronic Disorders of Consciousness (DoC). Electrical Deep Brain Stimulation (DBS) of the Thalamus has been reported to modulate arousal and ameliorate behavior in Minimally Conscious State (MCS) patients. However, there is no clear demonstration of the cerebral mechanisms for the specific and causal restoration of conscious access, i.e. awareness, with DBS. Here we hypothesized that specific thalamic DBS might restore both arousal and awareness through the restoration of thalamo-cortical activity and the subsequent reorganization of cortical dynamics. We first designed an experimental set-up combining DBS and functional Magnetic Resonance Imaging (fMRI) in Non-Human Primate (NHP) and applied finely tuned anesthesia to suppress consciousness. We recorded whole brain activity and developed a preprocessing pipeline, Pypreclin, to tackle the electrode-induced artifact. During deep sedation, Centro-Median Thalamic (CMT) DBS robustly induced arousal in an ON-OFF fashion. When CMT DBS was switched ON, fMRI signal increased in prefrontal, parietal and cingulate cortices, and gradually returned to baseline seconds after the stimulator was turned OFF. Moreover, CMT DBS led to a reconfiguration of Resting State cortical dynamics bydecreasing the function-structure similarity, previously described as a consciousness signature. Finally, CMT DBS restored a broad hierarchical response to global auditory regularities that was disrupted under general anesthesia. Thus, CMT DBS restored the two main dimensions of consciousness, i.e. arousal and awareness, paving the way to its therapeutical translation in patients with chronic DoC

Pypreclin: An automatic pipeline for macaque functional MRI preprocessing

International audienceNon-human primate functional MRI (fMRI) is a growing field in neuroscience. However, there is no standardized method for monkey fMRI data analysis, specifically for data preprocessing. The preprocessing of monkey fMRI data is challenged by several technical and experimental specificities of the monkey research such as artifacts related to body movements or to intracranial leads. Here we propose to address these challenges by developing a new versatile pipeline for macaque fMRI preprocessing. We developed a Python module, Pypreclin, to process raw images using state of the art algorithms embedded in a fully automatic pipeline. To evaluate its robustness, we applied Pypreclin to fMRI data acquired at 3T in both awake and anesthetized macaques, with or without iron oxide contrast agent, using single loop or multichannel phased-array coils, combined or not with intracranial implanted electrodes. We performed both resting-state and auditory evoked fMRI and compared the results of Pypreclin to a previously employed preprocessing pipeline. Pypreclin successfully achieved the registration of the fMRI data to the macaque brain template in all the experimental conditions. Moreover, Pypreclin enables more accurate locations of auditory evoked activations in relation to the gray matter at corrected level in the awake fMRI condition. Finally, using the Primate neuroimaging Data-Exchange open access platform, we could further validate Pypreclin for monkey fMRI images that were acquired at ultra-high fields, from other institutions and using different protocols. Pypreclin is a validated preprocessing tool that adapts to diverse experimental and technical situations of monkey fMRI. Pypreclin code is available on open source data sharing platform

Deep brain stimulation of the thalamus restores signatures of consciousness in a nonhuman primate model

International audienceLoss of consciousness is associated with the disruption of long-range thalamocortical and corticocortical brain communication. We tested the hypothesis that deep brain stimulation (DBS) of central thalamus might restore both arousal and awareness following consciousness loss. We applied anesthesia to suppress consciousness in nonhuman primates. During anesthesia, central thalamic stimulation induced arousal in an on-off manner and increased functional magnetic resonance imaging activity in prefrontal, parietal, and cingulate cortices. Moreover, DBS restored a broad dynamic repertoire of spontaneous resting-state activity, previously described as a signature of consciousness. None of these effects were obtained during the stimulation of a control site in the ventrolateral thalamus. Last, DBS restored a broad hierarchical response to auditory violations that was disrupted under anesthesia. Thus, DBS restored the two dimensions of consciousness, arousal and conscious access, following consciousness loss, paving the way to its therapeutical translation in patients with disorders of consciousness

Local orchestration of distributed functional patterns supporting loss and restoration of consciousness in the primate brain

International audienceA central challenge of neuroscience is to elucidate how brain function supports consciousness. Here, we combine the specificity of focal deep brain stimulation with fMRI coverage of the entire cortex, in awake and anaesthetised non-human primates. During propofol, sevoflurane, or ketamine anaesthesia, and subsequent restoration of responsiveness by electrical stimulation of the central thalamus, we investigate how loss of consciousness impacts distributed patterns of structure-function organisation across scales. We report that distributed brain activity under anaesthesia is increasingly constrained by brain structure across scales, coinciding with anaesthetic-induced collapse of multiple dimensions of hierarchical cortical organisation. These distributed signatures are observed across different anaesthetics, and they are reversed by electrical stimulation of the central thalamus, coinciding with recovery of behavioural markers of arousal. No such effects were observed upon stimulating the ventral lateral thalamus, demonstrating specificity. Overall, we identify consistent distributed signatures of consciousness that are orchestrated by specific thalamic nuclei

Local orchestration of distributed functional patterns supporting loss and restoration of consciousness in the primate brain

Acknowledgements: This work was supported by a Gates Cambridge Scholarship (OPP 1144) (to A.I.L.); a Travel Grant of the Boehringer Ingelheim Fonds (to A.I.L.); and the visitor program of the European Institute for Theoretical Neuroscience (to A.I.L.); the Fondation pour la Recherche Médicale (FRM grant number ECO20160736100, to J.T.); FNRS Belgium, project MIS/VA - F.4512.21 (to C.M.S.) and grant Embodied-Time – 40011405 (to C.M.S.); the Stephen Erskine Fellowship of Queens’ College, Cambridge (to E.A.S.); CNRS and the European Community (Human Brain Project, H2020-945539, to A.D. and R.C.); the Fondation Bettencourt Schueller (to B.J.); Fondation de France (to B.J.), Human Brain Project (Corticity project FLAG-ERA JTC2017, to B.J.); Institut National de la Santé et de la Recherche Médicale (to B.J.), UVSQ (to B.J.), Commissariat à l’Energie Atomique (to B.J.), Collège de France (to B.J.).AbstractA central challenge of neuroscience is to elucidate how brain function supports consciousness. Here, we combine the specificity of focal deep brain stimulation with fMRI coverage of the entire cortex, in awake and anaesthetised non-human primates. During propofol, sevoflurane, or ketamine anaesthesia, and subsequent restoration of responsiveness by electrical stimulation of the central thalamus, we investigate how loss of consciousness impacts distributed patterns of structure-function organisation across scales. We report that distributed brain activity under anaesthesia is increasingly constrained by brain structure across scales, coinciding with anaesthetic-induced collapse of multiple dimensions of hierarchical cortical organisation. These distributed signatures are observed across different anaesthetics, and they are reversed by electrical stimulation of the central thalamus, coinciding with recovery of behavioural markers of arousal. No such effects were observed upon stimulating the ventral lateral thalamus, demonstrating specificity. Overall, we identify consistent distributed signatures of consciousness that are orchestrated by specific thalamic nuclei.</jats:p

Local orchestration of distributed functional patterns supporting loss and restoration of consciousness in the primate brain.

A central challenge of neuroscience is to elucidate how brain function supports consciousness. Here, we combine the specificity of focal deep brain stimulation with fMRI coverage of the entire cortex, in awake and anaesthetised non-human primates. During propofol, sevoflurane, or ketamine anaesthesia, and subsequent restoration of responsiveness by electrical stimulation of the central thalamus, we investigate how loss of consciousness impacts distributed patterns of structure-function organisation across scales. We report that distributed brain activity under anaesthesia is increasingly constrained by brain structure across scales, coinciding with anaesthetic-induced collapse of multiple dimensions of hierarchical cortical organisation. These distributed signatures are observed across different anaesthetics, and they are reversed by electrical stimulation of the central thalamus, coinciding with recovery of behavioural markers of arousal. No such effects were observed upon stimulating the ventral lateral thalamus, demonstrating specificity. Overall, we identify consistent distributed signatures of consciousness that are orchestrated by specific thalamic nuclei.This work was supported by a Gates Cambridge Scholarship (OPP 1144) (to AIL); a Travel Grant of the Boehringer Ingelheim Fonds (to AIL); and the visitor program of the European Institute for Theoretical Neuroscience (to AIL); the Fondation pour la Recherche Médicale (FRM grant number ECO20160736100, to JT); FNRS Belgium, project MIS/VA - F.4512.21 (to CMS) and grant Embodied-Time – 40011405 (to CMS); the Stephen Erskine Fellowship of Queens’ College, Cambridge (to EAS); CNRS and the European Community (Human Brain Project, H2020-945539, to AD and RC); the Fondation Bettencourt Schueller (to BJ); Fondation de France (to BJ), Human Brain Project (Corticity project FLAG-ERA JTC2017, to BJ); Institut National de la Santé et de la Recherche Médicale (to BJ), UVSQ (to BJ), Commissariat à l’Energie Atomique (to BJ), Collège de France (to BJ)

Brain mechanisms of reversible symbolic reference: a potential singularity of the human brain

International audienceThe emergence of symbolic thinking has been proposed as a dominant cognitive criterion to distinguish humans from other primates during hominization. Although the proper definition of a symbol has been the subject of much debate, one of its simplest features is bidirectional attachment: the content is accessible from the symbol, and vice versa. Behavioral observations scattered over the past four decades suggest that this criterion might not be met in non-human primates, as they fail to generalize an association learned in one temporal order (A to B) to the reverse order (B to A). Here, we designed an implicit fMRI test to investigate the neural mechanisms of arbitrary audio-visual and visual-visual pairing in monkeys and humans and probe their spontaneous reversibility. After learning a unidirectional association, humans showed surprise signals when this learned association was violated. Crucially, this effect occurred spontaneously in both learned and reversed directions, within an extended network of high-level brain areas, including, but also going beyond the language network. In monkeys, by contrast, violations of association effects occurred solely in the learned direction and were largely confined to sensory areas. We propose that a human-specific brain network may have evolved the capacity for reversible symbolic reference

A Network-Based Approach to Glioma Surgery: Insights from Functional Neurosurgery

The evaluation and manipulation of structural and functional networks, which has been integral to advancing functional neurosurgery, is beginning to transcend classical subspecialty boundaries. Notably, its application in neuro-oncologic surgery has stimulated an exciting paradigm shift from the traditional localizationist approach, which is lacking in nuance and optimization. This manuscript reviews the existing literature and explores how structural and functional connectivity analyses have been leveraged to revolutionize and individualize pre-operative tumor evaluation and surgical planning. We describe how this novel approach may improve cognitive and neurologic preservation after surgery and attenuate tumor spread. Furthermore, we demonstrate how connectivity analysis combined with neuromodulation techniques can be employed to induce post-operative neuroplasticity and personalize neurorehabilitation. While the landscape of functional neuro-oncology is still evolving and requires further study to encourage more widespread adoption, this functional approach can transform the practice of neuro-oncologic surgery and improve the care and outcomes of patients with intra-axial tumors

Combining brain perturbation and neuroimaging in non-human primates

Brain perturbation studies allow detailed causal inferences of behavioral and neural processes. Because the combination of brain perturbation methods and neural measurement techniques is inherently challenging, research in humans has predominantly focused on non-invasive, indirect brain perturbations, or neurological lesion studies. Non-human primates have been indispensable as a neurobiological system that is highly similar to humans while simultaneously being more experimentally tractable, allowing visualization of the functional and structural impact of systematic brain perturbation. This review considers the state of the art in non-human primate brain perturbation with a focus on approaches that can be combined with neuroimaging. We consider both non-reversible (lesions) and reversible or temporary perturbations such as electrical, pharmacological, optical, optogenetic, chemogenetic, pathway-selective, and ultrasound based interference methods. Method-specific considerations from the research and development community are offered to facilitate research in this field and support further innovations. We conclude by identifying novel avenues for further research and innovation and by highlighting the clinical translational potential of the methods