scholarly journals BrainNetVis: An Open-Access Tool to Effectively Quantify and Visualize Brain Networks

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Eleni G. Christodoulou ◽  
Vangelis Sakkalis ◽  
Vassilis Tsiaras ◽  
Ioannis G. Tollis
Keyword(s):  
Open Access ◽  
Brain Network ◽  
Global Network ◽  
Control Group ◽  
Network Modelling ◽  
Network Information ◽  
Network Measures ◽  
Graph Metrics ◽  
Network Metrics ◽  
The Brain

This paper presents BrainNetVis, a tool which serves brain network modelling and visualization, by providing both quantitative and qualitative network measures of brain interconnectivity. It emphasizes the needs that led to the creation of this tool by presenting similar works in the field and by describing how our tool contributes to the existing scenery. It also describes the methods used for the calculation of the graph metrics (global network metrics and vertex metrics), which carry the brain network information. To make the methods clear and understandable, we use an exemplar dataset throughout the paper, on which the calculations and the visualizations are performed. This dataset consists of an alcoholic and a control group of subjects.

scholarly journals A Graphlet-Based Topological Characterization of the Resting-State Network in Healthy People

2021 ◽  
Vol 15 ◽  
Author(s):  
Paolo Finotelli ◽  
Carlo Piccardi ◽  
Edie Miglio ◽  
Paolo Dulio
Keyword(s):  
Resting State ◽  
Brain Regions ◽  
Brain Network ◽  
Induced Subgraphs ◽  
Topological Characterization ◽  
Network Information ◽  
The Subject ◽  
Euclidean Distances ◽  
The Brain

In this paper, we propose a graphlet-based topological algorithm for the investigation of the brain network at resting state (RS). To this aim, we model the brain as a graph, where (labeled) nodes correspond to specific cerebral areas and links are weighted connections determined by the intensity of the functional magnetic resonance imaging (fMRI). Then, we select a number of working graphlets, namely, connected and non-isomorphic induced subgraphs. We compute, for each labeled node, its Graphlet Degree Vector (GDV), which allows us to associate a GDV matrix to each one of the 133 subjects of the considered sample, reporting how many times each node of the atlas “touches” the independent orbits defined by the graphlet set. We focus on the 56 independent columns (i.e., non-redundant orbits) of the GDV matrices. By aggregating their count all over the 133 subjects and then by sorting each column independently, we obtain a sorted node table, whose top-level entries highlight the nodes (i.e., brain regions) most frequently touching each of the 56 independent graphlet orbits. Then, by pairwise comparing the columns of the sorted node table in the top-k entries for various values of k, we identify sets of nodes that are consistently involved with high frequency in the 56 independent graphlet orbits all over the 133 subjects. It turns out that these sets consist of labeled nodes directly belonging to the default mode network (DMN) or strongly interacting with it at the RS, indicating that graphlet analysis provides a viable tool for the topological characterization of such brain regions. We finally provide a validation of the graphlet approach by testing its power in catching network differences. To this aim, we encode in a Graphlet Correlation Matrix (GCM) the network information associated with each subject then construct a subject-to-subject Graphlet Correlation Distance (GCD) matrix based on the Euclidean distances between all possible pairs of GCM. The analysis of the clusters induced by the GCD matrix shows a clear separation of the subjects in two groups, whose relationship with the subject characteristics is investigated.

Assessment of Graph Metrics and Lateralization of Brain Connectivity in Progression of Alzheimer's Disease Using fMRI

2017 ◽  
Vol 9 (4) ◽  
pp. 46-66 ◽  
Author(s):  
Bhuvaneshwari Bhaskaran ◽  
Kavitha Anandan
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Default Mode Network ◽  
Brain Connectivity ◽  
Brain Network ◽  
Brain Disorder ◽  
Default Mode ◽  
Graph Metrics ◽  
Functional Topology ◽  
The Brain

Alzheimer's disease (AD) is a progressive brain disorder which has a long preclinical phase. The beta-amyloid plaques and tangles in the brain are considered as the main pathological causes. Functional connectivity is typically examined in capturing brain network dynamics in AD. A definitive underconnectivity is observed in patients through the progressive stages of AD. Graph theoretic modeling approaches have been effective in understanding the brain dynamics. In this article, the brain connectivity patterns and the functional topology through the progression of Alzheimer's disease are analysed using resting state fMRI. The altered network topology is analysed by graphed theoretical measures and explains cognitive deficits caused by the progression of this disease. Results show that the functional topology is disrupted in the default mode network regions as the disease progresses in patients. Further, it is observed that there is a lack of left lateralization involving default mode network regions as the severity in AD increases.

scholarly journals Transient brain networks underlying interpersonal strategies during synchronized action

2020 ◽  
Author(s):  
Ole Adrian Heggli ◽  
Ivana Konvalinka ◽  
Joana Cabral ◽  
Elvira Brattico ◽  
Morten L Kringelbach ◽  
...  
Keyword(s):  
Computational Models ◽  
Brain Activity ◽  
Brain Regions ◽  
Brain Network ◽  
Human Interaction ◽  
Action Perception ◽  
Network Information ◽  
Mutual Adaptation ◽  
Underlying Mechanisms ◽  
The Brain

Abstract Interpersonal coordination is a core part of human interaction, and its underlying mechanisms have been extensively studied using social paradigms such as joint finger-tapping. Here, individual and dyadic differences have been found to yield a range of dyadic synchronization strategies, such as mutual adaptation, leading–leading, and leading–following behaviour, but the brain mechanisms that underlie these strategies remain poorly understood. To identify individual brain mechanisms underlying emergence of these minimal social interaction strategies, we contrasted EEG-recorded brain activity in two groups of musicians exhibiting the mutual adaptation and leading–leading strategies. We found that the individuals coordinating via mutual adaptation exhibited a more frequent occurrence of phase-locked activity within a transient action–perception-related brain network in the alpha range, as compared to the leading–leading group. Furthermore, we identified parietal and temporal brain regions that changed significantly in the directionality of their within-network information flow. Our results suggest that the stronger weight on extrinsic coupling observed in computational models of mutual adaptation as compared to leading–leading might be facilitated by a higher degree of action–perception network coupling in the brain.

Is Transient Global Amnesia a Network Disease?

2018 ◽  
Vol 80 (5-6) ◽  
pp. 345-354 ◽  
Author(s):  
Kang Min Park ◽  
Byung In Lee ◽  
Sung Eun Kim
Keyword(s):  
White Matter ◽  
Healthy Subjects ◽  
Transient Global Amnesia ◽  
Brain Network ◽  
Network Measures ◽  
Postcentral Gyrus ◽  
Frontal Operculum ◽  
Global Amnesia ◽  
The Right ◽  
The Brain

Background: We evaluated a brain network using graph theoretical analysis and microstructural abnormalities of the white matter in patients with transient global amnesia (TGA). Methods: Twenty patients with TGA and healthy control subjects were recruited, and they underwent diffusion tensor imaging (DTI) scans. Graph theory was applied to obtain network measures based on DTI data. We investigated the network measures and microstructural abnormalities of white matter using tract-based spatial statistics (TBSS) analysis in the patients with TGA. Results: Measures of global topology were not different between the patients with TGA and healthy subjects. However, there were significant differences of hubs organization; the strength of the right superior and inferior orbitofrontal, the right inferior frontal operculum, the left superior parietal, and left postcentral gyrus, the cluster coefficient of the right middle orbitofrontal and left inferior parietal gyrus, the betweenness centrality of the left angular gyrus, and the pagerank centrality of the right superior and inferior orbitofrontal, right inferior frontal operculum, left superior parietal, and left postcentral gyrus in the patients with TGA were significantly lower than those in healthy subjects. Regarding the analysis of the white matter microstructure with TBSS, there were no differences in the fractional anisotropy and mean diffusivity values between the 2 groups. Conclusions: We newly identify a reorganization of network hubs of the brain network in patients with TGA, especially in the regions of the default-mode network. These alterations of the brain network may play a role in the pathophysiologic mechanism underlying TGA and suggest that TGA is a network disease.

scholarly journals Abnormal EEG Complexity and Functional Connectivity of Brain in Patients with Acute Thalamic Ischemic Stroke

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Shuang Liu ◽  
Jie Guo ◽  
Jiayuan Meng ◽  
Zhijun Wang ◽  
Yang Yao ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Functional Connectivity ◽  
Healthy Subjects ◽  
Brain Network ◽  
Control Group ◽  
Stroke Patients ◽  
Cerebral Disease ◽  
Essential Information ◽  
Stroke Group ◽  
The Brain

Ischemic thalamus stroke has become a serious cardiovascular and cerebral disease in recent years. To date the existing researches mostly concentrated on the power spectral density (PSD) in several frequency bands. In this paper, we investigated the nonlinear features of EEG and brain functional connectivity in patients with acute thalamic ischemic stroke and healthy subjects. Electroencephalography (EEG) in resting condition with eyes closed was recorded for 12 stroke patients and 11 healthy subjects as control group. Lempel-Ziv complexity (LZC), Sample Entropy (SampEn), and brain network using partial directed coherence (PDC) were calculated for feature extraction. Results showed that patients had increased mean LZC and SampEn than the controls, which implied the stroke group has higher EEG complexity. For the brain network, the stroke group displayed a trend of weaker cortical connectivity, which suggests a functional impairment of information transmission in cortical connections in stroke patients. These findings suggest that nonlinear analysis and brain network could provide essential information for better understanding the brain dysfunction in the stroke and assisting monitoring or prognostication of stroke evolution.

scholarly journals Identifying optimal working points of individual Virtual Brains: A large-scale brain network modelling study

2020 ◽  
Author(s):  
Paul Triebkorn ◽  
Joelle Zimmermann ◽  
Leon Stefanovski ◽  
Dipanjan Roy ◽  
Ana Solodkin ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Brain Function ◽  
Large Scale ◽  
Brain Activity ◽  
Brain Network ◽  
Model Parameters ◽  
Network Modelling ◽  
Neural Populations ◽  
Global Coupling ◽  
The Brain

AbstractUsing The Virtual Brain (TVB, thevirtualbrian.org) simulation platform, we explored for 50 individual adult human brains (ages 18-80), how personalized connectome based brain network modelling captures various empirical observations as measured by functional magnetic resonance imaging (fMRI) and electroencephalography (EEG). We compare simulated activity based on individual structural connectomes (SC) inferred from diffusion weighted imaging with fMRI and EEG in the resting state. We systematically explore the role of the following model parameters: conduction velocity, global coupling and graph theoretical features of individual SC. First, a subspace of the parameter space is identified for each subject that results in realistic brain activity, i.e. reproducing the following prominent features of empirical EEG-fMRI activity: topology of resting-state fMRI functional connectivity (FC), functional connectivity dynamics (FCD), electrophysiological oscillations in the delta (3-4 Hz) and alpha (8-12 Hz) frequency range and their bimodality, i.e. low and high energy modes. Interestingly, FCD fit, bimodality and static FC fit are highly correlated. They all show their optimum in the same range of global coupling. In other words, only when our local model is in a bistable regime we are able to generate switching of modes in our global network. Second, our simulations reveal the explicit network mechanisms that lead to electrophysiological oscillations, their bimodal behaviour and inter-regional differences. Third, we discuss biological interpretability of the Stefanescu-Jirsa-Hindmarsh-Rose-3D model when embedded inside the large-scale brain network and mechanisms underlying the emergence of bimodality of the neural signal.With the present study, we set the cornerstone for a systematic catalogue of spatiotemporal brain activity regimes generated with the connectome-based brain simulation platform The Virtual Brain.Author SummaryIn order to understand brain dynamics we use numerical simulations of brain network models. Combining the structural backbone of the brain, that is the white matter fibres connecting distinct regions in the grey matter, with dynamical systems describing the activity of neural populations we are able to simulate brain function on a large scale. In order to make accurate prediction with this network, it is crucial to determine optimal model parameters. We here use an explorative approach to adjust model parameters to individual brain activity, showing that subjects have their own optimal point in the parameter space, depending on their brain structure and function. At the same time, we investigate the relation between bistable phenomena on the scale of neural populations and the changed in functional connectivity on the brain network scale. Our results are important for future modelling approaches trying to make accurate predictions of brain function.

scholarly journals Brain connectivity during Alzheimer’s disease progression and its cognitive impact in a transgenic rat model

2020 ◽  
Vol 4 (2) ◽  
pp. 397-415
Author(s):  
Emma Muñoz-Moreno ◽  
Raúl Tudela ◽  
Xavier López-Gil ◽  
Guadalupe Soria
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Transgenic Animals ◽  
Brain Network ◽  
Control Group ◽  
Transgenic Rat ◽  
Disease Evolution ◽  
Early Stages ◽  
Graph Metrics ◽  
New Treatments

The research of Alzheimer’s disease (AD) in its early stages and its progression till symptomatic onset is essential to understand the pathology and investigate new treatments. Animal models provide a helpful approach to this research, since they allow for controlled follow-up during the disease evolution. In this work, transgenic TgF344-AD rats were longitudinally evaluated starting at 6 months of age. Every 3 months, cognitive abilities were assessed by a memory-related task and magnetic resonance imaging (MRI) was acquired. Structural and functional brain networks were estimated and characterized by graph metrics to identify differences between the groups in connectivity, its evolution with age, and its influence on cognition. Structural networks of transgenic animals were altered since the earliest stage. Likewise, aging significantly affected network metrics in TgF344-AD, but not in the control group. In addition, while the structural brain network influenced cognitive outcome in transgenic animals, functional network impacted how control subjects performed. TgF344-AD brain network alterations were present from very early stages, difficult to identify in clinical research. Likewise, the characterization of aging in these animals, involving structural network reorganization and its effects on cognition, opens a window to evaluate new treatments for the disease.

scholarly journals Spontaneous brain network activity: Analysis of its temporal complexity

2017 ◽  
Vol 1 (2) ◽  
pp. 100-115 ◽  
Author(s):  
Mangor Pedersen ◽  
Amir Omidvarnia ◽  
Jennifer M. Walz ◽  
Andrew Zalesky ◽  
Graeme D. Jackson
Keyword(s):  
Brain Network ◽  
Clustering Coefficient ◽  
Network Activity ◽  
Functional Magnetic Resonance ◽  
High Entropy ◽  
Temporal Complexity ◽  
Independent Replication ◽  
Network Metrics ◽  
The Brain ◽  
Complex Entropy

The brain operates in a complex way. The temporal complexity underlying macroscopic and spontaneous brain network activity is still to be understood. In this study, we explored the brain’s complexity by combining functional connectivity, graph theory, and entropy analyses in 25 healthy people using task-free functional magnetic resonance imaging. We calculated the pairwise instantaneous phase synchrony between 8,192 brain nodes for a total of 200 time points. This resulted in graphs for which time series of clustering coefficients (the “cliquiness” of a node) and participation coefficients (the between-module connectivity of a node) were estimated. For these two network metrics, sample entropy was calculated. The procedure produced a number of results: (1) Entropy is higher for the participation coefficient than for the clustering coefficient. (2) The average clustering coefficient is negatively related to its associated entropy, whereas the average participation coefficient is positively related to its associated entropy. (3) The level of entropy is network-specific to the participation coefficient, but not to the clustering coefficient. High entropy for the participation coefficient was observed in the default-mode, visual, and motor networks. These results were further validated using an independent replication dataset. Our work confirms that brain networks are temporally complex. Entropy is a good candidate metric to explore temporal network alterations in diseases with paroxysmal brain disruptions, including schizophrenia and epilepsy.

scholarly journals Modular-Level Alterations of Single-Subject Gray Matter Networks in Schizophrenia

2021 ◽  
Author(s):  
Jie Xiang ◽  
Yunxiao Ma ◽  
Gongshu Wang ◽  
Dandan Li ◽  
Tong Wang ◽  
...  
Keyword(s):  
Gray Matter ◽  
Inferior Frontal Gyrus ◽  
Brain Network ◽  
Control Group ◽  
Single Subject ◽  
Connection Strength ◽  
Schizophrenic Patients ◽  
Topological Characteristics ◽  
Structural Brain Network ◽  
The Brain

Abstract Schizophrenia is often regarded as a psychiatric disorder caused by disrupted connections in the brain. Evidence suggests that the gray matter of schizophrenia patients is damaged in a modular pattern. Recently, abnormal topological organization was observed in the gray matter networks of patients with schizophrenia. However, the modular-level alteration of gray matter networks in schizophrenia remains unclear. In this study, single-subject gray matter networks were constructed for a total of 217 subjects (116 patients with schizophrenia and 101 controls). We analyzed the topological characteristics of the brain network and the strengths of connections between and within modules. Compared with the outcomes in the control group, the global efficiency and participation coefficient values of the single-subject gray matter networks in schizophrenic patients were significantly reduced. The nodal participation coefficient of the regions involving the FPN, DMN and SCN were significantly decreased in subjects with schizophrenia. The intermodule connections between the FPN and VIS and between the DMN and SCN, in the FPN were significantly reduced in the patient group. In the FPN, the intramodule nodal connection strength of the left orbital inferior frontal gyrus and right inferior parietal gyrus was significantly decreased in schizophrenia patients. Reduced intermodule nodal connection strength between the FPN and VIS was associated with the severity of schizophrenia symptoms. These findings suggest that abnormal intramodule and intermodule connections in the structural brain network may a biomarker of schizophrenia symptoms.

scholarly journals Brain network motif topography may predict emergence from disorders of consciousness: a case series

2020 ◽  
Vol 2020 (1) ◽  
Author(s):  
Danielle Nadin ◽  
Catherine Duclos ◽  
Yacine Mahdid ◽  
Alexander Rokos ◽  
Mohamed Badawy ◽  
...  
Keyword(s):  
Case Series ◽  
Brain Network ◽  
Disorders Of Consciousness ◽  
Global Network ◽  
Network Motifs ◽  
Relative Power ◽  
Network Properties ◽  
Recovery From Anesthesia ◽  
The Brain ◽  
Recovery Of Consciousness

Abstract Neuroimaging methods have improved the accuracy of diagnosis in patients with disorders of consciousness (DOC), but novel, clinically translatable methods for prognosticating this population are still needed. In this case series, we explored the association between topographic and global brain network properties and prognosis in patients with DOC. We recorded high-density electroencephalograms in three patients with acute or chronic DOC, two of whom also underwent an anesthetic protocol. In these two cases, we compared functional network motifs, network hubs and power topography (i.e. topographic network properties), as well as relative power and graph theoretical measures (i.e. global network properties), at baseline, during exposure to anesthesia and after recovery from anesthesia. We also compared these properties to a group of healthy, conscious controls. At baseline, the topographic distribution of nodes participating in alpha motifs resembled conscious controls in patients who later recovered consciousness and high relative power in the delta band was associated with a negative outcome. Strikingly, the reorganization of network motifs, network hubs and power topography under anesthesia followed by their return to a baseline patterns upon recovery from anesthesia, was associated with recovery of consciousness. Our findings suggest that topographic network properties measured at the single-electrode level might provide more prognostic information than global network properties that are averaged across the brain network. In addition, we propose that the brain network’s capacity to reorganize in response to a perturbation is a precursor to the recovery of consciousness in DOC patients.

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