scholarly journals A hands-on tutorial on network and topological neuroscience

2021 ◽  
Author(s):  
Eduarda Gervini Zampieri Centeno ◽  
Giulia Moreni ◽  
Chris Vriend ◽  
Linda Douw ◽  
Fernando Antônio Nóbrega Santos
Keyword(s):  
Brain Networks ◽  
Three Dimensional ◽  
Brain Atlas ◽  
Topological Data Analysis ◽  
Hands On ◽  
Neuroimaging Data ◽  
Efficient Integration ◽  
New Feature ◽  
The Brain ◽  
Network Neuroscience

AbstractThe brain is an extraordinarily complex system that facilitates the efficient integration of information from different regions to execute its functions. With the recent advances in technology, researchers can now collect enormous amounts of data from the brain using neuroimaging at different scales and from numerous modalities. With that comes the need for sophisticated tools for analysis. The field of network neuroscience has been trying to tackle these challenges, and graph theory has been one of its essential branches through the investigation of brain networks. Recently, topological data analysis has gained more attention as an alternative framework by providing a set of metrics that go beyond pair-wise connections and offer improved robustness against noise. In this hands-on tutorial, our goal is to provide the computational tools to explore neuroimaging data using these frameworks and to facilitate their accessibility, data visualisation, and comprehension for newcomers to the field. We will start by giving a concise (and by no means complete) overview of the field to introduce the two frameworks, and then explain how to compute both well-established and newer metrics on resting-state functional magnetic resonance imaging. We use an open-source language (Python) and provide an accompanying publicly available Jupyter Notebook that uses data from the 1000 Functional Connectomes Project. Moreover, we would like to highlight one part of our notebook that is solely dedicated to realistic visualisation of high order interactions in brain networks. This pipeline provides three-dimensional (3-D) plots of pair-wise and higher-order interactions projected in a brain atlas, a new feature tailor-made for network neuroscience.

scholarly journals Intra- and Inter-Modular Connectivity Alterations in the Brain Structural Network of Spinocerebellar Ataxia Type 3

Entropy ◽  
2019 ◽  
Vol 21 (3) ◽  
pp. 317 ◽  
Author(s):  
Chi-Wen Jao ◽  
Bing-Wen Soong ◽  
Tzu-Yun Wang ◽  
Hsiu-Mei Wu ◽  
Chia-Feng Lu ◽  
...  
Keyword(s):  
Spinocerebellar Ataxia ◽  
Brain Networks ◽  
Structural Connectivity ◽  
Three Dimensional ◽  
Brain Network ◽  
Spinocerebellar Ataxia Type ◽  
Compensatory Mechanisms ◽  
Spinocerebellar Ataxia Type 3 ◽  
Type 3 ◽  
The Brain

In addition to cerebellar degeneration symptoms, patients with spinocerebellar ataxia type 3 (SCA3) exhibit extensive involvements with damage in the prefrontal cortex. A network model has been proposed for investigating the structural organization and functional mechanisms of clinical brain disorders. For neural degenerative diseases, a cortical feature-based structural connectivity network can locate cortical atrophied regions and indicate how their connectivity and functions may change. The brain network of SCA3 has been minimally explored. In this study, we investigated this network by enrolling 48 patients with SCA3 and 48 healthy subjects. A novel three-dimensional fractal dimension-based network was proposed to detect differences in network parameters between the groups. Copula correlations and modular analysis were then employed to categorize and construct the structural networks. Patients with SCA3 exhibited significant lateralized atrophy in the left supratentorial regions and significantly lower modularity values. Their cerebellar regions were dissociated from higher-level brain networks, and demonstrated decreased intra-modular connectivity in all lobes, but increased inter-modular connectivity in the frontal and parietal lobes. Our results suggest that the brain networks of patients with SCA3 may be reorganized in these regions, with the introduction of certain compensatory mechanisms in the cerebral cortex to minimize their cognitive impairment syndrome.

scholarly journals Combining network topology and information theory to construct representative brain networks

2020 ◽  
pp. 1-29 ◽  
Author(s):  
Andrea I. Luppi ◽  
Emmanuel A. Stamatakis
Keyword(s):  
Cost Optimization ◽  
Brain Networks ◽  
Network Construction ◽  
Information Theoretic ◽  
Human Connectome Project ◽  
Neuroimaging Data ◽  
Efficiency Cost ◽  
Network Topologies ◽  
Network Properties ◽  
Network Neuroscience

Network neuroscience employs graph theory to investigate the human brain as a complex network, and derive generalizable insights about the brain’s network properties. However, graph-theoretical results obtained from network construction pipelines that produce idiosyncratic networks may not generalize when alternative pipelines are employed. This issue is especially pressing because a wide variety of network construction pipelines have been employed in the human network neuroscience literature, making comparisons between studies problematic. Here, we investigate how to produce networks that are maximally representative of the broader set of brain networks obtained from the same neuroimaging data. We do so by minimizing an information-theoretic measure of divergence between network topologies, known as the portrait divergence. Based on functional and diffusion MRI data from the Human Connectome Project, we consider anatomical, functional, and multimodal parcellations at three different scales, and 48 distinct ways of defining network edges. We show that the highest representativeness can be obtained by using parcellations in the order of 200 regions and filtering functional networks based on efficiency-cost optimization—hough suitable alternatives are also highlighted. Overall, we identify specific node definition and thresholding procedures that neuroscientists can follow in order to derive representative networks from their human neuroimaging data.

scholarly journals Building Models of Functional Interactions Among Brain Domains that Encode Varying Information Complexity: A Schizophrenia Case Study

2020 ◽  
Author(s):  
Ishaan Batta ◽  
Anees Abrol ◽  
Zening Fu ◽  
Adrian Preda ◽  
Theo G.M. van Erp ◽  
...  
Keyword(s):  
Brain Networks ◽  
Training Data ◽  
Bayesian Optimization ◽  
Functional Interactions ◽  
Building Models ◽  
Complex Architectures ◽  
Neuroimaging Data ◽  
Model Subspace ◽  
Sophisticated Model ◽  
The Brain

ABSTRACTRevealing associations among various structural and functional patterns of the brain can yield highly informative results about the healthy and disordered brain. Studies using neuroimaging data have more recently begun to utilize the information within as well as across various functional and anatomical domains (i.e., groups of brain networks). However, most whole-brain approaches assume similar complexity of interactions throughout the brain. Here we investigate the hypothesis that interactions between brain networks capture varying amounts of complexity, and that we can better capture this information by varying the complexity of the model subspace structure based on available training data. To do this, we employ a Bayesian optimization-based framework known as the Tree Parzen Estimator (TPE) to identify, exploit and analyze patterns of variation in the information encoded by temporal information extracted from functional magnetic resonance imaging (fMRI) subdomains of the brain. Using a repeated cross-validation procedure on a schizophrenia classification task, we demonstrate evidence that interactions between specific functional subdomains are better characterized by more sophisticated model architectures compared to less complicated ones required by the others for optimally contributing towards classification and understanding the brain’s functional interactions. We show that functional subdomains known to be involved in schizophrenia require more complex architectures to optimally unravel discriminatory information about the disorder. Our study points to the need for adaptive, hierarchical learning frameworks that cater differently to the features from different subdomains, not only for a better prediction but also for enabling the identification of features predicting the outcome of interest.

scholarly journals Imaging transcriptomics: Convergent cellular, transcriptomic, and molecular neuroimaging signatures in the healthy adult human brain

2021 ◽  
Author(s):  
Daniel Martins ◽  
Alessio Giacomel ◽  
Steven CR Williams ◽  
Federico E Turkheimer ◽  
Ottavia Dipasquale ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Brain ◽  
Regional Distribution ◽  
Partial Least Square ◽  
Least Square ◽  
Synaptic Proteins ◽  
Brain Atlas ◽  
Wide Range ◽  
Neuroimaging Data ◽  
The Brain

The expansion of neuroimaging techniques over the last decades has opened a wide range of new possibilities to characterize brain dysfunction in several neurological and psychiatric disorders. However, the lack of specificity of most of these techniques, such as magnetic resonance imaging (MRI)-derived measures, to the underlying molecular and cellular properties of the brain tissue poses limitations to the amount of information one can extract to inform precise models of brain disease. The integration of transcriptomic and neuroimaging data, known as 'imaging transcriptomics', has recently emerged as an indirect way forward to test and/or generate hypotheses about potential cellular and transcriptomic pathways that might underly specific changes in neuroimaging MRI biomarkers. However, the validity of this approach is yet to be examined in-depth. Here, we sought to bridge this gap by performing imaging transcriptomic analyses of the regional distribution of well-known molecular markers, assessed by positron emission tomography (PET), in the healthy human brain. We focused on tracers spanning different elements of the biology of the brain, including neuroreceptors, synaptic proteins, metabolism, and glia. Using transcriptome-wide data from the Allen Brain Atlas, we applied partial least square regression to rank genes according to their level of spatial alignment with the regional distribution of these neuroimaging markers in the brain. Then, we performed gene set enrichment analyses to explore the enrichment for specific biological and cell-type pathways among the genes most strongly associated with each neuroimaging marker. Overall, our findings show that imaging transcriptomics can recover plausible transcriptomic and cellular correlates of the regional distribution of benchmark molecular imaging markers, independently of the type of parcellation used to map gene expression and neuroimaging data. Our data support the plausibility and robustness of imaging transcriptomics as an indirect approach for bridging gene expression, cells and macroscopical neuroimaging and improving our understanding of the biological pathways underlying regional variability in neuroimaging features

scholarly journals A robust image registration interface for large volume brain atlas

2018 ◽  
Author(s):  
Hong Ni ◽  
Chaozhen Tan ◽  
Zhao Feng ◽  
Shangbin Chen ◽  
Zoutao Zhang ◽  
...  
Keyword(s):  
Large Volume ◽  
Three Dimensional ◽  
Brain Structures ◽  
Cellular Level ◽  
Brain Atlas ◽  
Biological Images ◽  
Brain Functions ◽  
Streak Image ◽  
Dataset Size ◽  
The Brain

AbstractMapping the brain structures in three-dimensional accurately is critical for an in-depth understanding of the brain functions. By using the brain atlas as a hub, mapping detected datasets into a standard brain space enables efficiently use of various datasets. However, because of the heterogeneous and non-uniform characteristics of the brain structures at cellular level brought with the recently developed high-resolution whole-brain microscopes, traditional registration methods are difficult to apply to the robust mapping of various large volume datasets. Here, we proposed a robust Brain Spatial Mapping Interface (BrainsMapi) to address the registration of large volume datasets at cellular level by introducing the extract regional features of the anatomically invariant method and a strategy of parameter acquisition and large volume transformation. By performing validation on model data and biological images, BrainsMapi can not only achieve robust registration on sample tearing and streak image datasets, different individual and modality datasets accurately, but also are able to complete the registration of large volume dataset at cellular level which dataset size reaches 20 TB. Besides, it can also complete the registration of historical vectorized dataset. BrainsMapi would facilitate the comparison, reuse and integration of a variety of brain datasets.

scholarly journals A Practical Introduction to Network Neuroscience for Communication Researchers

2020 ◽  
Author(s):  
Jacob T. Fisher ◽  
Frederic R. Hopp ◽  
René Weber
Keyword(s):  
Statistical Tests ◽  
Brain Regions ◽  
Psychology Research ◽  
Media Psychology ◽  
Evolving Networks ◽  
Communication Processes ◽  
Neuroimaging Data ◽  
Neural Underpinnings ◽  
The Brain ◽  
Network Neuroscience

The increasing adoption of brain imaging methods has greatly augmented our understanding of the neural underpinnings of communication processes. Enabled by recent advancements in mathematics and computational infrastructure, researchers have begun to move beyond traditional univariate analytic techniques in favor of methods that consider the brain in terms of evolving networks of interactions between brain regions. This network neuroscience approach is a potential boon to communication and media psychology research but also requires a careful look at the complications inherent in adopting a novel (and complex) methodological tool. In this manuscript, we provide an overview of network neuroscience in view of the needs of communication neuroscientists, discussing considerations that must be considered when constructing networks from neuroimaging data and conducting statistical tests on these networks. Throughout the manuscript, we highlight research domains in which network neuroscience is likely to be particularly useful for increasing theoretical clarity in communication and media psychology research.

Lessons From the Neural Bases of Speech and Voice

2011 ◽  
Vol 21 (1) ◽  
pp. 5-14
Author(s):  
Christy L. Ludlow
Keyword(s):  
Brain Networks ◽  
Neural Substrates ◽  
Voice Behavior ◽  
Therapeutic Approaches ◽  
Neural Bases ◽  
Sound Foundation ◽  
The Brain ◽  
Normal Speech

The premise of this article is that increased understanding of the brain bases for normal speech and voice behavior will provide a sound foundation for developing therapeutic approaches to establish or re-establish these functions. The neural substrates involved in speech/voice behaviors, the types of muscle patterning for speech and voice, the brain networks involved and their regulation, and how they can be externally modulated for improving function will be addressed.

Finding Community of Brain Networks Based on Neighbor Index and DPSO with Dynamic Crossover

2020 ◽  
Vol 15 (4) ◽  
pp. 287-299
Author(s):  
Jie Zhang ◽  
Junhong Feng ◽  
Fang-Xiang Wu
Keyword(s):  
Brain Function ◽  
Brain Networks ◽  
Discrete Particle Swarm Optimization ◽  
Mri Brain ◽  
Mutation Operators ◽  
Neural Unit ◽  
Crossover And Mutation ◽  
The Brain ◽  
Index Table ◽  
Dynamic Crossover

Background: : The brain networks can provide us an effective way to analyze brain function and brain disease detection. In brain networks, there exist some import neural unit modules, which contain meaningful biological insights. Objective:: Therefore, we need to find the optimal neural unit modules effectively and efficiently. Method:: In this study, we propose a novel algorithm to find community modules of brain networks by combining Neighbor Index and Discrete Particle Swarm Optimization (DPSO) with dynamic crossover, abbreviated as NIDPSO. The differences between this study and the existing ones lie in that NIDPSO is proposed first to find community modules of brain networks, and dose not need to predefine and preestimate the number of communities in advance. Results: : We generate a neighbor index table to alleviate and eliminate ineffective searches and design a novel coding by which we can determine the community without computing the distances amongst vertices in brain networks. Furthermore, dynamic crossover and mutation operators are designed to modify NIDPSO so as to alleviate the drawback of premature convergence in DPSO. Conclusion: The numerical results performing on several resting-state functional MRI brain networks demonstrate that NIDPSO outperforms or is comparable with other competing methods in terms of modularity, coverage and conductance metrics.

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