Network scaling effects in graph analytic studies of human resting-state FMRI data

Saccades influence functional modularity in the human cortical vision network

Visual cortex is thought to show both dorsoventral and hemispheric modularity, but it is not known if the same functional modules emerge spontaneously from an unsupervised network analysis, or how they interact when saccades necessitate increased sharing of spatial information. Here, we address these issues by applying graph theory analysis to fMRI data obtained while human participants decided whether an object's shape or orientation changed, with or without an intervening saccade across the object. BOLD activation from 50 vision-related cortical nodes was used to identify local and global network properties. Modularity analysis revealed three sub-networks during fixation: a bilateral parietofrontal network linking areas implicated in visuospatial processing and two lateralized occipitotemporal networks linking areas implicated in object feature processing. When horizontal saccades required visual comparisons between visual hemifields, functional interconnectivity and information transfer increased, and the two lateralized ventral modules became functionally integrated into a single bilateral sub-network. This network included 'between module' connectivity hubs in lateral intraparietal cortex and dorsomedial occipital areas previously implicated in transsaccadic integration. These results provide support for functional modularity in the visual system and show that the hemispheric sub-networks are modified and functionally integrated during saccades.

Translational network neuroscience: Nine roadblocks and possible solutions

Translational network neuroscience aims to integrate advanced neuroimaging and data analysis techniques into clinical practice to better understand and treat neurological disorders. Despite the promise of technologies such as functional MRI and diffusion MRI combined with network analysis tools, the field faces several challenges that hinder its swift clinical translation. We have identified nine key roadblocks that impede this process: (a) theoretical and basic science foundations; (b) network construction, data interpretation, and validation; (c) MRI access, data variability, and protocol standardization; (d) data sharing; (e) computational resources and expertise; (f) interdisciplinary collaboration; (g) industry collaboration and commercialization; (h) operational efficiency, integration, and training; and (i) ethical and legal considerations. To address these challenges, we propose several possible solution strategies. By aligning scientific goals with clinical realities and establishing a sound ethical framework, translational network neuroscience can achieve meaningful advances in personalized medicine and ultimately improve patient care. We advocate for an interdisciplinary commitment to overcoming translational hurdles in network neuroscience and integrating advanced technologies into routine clinical practice.

Tutorial: a guide to diffusion MRI and structural connectomics

Diffusion magnetic resonance imaging (dMRI) is a versatile imaging technique that has gained popularity thanks to its sensitive ability to measure displacement of water molecules within a living tissue on a micrometer scale. Although dMRI has been around since the early 1990s, its applications are constantly evolving, primarily regarding the inference of structural connectomics from nerve fiber trajectories. However, these applications require expertise in image processing and statistics, and it can be difficult for a newcomer to choose an appropriate pipeline to fit their research needs, not least because dMRI is such a flexible methodology that dozens of acquisition and analysis pipelines have been developed over the years. This introductory guide is designed for graduate students and researchers in the neuroscience community who are interested in integrating this new methodology regardless of their background in neuroimaging and computational tools. The guide provides a brief overview of the basic dMRI methodologies but focuses on its applications in neuroplasticity and connectomics. The guide starts with dMRI experimental designs and a complete step-by-step pipeline for structural connectomics. The following section covers the basics of dMRI, including parameters and clinical applications (apparent diffusion coefficient, mean diffusivity, fractional anisotropy and microscopic fractional anisotropy), as well as different approaches and models. The final section focuses on structural connectomics, covering subjects from fiber tracking (techniques, evaluation and limitations) to structural networks (constructing, analyzing and visualizing a network).

Differential brain activity in patients with disorders of consciousness: a 3-month rs-fMRI study using amplitude of low-frequency fluctuation

Introduction

Disorders of consciousness (DoC) from severe brain injuries have significant impacts. However, further research on nuanced biomarkers is needed to fully understand the condition. This study employed resting-state functional MRI (rs-fMRI) and the amplitude of low-frequency fluctuation (ALFF) to investigate differential brain activity in patients with DoC following spinal cord stimulation (SCS) therapy. It also assessed the predictive value of rs-fMRI and ALFF in determining the consciousness levels at 3 months post-therapy.

Methods

We analyzed rs-fMRI data from 31 patients with traumatic brain injury (TBI) and 22 with non-traumatic brain injury (non-TBI) diagnosed with DoC. ALFF was measured before SCS therapy, and clinical outcomes were assessed 3 months later using the Coma Recovery Scale-Revised.

Results

Patients with TBI showed increased ALFF in the thalamus and anterior cingulate cortex, whereas the middle occipital lobe showed decreased ALFF. In the non-TBI group, a higher ALFF was noted in the precuneus, with a reduced ALFF in the occipital and temporal lobes. Patients with improved consciousness post-SCS exhibited distinct ALFF patterns compared with those with unchanged consciousness, particularly in the posterior cingulate and occipital regions.

Conclusion

The application of ALFF in rs-fMRI may be a predictive tool for post-treatment outcomes in patients with DoC of varying etiologies. Differential ALFF in specific brain regions could indicate the likelihood of improvement in consciousness following SCS therapy.

Clinical trial registration

https://www.chictr.org.cn/, Identifier ChiCTR2300069756.

Why experimental variation in neuroimaging should be embraced

In a perfect world, scientists would develop analyses that are guaranteed to reveal the ground truth of a research question. In reality, there are countless viable workflows that produce distinct, often conflicting, results. Although reproducibility places a necessary bound on the validity of results, it is not sufficient for claiming underlying validity, eventual utility, or generalizability. In this work we focus on how embracing variability in data analysis can improve the generalizability of results. We contextualize how design decisions in brain imaging can be made to capture variation, highlight examples, and discuss how variability capture may improve the quality of results.

Sex differences in functional and structural alterations of hippocampus region in chronic pain: a DTI and resting-state fMRI study

Introduction

It is well known that there are significant differences in the prevalence of chronic pain between males and females. Human and animal imaging studies have shown that chronic pain profoundly alters the structure and function of brain regions. However, there is limited research on the sex-specific mechanisms underlying the brain plasticity and adaptive changes associated with chronic pain. In this article, we conducted a multimodal study to evaluate how nerve injury-induced chronic pain affects the brain.

Methods

Male and female Sprague-Dawley (SD) rats with spared nerve injury (SNI) model underwent resting-state functional magnetic resonance imaging (rs-fMRI) (male sham group: n = 18; male SNI group: n = 18; female sham group: n = 20; female SNI group: n = 18) and magnetic resonance diffusion tensor imaging (DTI) (male sham group: n = 23; male SNI group: n = 21; female sham group: n = 20; female SNI group: n = 21) scanning. ICA method, Fractional amplitude of low-frequency fluctuations (fALFF), immunofluorescence staining, and graph theory analysis was utilized to extract the rs-fMRI changes of brain regions of each group.

Results

Using SNI model, which promotes long-lasting mechanical allodynia, we found that neuropathic pain deeply modified the intrinsic organization of the brain functional network in male and female rats (main effect of operation: F = 298.449, P < 0.001). 64 independent components (ICs) in the brain were divided and assigned to 16 systems. In male rats, we observed significant alterations in the microstructure of the hippocampal cornu ammonis 1 and cornu ammonis 2 (CA1/CA2) region, as indicated by increased mean diffusivity (MD) (CA1_L: P = 0.02; CA1_R: P = 0.031; CA2_L: P = 0.035; CA2_R: P = 0.015) and radial diffusivity (RD) (CA1_L: P = 0.028; CA1_R: P = 0.033; CA2_L: P = 0.037; CA2_R: P = 0.038) values, along with enhanced activating transcription factor 3 (ATF3) expression. Conversely, in female rats, we found significant increases in the fractional amplitude of low frequency fluctuations (fALFF) value within the hippocampal dentate gyrus (DG) (F = 5.419, P = 0.023), accompanied by elevated c-Fos signal (F = 6.269, P = 0.031). Furthermore, graph theory analysis revealed notable differences in the small-world network of the hippocampal system in female rats, characterized by reduced small-world attributes and increased inter-nodal transmission efficiency.

Discussion

Our study indicates sex differences in structural and functional alterations in the hippocampal system in rats under chronic pain conditions. The results suggest that the hippocampus system plays an important role in the different mechanisms of chronic pain in different sexes. These findings provide reliable insights to explore the complex mechanisms underlying sex differences in chronic pain.

Effects of connectivity hyperalignment (CHA) on estimated brain network properties: from coarse-scale to fine-scale

Recent gains in functional magnetic resonance imaging (fMRI) studies have been driven by increasingly sophisticated statistical and computational techniques and the ability to capture brain data at finer spatial and temporal resolution. These advances allow researchers to develop population-level models of the functional brain representations underlying behavior, performance, clinical status, and prognosis. However, even following conventional preprocessing pipelines, considerable inter-individual disparities in functional localization persist, posing a hurdle to performing compelling population-level inference. Persistent misalignment in functional topography after registration and spatial normalization will reduce power in developing predictive models and biomarkers, reduce the specificity of estimated brain responses and patterns, and provide misleading results on local neural representations and individual differences. This study aims to determine how connectivity hyperalignment (CHA)-an analytic approach for handling functional misalignment-can change estimated functional brain network topologies at various spatial scales from the coarsest set of parcels down to the vertex-level scale. The findings highlight the role of CHA in improving inter-subject similarities, while retaining individual-specific information and idiosyncrasies at finer spatial granularities. This highlights the potential for fine-grained connectivity analysis using this approach to reveal previously unexplored facets of brain structure and function.

Sex differences in human brain networks in normal and psychiatric populations from the perspective of small-world properties

Females and males are known to be different in the prevalences of multiple psychiatric disorders, while the underlying neural mechanisms are unclear. Based on non-invasive neuroimaging techniques and graph theory, many researchers have tried to use a small-world network model to elucidate sex differences in the brain. This manuscript aims to compile the related research findings from the past few years and summarize the sex differences in human brain networks in both normal and psychiatric populations from the perspective of small-world properties. We reviewed published reports examining altered small-world properties in both the functional and structural brain networks between males and females. Based on four patterns of altered small-world properties proposed: randomization, regularization, stronger small-worldization, and weaker small-worldization, we found that current results point to a significant trend toward more regularization in normal females and more randomization in normal males in functional brain networks. On the other hand, there seems to be no consensus to date on the sex differences in small-world properties of the structural brain networks in normal populations. Nevertheless, we noticed that the sample sizes in many published studies are small, and future studies with larger samples are warranted to obtain more reliable results. Moreover, the number of related studies conducted in psychiatric populations is still limited and more investigations might be needed. We anticipate that these conclusions will contribute to a deeper understanding of the sex differences in the brain, which may be also valuable for developing new methods in the treatment of psychiatric disorders.

Impact of brain parcellation on prediction performance in models of cognition and demographics

Brain connectivity analysis begins with the selection of a parcellation scheme that will define brain regions as nodes of a network whose connections will be studied. Brain connectivity has already been used in predictive modelling of cognition, but it remains unclear if the resolution of the parcellation used can systematically impact the predictive model performance. In this work, structural, functional and combined connectivity were each defined with five different parcellation schemes. The resolution and modality of the parcellation schemes were varied. Each connectivity defined with each parcellation was used to predict individual differences in age, education, sex, executive function, self-regulation, language, encoding and sequence processing. It was found that low-resolution functional parcellation consistently performed above chance at producing generalisable models of both demographics and cognition. However, no single parcellation scheme showed a superior predictive performance across all cognitive domains and demographics. In addition, although parcellation schemes impacted the graph theory measures of each connectivity type (structural, functional and combined), these differences did not account for the out-of-sample predictive performance of the models. Taken together, these findings demonstrate that while high-resolution parcellations may be beneficial for modelling specific individual differences, partial voluming of signals produced by the higher resolution of the parcellation likely disrupts model generalisability.

Analysis of Resting-State Functional Magnetic Resonance Imaging in Alzheimer's Disease

Alzheimer's disease (AD) has been characterized by widespread network disconnection among brain regions, widely overlapping with the hallmarks of the disease. Functional connectivity has been studied with an upward trend in the last two decades, predominantly in AD among other neuropsychiatric disorders, and presents a potential biomarker with various features that might provide unique contributions to foster our understanding of neural mechanisms of AD. The resting-state functional MRI (rs-fMRI) is usually used to measure the blood-oxygen-level-dependent signals that reflect the brain's functional connectivity. Nevertheless, the rs-fMRI is still underutilized, which might be due to the fairly complex acquisition and analytic methodology. In this chapter, we presented the common methods that have been applied in rs-fMRI literature, focusing on the studies on individuals in the continuum of AD. The key methodological aspects will be addressed that comprise acquiring, processing, and interpreting rs-fMRI data. More, we discussed the current and potential implications of rs-fMRI in AD.

Can hubs of the human connectome be identified consistently with diffusion MRI?

Recent years have seen a surge in the use of diffusion MRI to map connectomes in humans, paralleled by a similar increase in processing and analysis choices. Yet these different steps and their effects are rarely compared systematically. Here, in a healthy young adult population (n = 294), we characterized the impact of a range of analysis pipelines on one widely studied property of the human connectome: its degree distribution. We evaluated the effects of 40 pipelines (comparing common choices of parcellation, streamline seeding, tractography algorithm, and streamline propagation constraint) and 44 group-representative connectome reconstruction schemes on highly connected hub regions. We found that hub location is highly variable between pipelines. The choice of parcellation has a major influence on hub architecture, and hub connectivity is highly correlated with regional surface area in most of the assessed pipelines (ρ > 0.70 in 69% of the pipelines), particularly when using weighted networks. Overall, our results demonstrate the need for prudent decision-making when processing diffusion MRI data, and for carefully considering how different processing choices can influence connectome organization.

The effect of using group-averaged or individualized brain parcellations when investigating connectome dysfunction in psychosis

Functional magnetic resonance imaging (fMRI) is widely used to investigate functional coupling (FC) disturbances in a range of clinical disorders. Most analyses performed to date have used group-based parcellations for defining regions of interest (ROIs), in which a single parcellation is applied to each brain. This approach neglects individual differences in brain functional organization and may inaccurately delineate the true borders of functional regions. These inaccuracies could inflate or underestimate group differences in case-control analyses. We investigated how individual differences in brain organization influence group comparisons of FC using psychosis as a case study, drawing on fMRI data in 121 early psychosis patients and 57 controls. We defined FC networks using either a group-based parcellation or an individually tailored variant of the same parcellation. Individualized parcellations yielded more functionally homogeneous ROIs than did group-based parcellations. At the level of individual connections, case-control FC differences were widespread, but the group-based parcellation identified approximately 7.7% more connections as dysfunctional than the individualized parcellation. When considering differences at the level of functional networks, the results from both parcellations converged. Our results suggest that a substantial fraction of dysconnectivity previously observed in psychosis may be driven by the parcellation method, rather than by a pathophysiological process related to psychosis.

Altered Brain Connectivity and Network Topological Organization in a Non-ordinary State of Consciousness Induced by Hypnosis

Hypnosis has been shown to be of clinical utility; however, its underlying neural mechanisms remain unclear. This study aims to investigate altered brain dynamics during the non-ordinary state of consciousness induced by hypnosis. We studied high-density EEG in 9 healthy participants during eyes-closed wakefulness and during hypnosis, induced by a muscle relaxation and eyes fixation procedure. Using hypotheses based on internal and external awareness brain networks, we assessed region-wise brain connectivity between six ROIs (right and left frontal, right and left parietal, upper and lower midline regions) at the scalp level and compared across conditions. Data-driven, graph-theory analyses were also carried out to characterize brain network topology in terms of brain network segregation and integration. During hypnosis, we observed (1) increased delta connectivity between left and right frontal, as well as between right frontal and parietal regions; (2) decreased connectivity for alpha (between right frontal and parietal and between upper and lower midline regions) and beta-2 bands (between upper midline and right frontal, frontal and parietal, also between upper and lower midline regions); and (3) increased network segregation (short-range connections) in delta and alpha bands, and increased integration (long-range connections) in beta-2 band. This higher network integration and segregation was measured bilaterally in frontal and right parietal electrodes, which were identified as central hub regions during hypnosis. This modified connectivity and increased network integration-segregation properties suggest a modification of the internal and external awareness brain networks that may reflect efficient cognitive-processing and lower incidences of mind-wandering during hypnosis.

Graph Neural Networks in Network Neuroscience

Noninvasive medical neuroimaging has yielded many discoveries about the brain connectivity. Several substantial techniques mapping morphological, structural and functional brain connectivities were developed to create a comprehensive road map of neuronal activities in the human brain -namely brain graph. Relying on its non-euclidean data type, graph neural network (GNN) provides a clever way of learning the deep graph structure and it is rapidly becoming the state-of-the-art leading to enhanced performance in various network neuroscience tasks. Here we review current GNN-based methods, highlighting the ways that they have been used in several applications related to brain graphs such as missing brain graph synthesis and disease classification. We conclude by charting a path toward a better application of GNN models in network neuroscience field for neurological disorder diagnosis and population graph integration. The list of papers cited in our work is available at https://github.com/basiralab/GNNs-in-Network-Neuroscience.

Individualized network analysis: A novel approach to investigate tau PET using graph theory in the Alzheimer's disease continuum

Introduction

Tau PET imaging has emerged as an important tool to detect and monitor tangle burden in vivo in the study of Alzheimer's disease (AD). Previous studies demonstrated the association of tau burden with cognitive decline in probable AD cohorts. This study introduces a novel approach to analyze tau PET data by constructing individualized tau network structure and deriving its graph theory-based measures. We hypothesize that the network- based measures are a measure of the total tau load and the stage through disease.

Methods

Using tau PET data from the AD Neuroimaging Initiative from 369 participants, we determine the network measures, global efficiency, global strength, and limbic strength, and compare with two regional measures entorhinal and tau composite SUVR, in the ability to differentiate, cognitively unimpaired (CU), MCI and AD. We also investigate the correlation of these network and regional measures and a measure of memory performance, auditory verbal learning test for long-term recall memory (AVLT-LTM). Finally, we determine the stages based on global efficiency and limbic strength using conditional inference trees and compare with Braak staging.

Results

We demonstrate that the derived network measures are able to differentiate three clinical stages of AD, CU, MCI, and AD. We also demonstrate that these network measures are strongly correlated with memory performance overall. Unlike regional tau measurements, the tau network measures were significantly associated with AVLT-LTM even in cognitively unimpaired individuals. Stages determined from global efficiency and limbic strength, visually resembled Braak staging.

Discussion

The strong correlations with memory particularly in CU suggest the proposed technique may be used to characterize subtle early tau accumulation. Further investigation is ongoing to examine this technique in a longitudinal setting.

TOPOLOGICAL LEARNING FOR BRAIN NETWORKS

This paper proposes a novel topological learning framework that integrates networks of different sizes and topology through persistent homology. Such challenging task is made possible through the introduction of a computationally efficient topological loss. The use of the proposed loss bypasses the intrinsic computational bottleneck associated with matching networks. We validate the method in extensive statistical simulations to assess its effectiveness when discriminating networks with different topology. The method is further demonstrated in a twin brain imaging study where we determine if brain networks are genetically heritable. The challenge here is due to the difficulty of overlaying the topologically different functional brain networks obtained from resting-state functional MRI onto the template structural brain network obtained through diffusion MRI.

Disrupted topological organization of functional brain networks in Alzheimer's disease patients with depressive symptoms

BACKGROUND

Depression is a common symptom of Alzheimer's disease (AD), but the underlying neural mechanism is unknown. The aim of this study was to explore the topological properties of AD patients with depressive symptoms (D-AD) using graph theoretical analysis.

METHODS

We obtained 3-Tesla rsfMRI data from 24 D-AD patients, 20 non-depressed AD patients (nD-AD), and 20 normal controls (NC). Resting state networks were identified using graph theory analysis. ANOVA with a two-sample t-test post hoc analysis in GRETNA was used to assess the topological measurements.

RESULTS

Our results demonstrate that the three groups show characteristic properties of a small-world network. NCs showed significantly larger global and local efficiency than D-AD and nD-AD patients. Compared with nD-AD patients, D-AD patients showed decreased nodal centrality in the pallidum, putamen, and right superior temporal gyrus. They also showed increased nodal centrality in the right superior parietal gyrus, the medial orbital portion of the right superior frontal gyrus, and the orbital portion of the right superior frontal gyrus. Compared with nD-AD patients, NC showed decreased nodal betweenness in the right superior temporal gyrus, and increased nodal betweenness in medial orbital part of the right superior frontal gyrus.

CONCLUSIONS

These results indicate that D-AD is associated with alterations of topological structure. Our study provides new insights into the brain mechanisms underlying D-AD.

Test-retest reliability of modular-relevant analysis in brain functional network

Introduction

The human brain could be modeled as a complex network via functional magnetic resonance imaging (fMRI), and the architecture of these brain functional networks can be studied from multiple spatial scales with different graph theory tools. Detecting modules is an important mesoscale network measuring approach that has provided crucial insights for uncovering how brain organizes itself among different functional subsystems. Despite its successful application in a wide range of brain network studies, the lack of comprehensive reliability assessment prevents its potential extension to clinical trials.

Methods

To fill this gap, this paper, using resting-state test-retest fMRI data, systematically explored the reliabilities of five popular network metrics derived from modular structure. Considering the repeatability of network partition depends heavily on network size and module detection algorithm, we constructed three types of brain functional networks for each subject by using a set of coarse-to-fine brain atlases and adopted four methods for single-subject module detection and twelve methods for group-level module detection.

Results

The results reported moderate-to-good reliability in modularity, intra- and inter-modular functional connectivities, within-modular degree and participation coefficient at both individual and group levels, indicating modular-relevant network metrics can provide robust evaluation results. Further analysis identified the significant influence of module detection algorithm and node definition approach on reliabilities of network partitions and its derived network analysis results.

Discussion

This paper provides important guidance for choosing reliable modular-relevant network metrics and analysis strategies in future studies.

Wide-Field Calcium Imaging of Neuronal Network Dynamics In Vivo

A central tenet of neuroscience is that sensory, motor, and cognitive behaviors are generated by the communications and interactions among neurons, distributed within and across anatomically and functionally distinct brain regions. Therefore, to decipher how the brain plans, learns, and executes behaviors requires characterizing neuronal activity at multiple spatial and temporal scales. This includes simultaneously recording neuronal dynamics at the mesoscale level to understand the interactions among brain regions during different behavioral and brain states. Wide-field Ca2+ imaging, which uses single photon excitation and improved genetically encoded Ca2+ indicators, allows for simultaneous recordings of large brain areas and is proving to be a powerful tool to study neuronal activity at the mesoscopic scale in behaving animals. This review details the techniques used for wide-field Ca2+ imaging and the various approaches employed for the analyses of the rich neuronal-behavioral data sets obtained. Also discussed is how wide-field Ca2+ imaging is providing novel insights into both normal and altered neural processing in disease. Finally, we examine the limitations of the approach and new developments in wide-field Ca2+ imaging that are bringing new capabilities to this important technique for investigating large-scale neuronal dynamics.

Meta-connectomic analysis maps consistent, reproducible, and transcriptionally relevant functional connectome hubs in the human brain

Human brain connectomes include sets of densely connected hub regions. However, the consistency and reproducibility of functional connectome hubs have not been established to date and the genetic signatures underlying robust hubs remain unknown. Here, we conduct a worldwide harmonized meta-connectomic analysis by pooling resting-state functional MRI data of 5212 healthy young adults across 61 independent cohorts. We identify highly consistent and reproducible connectome hubs in heteromodal and unimodal regions both across cohorts and across individuals, with the greatest effects observed in lateral parietal cortex. These hubs show heterogeneous connectivity profiles and are critical for both intra- and inter-network communications. Using post-mortem transcriptome datasets, we show that as compared to non-hubs, connectome hubs have a spatiotemporally distinctive transcriptomic pattern dominated by genes involved in the neuropeptide signaling pathway, neurodevelopmental processes, and metabolic processes. These results highlight the robustness of macroscopic connectome hubs and their potential cellular and molecular underpinnings, which markedly furthers our understanding of how connectome hubs emerge in development, support complex cognition in health, and are involved in disease.

Resting-State fMRI Whole Brain Network Function Plasticity Analysis in Attention Deficit Hyperactivity Disorder

Attention deficit hyperactivity disorder (ADHD) is a common mental disorder in children, which is related to inattention and hyperactivity. These symptoms are associated with abnormal interactions of brain networks. We used resting-state functional magnetic resonance imaging (rs-fMRI) based on the graph theory to explore the topology property changes of brain networks between an ADHD group and a normal group. The more refined AAL_1024 atlas was used to construct the functional networks with high nodal resolution, for detecting more subtle changes in brain regions and differences among groups. We compared altered topology properties of brain network between the groups from multilevel, mainly including modularity at mesolevel. Specifically, we analyzed the similarities and differences of module compositions between the two groups. The results found that the ADHD group showed stronger economic small-world network property, while the clustering coefficient was significantly lower than the normal group; the frontal and occipital lobes showed smaller node degree and global efficiency between disease statuses. The modularity results also showed that the module number of the ADHD group decreased, and the ADHD group had short-range overconnectivity within module and long-range underconnectivity between modules. Moreover, modules containing long-range connections between the frontal and occipital lobes disappeared, indicating that there was lack of top-down control information between the executive control region and the visual processing region in the ADHD group. Our results suggested that these abnormal regions were related to executive control and attention deficit of ADHD patients. These findings helped to better understand how brain function correlates with the ADHD symptoms and complement the fewer modularity elaboration of ADHD research.

Dynamic Brain Connectivity in Resting-State FMRI Using Spectral ICA and Graph Approach: Application to Healthy Controls and Multiple Sclerosis

Multiple sclerosis (MS) is a neuroinflammatory disease that involves structural and functional damage to the brain. It changes the functional connectivity of the brain between and within networks. Resting-state functional magnetic resonance imaging (fMRI) enables us to measure functional correlation and independence between different brain regions. In recent years, statistical methods, including independent component analysis (ICA) and graph-based analysis, have been widely used in fMRI studies. Furthermore, topological properties of the brain have been appeared as significant features of neuroscience studies. Most studies are focused on graph analysis and ICA methods, rather than considering spectral approaches. Here, we developed a new framework to measure brain connectivity (in static and dynamic formats) and incorporate it to study fMRI data from MS patients and healthy controls (HCs). For this purpose, a spectral ICA method is proposed to extract the nodes of the brain graph. Spectral ICA extracts more reliable components and decreases the processing time in calculation of the static brain connectivity. Compared to Infomax ICA, dynamic range and low-frequency to high-frequency power ratio (fALFF) show better results using the proposed ICA. It is also helpful in selection of the states for dynamic connectivity. Furthermore, the dynamic connectivity-based extracted components from spectral ICA are estimated using a mutual information method and based on correlation of sliding time-windowed on selected IC time courses. First-level and second-level connectivity states are calculated using correlations of connectivity strength between graph nodes (spectral ICA components). Finally, static and dynamic connectivity are analyzed based on correlation nodes percolated by an anatomical automatic labeling (AAL) atlas. Despite static and dynamic connectivity results of AAL correlations not showing any significant changes between MS and HC, our results based on spectral ICA in static and dynamic connectivity showed significantly decreased connectivity in MS patients in the anterior cingulate cortex, whereas it was significantly weaker in the core but stronger at the periphery of the posterior cingulate cortex.

Combination of structural and functional connectivity explains unique variation in specific domains of cognitive function

The relationship between structural and functional brain networks has been characterised as complex: the two networks mirror each other and show mutual influence but they also diverge in their organisation. This work explored whether a combination of structural and functional connectivity can improve the fit of regression models of cognitive performance. Principal Component Analysis (PCA) was first applied to cognitive data from the Human Connectome Project to identify latent cognitive components: Executive Function, Self-regulation, Language, Encoding and Sequence Processing. A Principal Component Regression approach with embedded Step-Wise Regression (SWR-PCR) was then used to fit regression models of each cognitive domain based on structural (SC), functional (FC) or combined structural-functional (CC) connectivity. Executive Function was best explained by the CC model. Self-regulation was equally well explained by SC and FC. Language was equally well explained by CC and FC models. Encoding and Sequence Processing were best explained by SC. Evaluation of out-of-sample models' skill via cross-validation showed that SC, FC and CC produced generalisable models of Language performance. SC models performed most effectively at predicting Language performance in unseen sample. Executive Function was most effectively predicted by SC models, followed only by CC models. Self-regulation was only effectively predicted by CC models and Sequence Processing was only effectively predicted by FC models. The present study demonstrates that integrating structural and functional connectivity can help explaining cognitive performance, but that the added explanatory value (in sample) may be domain-specific and can come at the expense of reduced generalisation performance (out-of-sample).

Sparse Hierarchical Representation Learning on Functional Brain Networks for Prediction of Autism Severity Levels

Machine learning algorithms have been widely applied in diagnostic tools for autism spectrum disorder (ASD), revealing an altered brain connectivity. However, little is known about whether an magnetic resonance imaging (MRI)-based brain network is related to the severity of ASD symptoms in a large-scale cohort. We propose a graph convolution neural network-based framework that can generate sparse hierarchical graph representations for functional brain connectivity. Instead of assigning initial features for each node, we utilized a feature extractor to derive node features and the extracted representations can be fed to a hierarchical graph self-attention framework to effectively represent the entire graph. By incorporating connectivity embeddings in the feature extractor, we propose adjacency embedding networks to characterize the heterogeneous representations of the brain connectivity. Our proposed model variants outperform the benchmarking model with different configurations of adjacency embedding networks and types of functional connectivity matrices. Using this approach with the best configuration (SHEN atlas for node definition, Tikhonov correlation for connectivity estimation, and identity-adjacency embedding), we were able to predict individual ASD severity levels with a meaningful accuracy: the mean absolute error (MAE) and correlation between predicted and observed ASD severity scores resulted in 0.96, and r = 0.61 (P < 0.0001), respectively. To obtain a better understanding on how to generate better representations, we investigate the relationships between the extracted feature embeddings and the graph theory-based nodal measurements using canonical correlation analysis. Finally, we visualized the model to identify the most contributive functional connections for predicting ASD severity scores.

Evaluation of functional MRI-based human brain parcellation: a review

Brain parcellations play a crucial role in the analysis of brain imaging data sets, as they can significantly affect the outcome of the analysis. In recent years, several novel approaches for constructing MRI-based brain parcellations have been developed with promising results. In the absence of ground truth, several evaluation approaches have been used to evaluate currently available brain parcellations. In this article, we review and critique methods used for evaluating functional brain parcellations constructed using fMRI data sets. We also describe how some of these evaluation methods have been used to estimate the optimal parcellation granularity. We provide a critical discussion of the current approach to the problem of identifying the optimal brain parcellation that is suited for a given neuroimaging study. We argue that the criteria for an optimal brain parcellation must depend on the application the parcellation is intended for. We describe a teleological approach to the evaluation of brain parcellations, where brain parcellations are evaluated in different contexts and optimal brain parcellations for each context are identified separately. We conclude by discussing several directions for further research that would result in improved evaluation strategies.

Alzheimer's Disease Diagnosis and Biomarker Analysis Using Resting-State Functional MRI Functional Brain Network With Multi-Measures Features and Hippocampal Subfield and Amygdala Volume of Structural MRI

Accurate diagnosis of the initial phase of Alzheimer's disease (AD) is essential and crucial. The objective of this research was to employ efficient biomarkers for the diagnostic analysis and classification of AD based on combining structural MRI (sMRI) and resting-state functional MRI (rs-fMRI). So far, several anatomical MRI imaging markers for AD diagnosis have been identified. The use of cortical and subcortical volumes, the hippocampus, and amygdala volume, as well as genetic patterns, has proven to be beneficial in distinguishing patients with AD from the healthy population. The fMRI time series data have the potential for specific numerical information as well as dynamic temporal information. Voxel and graphical analyses have gained popularity for analyzing neurodegenerative diseases, such as Alzheimer's and its prodromal phase, mild cognitive impairment (MCI). So far, these approaches have been utilized separately for the diagnosis of AD. In recent studies, the classification of cases of MCI into those that are not converted for a certain period as stable MCI (MCIs) and those that converted to AD as MCIc has been less commonly reported with inconsistent results. In this study, we verified and validated the potency of a proposed diagnostic framework to identify AD and differentiate MCIs from MCIc by utilizing the efficient biomarkers obtained from sMRI, along with functional brain networks of the frequency range .01-.027 at the resting state and the voxel-based features. The latter mainly included default mode networks (amplitude of low-frequency fluctuation [ALFF], fractional ALFF [ALFF], and regional homogeneity [ReHo]), degree centrality (DC), and salience networks (SN). Pearson's correlation coefficient for measuring fMRI functional networks has proven to be an efficient means for disease diagnosis. We applied the graph theory to calculate nodal features (nodal degree [ND], nodal path length [NL], and between centrality [BC]) as a graphical feature and analyzed the connectivity link between different brain regions. We extracted three-dimensional (3D) patterns to calculate regional coherence and then implement a univariate statistical t-test to access a 3D mask that preserves voxels showing significant changes. Similarly, from sMRI, we calculated the hippocampal subfield and amygdala nuclei volume using Freesurfer (version 6). Finally, we implemented and compared the different feature selection algorithms to integrate the structural features, brain networks, and voxel features to optimize the diagnostic identifications of AD using support vector machine (SVM) classifiers. We also compared the performance of SVM with Random Forest (RF) classifiers. The obtained results demonstrated the potency of our framework, wherein a combination of the hippocampal subfield, the amygdala volume, and brain networks with multiple measures of rs-fMRI could significantly enhance the accuracy of other approaches in diagnosing AD. The accuracy obtained by the proposed method was reported for binary classification. More importantly, the classification results of the less commonly reported MCIs vs. MCIc improved significantly. However, this research involved only the AD Neuroimaging Initiative (ADNI) cohort to focus on the diagnosis of AD advancement by integrating sMRI and fMRI. Hence, the study's primary disadvantage is its small sample size. In this case, the dataset we utilized did not fully reflect the whole population. As a result, we cannot guarantee that our findings will be applicable to other populations.

Reorganized Brain Functional Network Topology in Presbycusis

Purpose

Presbycusis is characterized by bilateral sensorineural hearing loss at high frequencies and is often accompanied by cognitive decline. This study aimed to identify the topological reorganization of brain functional network in presbycusis with/without cognitive decline by using graph theory analysis approaches based on resting-state functional magnetic resonance imaging (rs-fMRI).

Methods

Resting-state fMRI scans were obtained from 30 presbycusis patients with cognitive decline, 30 presbycusis patients without cognitive decline, and 50 age-, sex-, and education-matched healthy controls. Graph theory was applied to analyze the topological properties of brain functional networks including global and nodal metrics, modularity, and rich-club organization.

Results

At the global level, the brain functional networks of all participants were found to possess small-world properties. Also, significant group differences in global network metrics were observed among the three groups such as clustering coefficient, characteristic path length, normalized characteristic path length, and small-worldness. At the nodal level, several nodes with abnormal betweenness centrality, degree centrality, nodal efficiency, and nodal local efficiency were detected in presbycusis patients with/without cognitive decline. Changes in intra-modular connections in frontal lobe module and inter-modular connections in prefrontal subcortical lobe module were found in presbycusis patients exposed to modularity analysis. Rich-club nodes were reorganized in presbycusis patients, while the connections among them had no significant group differences.

Conclusion

Presbycusis patients exhibited topological reorganization of the whole-brain functional network, and presbycusis patients with cognitive decline showed more obvious changes in these topological properties than those without cognitive decline. Abnormal changes of these properties in presbycusis patients may compensate for cognitive impairment by mobilizing additional neural resources.

Whole-Brain Network Models: From Physics to Bedside

Computational neuroscience has come a long way from its humble origins in the pioneering work of Hodgkin and Huxley. Contemporary computational models of the brain span multiple spatiotemporal scales, from single neuronal compartments to models of social cognition. Each spatial scale comes with its own unique set of promises and challenges. Here, we review models of large-scale neural communication facilitated by white matter tracts, also known as whole-brain models (WBMs). Whole-brain approaches employ inputs from neuroimaging data and insights from graph theory and non-linear systems theory to model brain-wide dynamics. Over the years, WBM models have shown promise in providing predictive insights into various facets of neuropathologies such as Alzheimer's disease, Schizophrenia, Epilepsy, Traumatic brain injury, while also offering mechanistic insights into large-scale cortical communication. First, we briefly trace the history of WBMs, leading up to the state-of-the-art. We discuss various methodological considerations for implementing a whole-brain modeling pipeline, such as choice of node dynamics, model fitting and appropriate parcellations. We then demonstrate the applicability of WBMs toward understanding various neuropathologies. We conclude by discussing ways of augmenting the biological and clinical validity of whole-brain models.

Episodic Past, Future, and counterfactual thinking in Relapsing-Remitting Multiple sclerosis

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Performance in episodic past, future or counterfactual thinking in relapsing-remitting MS and controls was explored.

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Behavioral and diffusion weighted imaging were used to evaluate associations between white matter integrity and group differences in performance.

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Relative to controls, MS patients showed reductions in episodic details across all three simulations.

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Reduced white matter integrity in three association tracts predicted this reduction in episodic details during counterfactual simulations.

Multiple sclerosis (MS) is a progressive disease characterized by widespread white matter lesions in the brain and spinal cord. In addition to well-characterized motor deficits, MS results in cognitive impairments in several domains, notably in episodic autobiographical memory. Recent studies have also revealed that patients with MS exhibit deficits in episodic future thinking, i.e., our capacity to imagine possible events that may occur in our personal future. Both episodic memory and episodic future thinking have been shown to share cognitive and neural mechanisms with a related kind of hypothetical simulation known as episodic counterfactual thinking: our capacity to imagine alternative ways in which past personal events could have occurred but did not. However, the extent to which episodic counterfactual thinking is affected in MS is still unknown. The current study sought to explore this issue by comparing performance in mental simulation tasks involving either past, future or counterfactual thoughts in relapsing-remitting MS. Diffusion weighted imaging (DWI) measures were also extracted to determine whether changes in structural pathways connecting the brain’s default mode network (DMN) would be associated with group differences in task performance. Relative to controls, patients showed marked reductions in the number of internal details across all mental simulations, but no differences in the number of external and semantic-based details. It was also found that, relative to controls, patients with relapsing-remitting MS reported reduced composition ratings for episodic simulations depicting counterfactual events, but not so for actual past or possible future episodes. Additionally, three DWI measures of white matter integrity—fractional anisotropy, radial diffusivity and streamline counts—showed reliable differences between patients with relapsing-remitting MS and matched healthy controls. Importantly, DWI measures associated with reduced white matter integrity in three association tracts on the DMN—the right superior longitudinal fasciculus, the left hippocampal portion of the cingulum and the left inferior longitudinal fasciculus—predicted reductions in the number of internal details during episodic counterfactual simulations. Taken together, these results help to illuminate impairments in episodic simulation in relapsing-remitting MS and show, for the first time, a differential association between white matter integrity and deficits in episodic counterfactual thinking in individuals with relapsing-remitting MS.

Altered topological properties of the intrinsic functional brain network in patients with right-sided unilateral hearing loss caused by acoustic neuroma

Neuroimaging studies have identified alterations in functional connectivity between specific brain regions in patients with unilateral hearing loss (UHL) and different influence of the side of UHL on neural plasticity. However, little is known about changes of whole-brain functional networks in patients with UHL and whether differences exist in topological organization between right-sided UHL (RUHL) and left-sided UHL (LUHL). To address this issue, we employed resting-state fMRI (rs-fMRI) and graph-theoretical approaches to investigate the topological alterations of brain functional connectomes in patients with RUHL and LUHL. Data from 44 patients with UHL (including 22 RUHL patients and 22 LUHL patients) and 37 healthy control subjects (HCs) were collected. Functional brain networks were constructed for each participant, following by graph-theoretical network analyses at connectional and global (e.g., small-worldness) levels. The correlations between brain network topologies and clinical variables were further studied. Using network-based analysis, we found a subnetwork in the visual cortex which had significantly lower connectivity strength in patients with RUHL as compared to HCs. At global level, all participants showed small-world architecture in functional brain networks, however, significantly lower normalized clustering coefficient and small-worldness were observed in patients with RUHL than in HCs. Moreover, these abnormal network metrics were demonstrated to be correlated with the clinical variables and cognitive performance of patients with RUHL. Notably, no significant alterations in the functional brain networks were found in patients with LUHL. Our findings demonstrate that RUHL (rather than LUHL) is accompanied with aberrant topological organization of the functional brain connectome, indicating different pathophysiological mechanisms between RUHL and LUHL from a viewpoint of network topology.

Decreasing Shortest Path Length of the Sensorimotor Network Induces Frontal Glioma-Related Epilepsy

Background

Glioma-related epilepsy (GRE) is a common symptom in patients with prefrontal glioma. Epilepsy onset is associated with functional network alterations. This study investigated alterations of functional networks in patients with prefrontal glioma and GRE.

Methods

Sixty-five patients with prefrontal lobe gliomas were retrospectively assessed and classified into GRE and non-GRE groups. Additionally, 25 healthy participants were enrolled after matching for general information. Imaging data were acquired within 72 h in pre-operation. The sensorimotor network was used to delineate alterations in functional connectivity (FC) and topological properties. One-way analysis of variance and post-hoc analysis with Bonferroni correction were used to calculate differences of FC and topological properties.

Results

All significant alterations were solely found in the sensorimotor network. Irrespective of gliomas located in the left or right prefrontal lobes, the edge between medial Brodmann area 6 and caudal ventrolateral Brodmann area 6 decreased FC in the GRE group compared with the non-GRE group [p < 0.0001 (left glioma), p = 0.0002 (right glioma)]. Moreover, the shortest path length decrease was found in the GRE group compared with the non-GRE group [p = 0.0292 (left glioma) and p = 0.0129 (right glioma)].

Conclusions

The reduction of FC between the medial BA 6 (supplementary motor area) and caudal ventrolateral BA 6 in the ipsilateral hemisphere and the shortening of the path length of the sensorimotor network were characteristics alterations in patients with GRE onset. These findings fill in the gap which is the relationship between GRE onset and the alterations of functional networks in patients with prefrontal glioma.

Significance Statement

Glioma related epilepsy is the most common symptom of prefrontal glioma. It is important to identify characteristic alterations in functional networks in patients with GRE. We found that all significant alterations occurred in the sensorimotor network. Moreover, a decreased FC in the supplementary motor area and a shortening of the path’s length are additional characteristics of glioma-related epilepsy. We believe that our findings indicate new directions of research that will contribute to future investigations of glioma-related epilepsy onset.

Multimodal Brain Connectomics-Based Prediction of Parkinson’s Disease Using Graph Attention Networks

Background

A multimodal connectomic analysis using diffusion and functional MRI can provide complementary information on the structure–function network dynamics involved in complex neurodegenerative network disorders such as Parkinson’s disease (PD). Deep learning-based graph neural network models generate higher-level embeddings that could capture intricate structural and functional regional interactions related to PD.

Objective

This study aimed at investigating the role of structure–function connections in predicting PD, by employing an end-to-end graph attention network (GAT) on multimodal brain connectomes along with an interpretability framework.

Methods

The proposed GAT model was implemented to generate node embeddings from the structural connectivity matrix and multimodal feature set containing morphological features and structural and functional network features of PD patients and healthy controls. Graph classification was performed by extracting topmost node embeddings, and the interpretability framework was implemented using saliency analysis and attention maps. Moreover, we also compared our model with unimodal models as well as other state-of-the-art models.

Results

Our proposed GAT model with a multimodal feature set demonstrated superior classification performance over a unimodal feature set. Our model demonstrated superior classification performance over other comparative models, with 10-fold CV accuracy and an F1 score of 86% and a moderate test accuracy of 73%. The interpretability framework highlighted the structural and functional topological influence of motor network and cortico-subcortical brain regions, among which structural features were correlated with onset of PD. The attention maps showed dependency between large-scale brain regions based on their structural and functional characteristics.

Conclusion

Multimodal brain connectomic markers and GAT architecture can facilitate robust prediction of PD pathology and provide an attention mechanism-based interpretability framework that can highlight the pathology-specific relation between brain regions.

Test-retest reliability of regression dynamic causal modeling

Regression dynamic causal modeling (rDCM) is a novel and computationally highly efficient method for inferring effective connectivity at the whole-brain level. While face and construct validity of rDCM have already been demonstrated, here we assessed its test-retest reliability—a test-theoretical property of particular importance for clinical applications—together with group-level consistency of connection-specific estimates and consistency of whole-brain connectivity patterns over sessions. Using the Human Connectome Project dataset for eight different paradigms (tasks and rest) and two different parcellation schemes, we found that rDCM provided highly consistent connectivity estimates at the group level across sessions. Second, while test-retest reliability was limited when averaging over all connections (range of mean intraclass correlation coefficient 0.24–0.42 over tasks), reliability increased with connection strength, with stronger connections showing good to excellent test-retest reliability. Third, whole-brain connectivity patterns by rDCM allowed for identifying individual participants with high (and in some cases perfect) accuracy. Comparing the test-retest reliability of rDCM connectivity estimates with measures of functional connectivity, rDCM performed favorably—particularly when focusing on strong connections. Generally, for all methods and metrics, task-based connectivity estimates showed greater reliability than those from the resting state. Our results underscore the potential of rDCM for human connectomics and clinical applications.

Associations of the Disrupted Functional Brain Network and Cognitive Function in End-Stage Renal Disease Patients on Maintenance Hemodialysis: A Graph Theory-Based Study of Resting-State Functional Magnetic Resonance Imaging

Objective: Cognitive impairment (CI) is a common neurological complication in patients with end-stage renal disease undergoing maintenance hemodialysis (MHD). Brain network analysis based on graph theory is a promising tool for studying CI. Therefore, the purpose of this study was to analyze the changes of functional brain networks in patients on MHD with and without CI by using graph theory and further explore the underlying neuropathological mechanism of CI in these patients. Methods: A total of 39 patients on MHD (19 cases with CI and 20 without) and 25 healthy controls (HCs) matched for age, sex, and years of education were enrolled in the study. Resting-state functional magnetic resonance imaging (rs-fMRI) and T1-weighted high-resolution anatomical data were obtained, and functional brain networks for each subject were constructed. The brain network parameters at the global and regional levels were calculated, and a one-way analysis of covariance was used to compare the differences across the three groups. The associations between the changed graph-theory parameters and cognitive function scores in patients on MHD were evaluated using Spearman correlation analysis. Results: Compared with HCs, the global parameters [sigma, gamma, and local efficiency (Eloc)] in both patient groups decreased significantly (p < 0.05, Bonferroni corrected). The clustering coefficient (Cp) in patients with CI was significantly lower than that in the other two groups (p < 0.05, Bonferroni corrected). The regional parameters were significantly lower in the right superior frontal gyrus, dorsolateral (SFGdor) and gyrus rectus (REC) of patients with CI than those of patients without CI; however the nodal local efficiency in the left amygdala was significantly increased (all p < 0.05, Bonferroni corrected). The global Cp and regional parameters in the three brain regions (right SFGdor, REC, and left amygdala) were significantly correlated with the cognitive function scores (all FDR q < 0.05). Conclusion: This study confirmed that the topology of the functional brain network was disrupted in patients on MHD with and without CI and the disruption of brain network was more severe in patients with CI. The abnormal brain network parameters are closely related to cognitive function in patients on MHD.

Multiscale dynamic mean field (MDMF) model relates resting-state brain dynamics with local cortical excitatory-inhibitory neurotransmitter homeostasis

Previous computational models have related spontaneous resting-state brain activity with local excitatory–inhibitory balance in neuronal populations. However, how underlying neurotransmitter kinetics associated with E–I balance govern resting-state spontaneous brain dynamics remains unknown. Understanding the mechanisms by virtue of which fluctuations in neurotransmitter concentrations, a hallmark of a variety of clinical conditions, relate to functional brain activity is of critical importance. We propose a multiscale dynamic mean field (MDMF) model—a system of coupled differential equations for capturing the synaptic gating dynamics in excitatory and inhibitory neural populations as a function of neurotransmitter kinetics. Individual brain regions are modeled as population of MDMF and are connected by realistic connection topologies estimated from diffusion tensor imaging data. First, MDMF successfully predicts resting-state functional connectivity. Second, our results show that optimal range of glutamate and GABA neurotransmitter concentrations subserve as the dynamic working point of the brain, that is, the state of heightened metastability observed in empirical blood-oxygen-level-dependent signals. Third, for predictive validity the network measures of segregation (modularity and clustering coefficient) and integration (global efficiency and characteristic path length) from existing healthy and pathological brain network studies could be captured by simulated functional connectivity from an MDMF model.

How changes in neurotransmitter kinetics impact the organization of large-scale neurocognitive networks is an open question in neuroscience. Here, we propose a multiscale dynamic mean field (MDMF) model that incorporates biophysically realistic kinetic parameters of receptor binding in a dynamic mean field model and captures brain dynamics from the “whole brain.” MDMF could reliably reproduce the resting-state brain functional connectivity patterns. Further employing graph theoretic methods, MDMF could qualitatively explain the idiosyncrasies of network integration and segregation measures reported by previous clinical studies.

Interhemispheric Cortical Network Connectivity Reorganization Predicts Vision Impairment in Stroke

Stroke is one of the main causes of disability in human beings, and when the occipital lobe is affected, this leads to partial vision loss (homonymous hemianopia). To understand brain mechanisms of vision loss and recovery, graph theory-based brain functional connectivity network (FCN) analysis was recently introduced. However, few brain network studies exist that have studied if the strength of the damaged FCN can predict the extent of functional impairment. We now characterized the brain FCN using deep neural network analysis to describe multiscale brain networks and explore their corresponding physiological patterns. In a group of 24 patients and 24 controls, Bi-directional long short-term memory (Bi-LSTM) was evaluated to reveal the cortical network pattern learning efficiency compared with other traditional algorithms. Bi-LSTM achieved the best balanced-overall accuracy of 73% with sensitivity of 70% and specificity and 75% in the low alpha band. This demonstrates that bi-directional learning can capture the brain network feature representation of both hemispheres. It shows that brain damage leads to reorganized FCN patterns with a greater number of functional connections of intermediate density in the high alpha band. Future studies should explore how this understanding of brain FCN can be used for clinical diagnostics and rehabilitation.

Revealing the Relevant Spatiotemporal Scale Underlying Whole-Brain Dynamics

The brain rapidly processes and adapts to new information by dynamically transitioning between whole-brain functional networks. In this whole-brain modeling study we investigate the relevance of spatiotemporal scale in whole-brain functional networks. This is achieved through estimating brain parcellations at different spatial scales (100-900 regions) and time series at different temporal scales (from milliseconds to seconds) generated by a whole-brain model fitted to fMRI data. We quantify the richness of the dynamic repertoire at each spatiotemporal scale by computing the entropy of transitions between whole-brain functional networks. The results show that the optimal relevant spatial scale is around 300 regions and a temporal scale of around 150 ms. Overall, this study provides much needed evidence for the relevant spatiotemporal scales and recommendations for analyses of brain dynamics.

Aberrant brain network topology in the frontoparietal-limbic circuit in bipolar disorder: a graph-theory study

Characterizing the properties of brain networks across mood states seen in bipolar disorder (BP) can provide a deeper insight into the mechanisms involved in this type of affective disorder. In this study, graph theoretical methods were used to examine global, modular and nodal brain network topology in the resting state using functional magnetic resonance imaging data acquired from 95 participants, including those with bipolar depression (BPD; n = 30) and bipolar mania (BPM; n = 39) and healthy control (HC) subjects (n = 26). The threshold value of the individual subjects' connectivity matrix varied from 0.15 to 0.30 with steps of 0.01. We found that: (1) at the global level, BP patients showed a significantly increased global efficiency and synchronization and a decreased path length; (2) at the nodal level, BP patients showed impaired nodal parameters, predominantly within the frontoparietal and limbic sub-network; (3) at the module level, BP patients were characterized by denser FCs (edges) between Module III (the front-parietal system) and Module V (limbic/paralimbic systems); (4) at the nodal level, the BPD and BPM groups showed state-specific differences in the orbital part of the left superior-frontal gyrus, right putamen, right parahippocampal gyrus and left fusiform gyrus. These results revealed abnormalities in topological organization in the whole brain, especially in the frontoparietal-limbic circuit in both BPD and BPM. These deficits may reflect the pathophysiological processes occurring in BP. In addition, state-specific regional nodal alterations in BP could potentially provide biomarkers of conversion across different mood states.

Pregnancy leads to changes in the brain functional network: a connectome analysis

Pregnancy leads to long-lasting changes in human brain structure; however, little is known regarding alterations in the topological organization of functional networks. In this study, we investigated the effect of pregnancy on human brain function networks. Resting-state fMRI data was collected from eighteen primiparous mothers and twenty-four nulliparous control women of similar age, education level and body mass index (BMI). The functional brain network and topological properties were calculated by using GRETNA toolbox. The demographic data differences between two groups were computed by the independent two sample t-test. We tested group differences in network metrics' area under curve (AUC) using non-parametric permutation test of 1,000 permutations and corrected for false discovery rate (FDR). Differences in regional networks between groups were evaluated using non-parametric permutation tests by network-based statistical analysis (NBS). Compared with the nulliparous control women, a hub node changed from left inferior temporal gyrus to right precentral gyrus in primiparous mothers, while primiparous mothers showed enhanced network global efficiency (p = 0.247), enhanced local efficiency (p = 0.410), larger clustering coefficient (p = 0.410), but shorter characteristic path length (p = 0.247), smaller normalized clustering coefficient (p = 0.111), and shorter normalized characteristic path length (p = 0.705). Although both groups of functional networks have small-world property (σ > 1), the σ values of primiparous mothers were decreased significantly. NBS evaluation showed the majority of altered connected sub-network in the primiparous mothers occurred in the bilateral frontal lobe gyrus (p < 0.05). Altered functional network metrics and an abnormal sub-network were found in primiparous mothers, suggested that pregnancy may lead to changes in the brain functional network.

Principles and open questions in functional brain network reconstruction

Graph theory is now becoming a standard tool in system-level neuroscience. However, endowing observed brain anatomy and dynamics with a complex network representation involves often covert theoretical assumptions and methodological choices which affect the way networks are reconstructed from experimental data, and ultimately the resulting network properties and their interpretation. Here, we review some fundamental conceptual underpinnings and technical issues associated with brain network reconstruction, and discuss how their mutual influence concurs in clarifying the organization of brain function.

Neural Kinesthetic Contribution to Motor Imagery of Body Parts: Tongue, Hands, and Feet

Motor imagery (MI) is assimilated to a perception-action process, which is mentally represented. Although several models suggest that MI, and its equivalent motor execution, engage very similar brain areas, the mechanisms underlying MI and their associated components are still under investigation today. Using 22 Ag/AgCl EEG electrodes, 19 healthy participants (nine males and 10 females) with an average age of 25.8 years old (sd = 3.5 years) were required to imagine moving several parts of their body (i.e., first-person perspective) one by one: left and right hand, tongue, and feet. Network connectivity analysis based on graph theory, together with a correlational analysis, were performed on the data. The findings suggest evidence for motor and somesthetic neural synchronization and underline the role of the parietofrontal network for the tongue imagery task only. At both unilateral and bilateral cortical levels, only the tongue imagery task appears to be associated with motor and somatosensory representations, that is, kinesthetic representations, which might contribute to verbal actions. As such, the present findings suggest the idea that imagined tongue movements, involving segmentary kinesthetic actions, could be the prerequisite of language.

Mean-Field Modeling of Brain-Scale Dynamics for the Evaluation of EEG Source-Space Networks

Understanding the dynamics of brain-scale functional networks at rest and during cognitive tasks is the subject of intense research efforts to unveil fundamental principles of brain functions. To estimate these large-scale brain networks, the emergent method called "electroencephalography (EEG) source connectivity" has generated increasing interest in the network neuroscience community, due to its ability to identify cortical brain networks with satisfactory spatio-temporal resolution, while reducing mixing and volume conduction effects. However, no consensus has been reached yet regarding a unified EEG source connectivity pipeline, and several methodological issues have to be carefully accounted to avoid pitfalls. Thus, a validation toolbox that provides flexible "ground truth" models is needed for an objective methods/parameters evaluation and, thereby an optimization of the EEG source connectivity pipeline. In this paper, we show how a recently developed large-scale model of brain-scale activity, named COALIA, can provide to some extent such ground truth by providing realistic simulations of source-level and scalp-level activity. Using a bottom-up approach, the model bridges cortical micro-circuitry and large-scale network dynamics. Here, we provide an example of the potential use of COALIA to analyze, in the context of epileptiform activity, the effect of three key factors involved in the "EEG source connectivity" pipeline: (i) EEG sensors density, (ii) algorithm used to solve the inverse problem, and (iii) functional connectivity measure. Results showed that a high electrode density (at least 64 channels) is required to accurately estimate cortical networks. Regarding the inverse solution/connectivity measure combination, the best performance at high electrode density was obtained using the weighted minimum norm estimate (wMNE) combined with the weighted phase lag index (wPLI). Although those results are specific to the considered aforementioned context (epileptiform activity), we believe that this model-based approach can be successfully applied to other experimental questions/contexts. We aim at presenting a proof-of-concept of the interest of COALIA in the network neuroscience field, and its potential use in optimizing the EEG source-space network estimation pipeline.

Dynamical consequences of regional heterogeneity in the brain's transcriptional landscape

Brain regions vary in their molecular and cellular composition, but how this heterogeneity shapes neuronal dynamics is unclear. Here, we investigate the dynamical consequences of regional heterogeneity using a biophysical model of whole-brain functional magnetic resonance imaging (MRI) dynamics in humans. We show that models in which transcriptional variations in excitatory and inhibitory receptor (E:I) gene expression constrain regional heterogeneity more accurately reproduce the spatiotemporal structure of empirical functional connectivity estimates than do models constrained by global gene expression profiles or MRI-derived estimates of myeloarchitecture. We further show that regional transcriptional heterogeneity is essential for yielding both ignition-like dynamics, which are thought to support conscious processing, and a wide variance of regional-activity time scales, which supports a broad dynamical range. We thus identify a key role for E:I heterogeneity in generating complex neuronal dynamics and demonstrate the viability of using transcriptomic data to constrain models of large-scale brain function.

The Time Varying Networks of the Interoceptive Attention and Rest

Focused attention to spontaneous sensations is a dynamic process that demands interoceptive abilities. Failure to control it has been linked to neuropsychiatric disorders like illness-anxiety disorder. Regulatory strategies, such as focused attention meditation (FAM), may enhance the ability to control focused attention particularly to body sensations, which can be reflected on functional neuroanatomy. The functional connectivity (FC) related to focused attention has been described, however, the dynamic brain organization associated to this process and the differences to the resting state remains to be studied. To quantify the cerebral dynamic counterpart of focused attention to interoception, we examined fifteen experienced meditators while performing a 20-min attentional task to spontaneous sensations. Subjects underwent three scanning sessions obtaining a resting-state scan before and after the task. Sliding window dynamic FC (DFC) and k-means clustering identified five recurrent FC patterns along the dorsal attention network (DAN), default mode network (DMN), and frontoparietal network (FPN). Subjects remained longer in a low connectivity brain pattern during the resting conditions. By contrast, subjects spent a higher proportion of time in complex patterns during the task than rest. Moreover, a carry-over effect in FC was observed following the interoceptive task performance, suggestive of an active role in the learning process linked to cognitive training. Our results suggest that focused attention to interoceptive processes, demands a dynamic brain organization with specific features that distinguishes it from the resting condition. This approach may provide new insights characterizing the neural basis of the focused attention, an essential component for human adaptability.

Spontaneous eye movements during eyes-open rest reduce resting-state-network modularity by increasing visual-sensorimotor connectivity

During wakeful rest, individuals make small eye movements during fixation. We examined how these endogenously driven oculomotor patterns impact topography and topology of functional brain networks. We used a dataset consisting of eyes-open resting-state (RS) fMRI data with simultaneous eye tracking. The eye-tracking data indicated minor movements during rest, which correlated modestly with RS BOLD data. However, eye-tracking data correlated well with echo-planar imaging time series sampled from the area of the eye-orbit (EO-EPI), which is a signal previously used to identify eye movements during exogenous saccades and movie viewing. Further analyses showed that EO-EPI data were correlated with activity in an extensive motor and sensorimotor network, including components of the dorsal attention network and the frontal eye fields. Partialling out variance related to EO-EPI from RS data reduced connectivity, primarily between sensorimotor and visual areas. It also produced networks with higher modularity, lower mean connectivity strength, and lower mean clustering coefficient. Our results highlight new aspects of endogenous eye movement control during wakeful rest. They show that oculomotor-related contributions form an important component of RS network topology, and that those should be considered in interpreting differences in network structure between populations or as a function of different experimental conditions.

We studied how subtle eye movements made during fixation, in absence of any other task, are related to resting-state connectivity measured using fMRI. We used a dataset for which eye tracking and BOLD resting-state were acquired simultaneously. We correlated brain activity with both eye-tracking metrics as well as time series sampled from the area of the eye orbits (EO-EPI). Eye-tracking data correlated well with the EO-EPI data. Furthermore, EO-EPI correlated with BOLD signal in sensorimotor and visual brain systems. Removing variance related to EO-EPI reduced connectivity between sensorimotor and visual areas and resulted in more modular resting-state networks. Our findings show that oculomotor-related contributions are an important component of resting-state network topology, and that they can be studied using EPI data from the eye orbits.

The functional connectome in posttraumatic stress disorder

BACKGROUND

Previous fMRI studies of posttraumatic stress disorder (PTSD) have investigated region-specific alterations in intrinsic connectivity but connectome-wide changes in connectivity are yet to be characterized. Understanding the neurobiology of this is important to develop novel treatment interventions for PTSD. This study aims to identify connectome-wide disruptions in PTSD to provide a more comprehensive analysis of nseural networks in this disorder.

METHODS

A functional MRI scan was completed by 138 individuals (67 PTSD and 71 non-trauma-exposed healthy controls [HC]). For every individual, inter-regional intrinsic functional connectivity was estimated between 436 brain regions, comprising intra and inter-network connectivity of eight large-scale brain networks. Group-wise differences between PTSD and HC were investigated using network-based statistics at a family-wise error rate of p < 0.05. Significant network differences were then further investigated in 27 individuals with trauma exposure but no PTSD [TC]).

RESULTS

Compared to HC, PTSD displayed lower intrinsic functional connectivity in a network of 203 connections between 420 regions within and between mid-posterior default mode, central executive, limbic, visual and somatomotor regions. Additionally, PTSD displayed higher connectivity across a network of 50 connections from thalamic and limbic to sensory and default-mode regions. Connectivity in TC in both these networks was intermediate and significantly different to PTSD and HC.

CONCLUSION

A large-scale imbalance between hypoconnectivity of higher-order cortical networks and hyperconnectivity of emotional and arousal response systems seems to occur on a sliding scale from trauma exposure to clinical manifestation as PTSD. Novel interventions that target this systemic functional imbalance could provide potential mitigation of PTSD.

Network-level functional topological changes after mindfulness-based cognitive therapy in mood dysregulated adolescents at familial risk for bipolar disorder: a pilot study

BACKGROUND

Given that psychopharmacological approaches routinely used to treat mood-related problems may result in adverse outcomes in mood dysregulated adolescents at familial risk for bipolar disorder (BD), Mindfulness-Based Cognitive Therapy for Children (MBCT-C) provides an alternative effective and safe option. However, little is known about the brain mechanisms of beneficial outcomes from this intervention. Herein, we aimed to investigate the network-level neurofunctional effects of MBCT-C in mood dysregulated adolescents.

METHODS

Ten mood dysregulated adolescents at familial risk for BD underwent a 12-week MBCT-C intervention. Resting-state functional magnetic resonance imaging (fMRI) was performed prior to and following MBCT-C. Topological metrics of three intrinsic functional networks (default mode network (DMN), fronto-parietal network (FPN) and cingulo-opercular network (CON)) were investigated respectively using graph theory analysis.

RESULTS

Following MBCT-C, mood dysregulated adolescents showed increased global efficiency and decreased characteristic path length within both CON and FPN. Enhanced functional connectivity strength of frontal and limbic areas were identified within the DMN and CON. Moreover, change in characteristic path length within the CON was suggested to be significantly related to change in the Emotion Regulation Checklist score.

CONCLUSIONS

12-week MBCT-C treatment in mood dysregulated adolescents at familial risk for BD yield network-level neurofunctional effects within the FPN and CON, suggesting enhanced functional integration of the dual-network. Decreased characteristic path length of the CON may be associated with the improvement of emotion regulation following mindfulness training. However, current findings derived from small sample size should be interpreted with caution. Future randomized controlled trials including larger samples are critical to validate our findings.

Abnormalities in the thalamo-cortical network in patients with functional constipation

Functional constipation (FCon) is a common functional gastrointestinal disorder (FGID); neuroimaging studies have shown brain functional abnormalities in thalamo-cortical regions in patients with FGID. However, association between FCon and topological characteristics of brain networks remains largely unknown. We employed resting-state functional magnetic resonance imaging (RS-fMRI) and graph theory approach to investigate functional brain topological organization in 42 patients with FCon and 41 healthy controls (HC) from perspectives of global, regional and modular levels. Results showed patients with FCon had a significantly lower normalized clustering coefficient and small-worldness, implying decreased brain functional connectivity. Regions showed altered nodal degree and efficiency mainly located in the thalamus, rostral anterior cingulate cortex (rACC), and supplementary motor area (SMA), which are involved in somatic/sensory, emotional processing and motor-control. For the modular analysis, thalamus, rACC and SMA had an aberrant within-module nodal degree and nodal efficiency, and thalamus-related network exhibited abnormal interaction with the limbic network (amygdala and hippocampal gyrus). Nodal degree in the thalamus was negatively correlated with difficulty of defecation, and nodal degree in the rACC was negatively correlated with sensation of incomplete evacuation. These findings indicated that FCon was associated with abnormalities in the thalamo-cortical network.

Associations of cannabis use disorder with cognition, brain structure, and brain function in African Americans

Although previous studies have highlighted associations of cannabis use with cognition and brain morphometry, critical questions remain with regard to the association between cannabis use and brain structural and functional connectivity. In a cross-sectional community sample of 205 African Americans (age 18-70) we tested for associations of cannabis use disorder (CUD, n = 57) with multi-domain cognitive measures and structural, diffusion, and resting state brain-imaging phenotypes. Post hoc model evidence was computed with Bayes factors (BF) and posterior probabilities of association (PPA) to account for multiple testing. General cognitive functioning, verbal intelligence, verbal memory, working memory, and motor speed were lower in the CUD group compared with non-users (p < .011; 1.9 < BF < 3,217). CUD was associated with altered functional connectivity in a network comprising the motor-hand region in the superior parietal gyri and the anterior insula (p < .04). These differences were not explained by alcohol, other drug use, or education. No associations with CUD were observed in cortical thickness, cortical surface area, subcortical or cerebellar volumes (0.12 < BF < 1.5), or graph-theoretical metrics of resting state connectivity (PPA < 0.01). In a large sample collected irrespective of cannabis used to minimize recruitment bias, we confirm the literature on poorer cognitive functioning in CUD, and an absence of volumetric brain differences between CUD and non-CUD. We did not find evidence for or against a disruption of structural connectivity, whereas we did find localized resting state functional dysconnectivity in CUD. There was sufficient proof, however, that organization of functional connectivity as determined via graph metrics does not differ between CUD and non-user group.

Altered electroencephalographic networks in developmental dyslexia after remedial training: a prospective case-control study

Electroencephalographic studies using graph theoretic analysis have found aberrations in functional connectivity in children with developmental dyslexia. However, how the training with visual tasks can change the functional connectivity of the semantic network in developmental dyslexia is still unclear. We looked for differences in local and global topological properties of functional networks between 21 healthy controls and 22 dyslexic children (8-9 years old) before and after training with visual tasks in this prospective case-control study. The minimum spanning tree method was used to construct the subjects' brain networks in multiple electroencephalographic frequency ranges during a visual word/pseudoword discrimination task. We found group differences in the theta, alpha, beta and gamma bands for four graph measures suggesting a more integrated network topology in dyslexics before the training compared to controls. After training, the network topology of dyslexic children had become more segregated and similar to that of the controls. In the θ, α and β1-frequency bands, compared to the controls, the pre-training dyslexics exhibited a reduced degree and betweenness centrality of the left anterior temporal and parietal regions. The simultaneous appearance in the left hemisphere of hubs in temporal and parietal (α, β1), temporal and superior frontal cortex (θ, α), parietal and occipitotemporal cortices (β1), identified in the networks of normally developing children was not present in the brain networks of dyslexics. After training, the hub distribution for dyslexics in the theta and beta1 bands had become similar to that of the controls. In summary, our findings point to a less efficient network configuration in dyslexics compared to a more optimal global organization in the controls. This is the first study to investigate the topological organization of functional brain networks of Bulgarian dyslexic children. Approval for the study was obtained from the Ethics Committee of the Institute of Neurobiology and the Institute for Population and Human Studies, Bulgarian Academy of Sciences (approval No. 02-41/12.07.2019) on March 28, 2017, and the State Logopedic Center and the Ministry of Education and Science (approval No. 09-69/14.03.2017) on July 12, 2019.