Minimum spanning tree analysis of the human connectome

Crochet increases attention through a requiring motor skill learning

In this study, we compared the effects promoted by a brief single session of crochet in a group of skilled knitters (CRO) and a control group (CRT) on the Attentional Network Test (ANT) and the whole brain Functional Connectivity (FC) revealed by Magnetoencephalography (MEG). Data revealed that crochet determined a significant effect (before, T0, vs after, T1, the crochet session) on reaction times (for all cue and stimulus types), improving alertness and orienting networks (but not executive control) only in the CRO group. Data of FC are coherent with the behavioural ones. We observed that the Betweenness Centrality maximum (BCmax) index in the beta band significantly increased, and global FC in the alpha band significantly increased at T1 for the CRO group but not for the CTR group. Increased global BCmax in the beta band after the crochet activity correlated with better performance (reduced reaction times), suggesting that the brain has become more efficiently integrated, thus increasing the information exchange between different brain areas. Decreased global FC in the alpha band may reflect a transition from a quiet, global rest to a condition of increased alertness and readiness to stimuli. Finally, we discuss the hypothesis that these results could be the reinforcement of connections between motor and attentional networks promoted by learning the complex motor skills of crochet.

Comparison of dry and wet electroencephalography for the assessment of cognitive evoked potentials and sensor-level connectivity

Background

Multipin dry electrodes (dry EEG) provide faster and more convenient application than wet EEG, enabling extensive data collection. This study aims to compare task-related time-frequency representations and resting-state connectivity between wet and dry EEG methods to establish a foundation for using dry EEG in investigations of brain activity in neuropsychiatric disorders.

Methods

In this counterbalanced cross-over study, we acquired wet and dry EEG in 33 healthy participants [n = 22 females, mean age (SD) = 24.3 (± 3.4) years] during resting-state and an auditory oddball paradigm. We computed mismatch negativity (MMN), theta power in task EEG, and connectivity measures from resting-state EEG using phase lag index (PLI) and minimum spanning tree (MST). Agreement between wet and dry EEG was assessed using Bland-Altman bias.

Results

MMN was detectable with both systems in time and frequency domains, but dry EEG underestimated MMN mean amplitude, peak latency, and theta power compared to wet EEG. Resting-state connectivity was reliably estimated with dry EEG using MST diameter in all except the very low frequencies (0.5-4 Hz). PLI showed larger differences between wet and dry EEG in all frequencies except theta.

Conclusion

Dry EEG reliably detected MMN and resting-state connectivity despite a lower signal-to-noise ratio. This study provides the methodological basis for using dry EEG in studies investigating the neural processes underlying psychiatric and neurological conditions.

Minimum spanning tree analysis of unimpaired individuals at risk of Alzheimer's disease

Identifying early and non-invasive biomarkers to detect individuals in the earliest stages of the Alzheimer's disease continuum is crucial. As a result, electrophysiology and plasma biomarkers are emerging as great candidates in this pursuit due to their low invasiveness. This is the first magnetoencephalography study to assess the relationship between minimum spanning tree parameters, an alternative to overcome the comparability and thresholding problem issues characteristic of conventional brain network analyses, and plasma phosphorylated tau231 levels in unimpaired individuals, with different risk levels of Alzheimer's disease. Seventy-six individuals with available magnetoencephalography recordings and phosphorylated tau231 plasma determination were included. The minimum spanning tree for the theta, alpha and beta bands for each subject was obtained, and the leaf fraction, tree hierarchy and diameter were calculated. To study the relationship between these topological parameters and phosphorylated tau231, we performed correlation analyses, for the whole sample and considering the two risk sub-groups separately. Increasing concentrations of phosphorylated tau231 were associated with greater leaf fraction and tree hierarchy values, along with lower diameter values, for the alpha and theta frequency bands. These results emerged for the whole sample and the higher risk group, but not for the lower risk group. Our results indicate that the network topology of cognitively unimpaired individuals with elevated plasma phosphorylated tau231 levels, a marker of Alzheimer's disease pathology and amyloid-β accumulation, is already altered, shifting towards a more integrated network increasing its vulnerability and hub-dependency, mostly in the alpha band. This is indicated by increases in leaf fraction and tree hierarchy, along with reductions in diameter. These results match the initial trajectory proposed by theoretical models of disease progression and network disruption and suggest that changes in brain function and organization begin early on.

Functional Connectivity Analysis of Prej udice Among Colombian Armed Conflict Former Actors

Despite institutional efforts, reconciliation among former actors of the Colombian armed conflict has yet to be achieved, with prejudice being one direct driver of this drawback. We present an EEG-based functional connectivity study applied to four groups of former actors who completed an Implicit Association Test designed to measure prejudice toward victims or combatants. We analyzed seven measures of functional connectivity calculated in six different frequency bands and two experimental conditions. In the behavioral task, we found more prejudice toward victims from the same victims and more prejudice of civilians toward combatants. For the connectivity measures, we found differences in theta band among the victims' and ex-paramilitaries' groups concerning the civilians' and ex-guerrillas' groups, and differences in the beta2 band among the victims' and ex-guerrillas' groups concerning the ex-paramilitaries' group. The results help us design more effective socio-cognitive interventions to reduce prejudice.

Predicting the Conversion from Mild Cognitive Impairment to Alzheimer's Disease Using Graph Frequency Bands and Functional Connectivity-Based Features

Accurate prediction of the progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD) is crucial for disease management. Machine learning techniques have demonstrated success in classifying AD and MCI cases, particularly with the use of resting-state functional magnetic resonance imaging (rs-fMRI) data.This study utilized three years of rs-fMRI data from the ADNI, involving 142 patients with stable MCI (sMCI) and 136 with progressive MCI (pMCI). Graph signal processing was applied to filter rs-fMRI data into low, middle, and high frequency bands. Connectivity-based features were derived from both filtered and unfiltered data, resulting in a comprehensive set of 100 features, including global graph metrics, minimum spanning tree (MST) metrics, triadic interaction metrics, hub tendency metrics, and the number of links. Feature selection was enhanced using particle swarm optimization (PSO) and simulated annealing (SA). A support vector machine (SVM) with a radial basis function (RBF) kernel and a 10-fold cross-validation setup were employed for classification. The proposed approach demonstrated superior performance, achieving optimal accuracy with minimal feature utilization. When PSO selected five features, SVM exhibited accuracy, specificity, and sensitivity rates of 77%, 70%, and 83%, respectively. The identified features were as follows: (Mean of clustering coefficient, Mean of strength)/Radius/(Mean Eccentricity, and Modularity) from low/middle/high frequency bands of graph. The study highlights the efficacy of the proposed framework in identifying individuals at risk of AD development using a parsimonious feature set. This approach holds promise for advancing the precision of MCI to AD progression prediction, aiding in early diagnosis and intervention strategies.

Minimum spanning tree analysis of EEG resting-state functional networks in schizophrenia

Schizophrenia is a serious and complex mental disease, known to be associated with various subtle structural and functional deviations in the brain. Recently, increased attention is given to the analysis of brain-wide, global mechanisms, strongly altering the communication of long-distance brain areas in schizophrenia. Data of 32 patients with schizophrenia and 28 matched healthy control subjects were analyzed. Two minutes long 64-channel EEG recordings were registered during resting, eyes closed condition. Average connectivity strength was estimated with Weighted Phase Lag Index (wPLI) in lower frequencies: delta and theta, and Amplitude Envelope Correlation with leakage correction (AEC-c) in higher frequencies: alpha, beta, lower gamma and higher gamma. To analyze functional network topology Minimum Spanning Tree (MST) algorithms were applied. Results show that patients have weaker functional connectivity in delta and alpha frequency bands. Concerning network differences, the result of lower diameter, higher leaf number, and also higher maximum degree and maximum betweenness centrality in patients suggest a star-like, and more random network topology in patients with schizophrenia. Our findings are in accordance with some previous findings based on resting-state EEG (and fMRI) data, suggesting that MST network structure in schizophrenia is biased towards a less optimal, more centralized organization.

Low Functional network integrity in cognitively unimpaired and MCI subjects with depressive symptoms: results from a multi-center fMRI study

Evidence suggests that depressive symptomatology is a consequence of network dysfunction rather than lesion pathology. We studied whole-brain functional connectivity using a Minimum Spanning Tree as a graph-theoretical approach. Furthermore, we examined functional connectivity in the Default Mode Network, the Frontolimbic Network (FLN), the Salience Network, and the Cognitive Control Network. All 183 elderly subjects underwent a comprehensive neuropsychological evaluation and a 3 Tesla brain MRI scan. To assess the potential presence of depressive symptoms, the 13-item version of the Beck Depression Inventory (BDI) or the Geriatric Depression Scale (GDS) was utilized. Participants were assigned into three groups based on their cognitive status: amnestic mild cognitive impairment (MCI), non-amnestic MCI, and healthy controls. Regarding affective symptoms, subjects were categorized into depressed and non-depressed groups. An increased mean eccentricity and network diameter were found in patients with depressive symptoms relative to non-depressed ones, and both measures showed correlations with depressive symptom severity. In patients with depressive symptoms, a functional hypoconnectivity was detected between the Anterior Cingulate Cortex (ACC) and the right amygdala in the FLN, which impairment correlated with depressive symptom severity. While no structural difference was found in subjects with depressive symptoms, the volume of the hippocampus and the thickness of the precuneus and the entorhinal cortex were decreased in subjects with MCI, especially in amnestic MCI. The increase in eccentricity and diameter indicates a more path-like functional network configuration that may lead to an impaired functional integration in depression, a possible cause of depressive symptomatology in the elderly.

Potential long consequences from internal and external ecology: loss of gut microbiota antifragility in children from an industrialized population compared with an indigenous rural lifestyle

Human health is strongly mediated by the gut microbiota ecosystem, which, in turn, depends not only on its state but also on its dynamics and how it responds to perturbations. Healthy microbiota ecosystems tend to be in criticality and antifragile dynamics corresponding to a maximum complexity configuration, which may be assessed with information and network theory analysis. Under this complex system perspective, we used a new analysis of published data to show that a children's population with an industrialized urban lifestyle from Mexico City exhibits informational and network characteristics similar to parasitized children from a rural indigenous population in the remote mountainous region of Guerrero, México. We propose then, that in this critical age for gut microbiota maturation, the industrialized urban lifestyle could be thought of as an external perturbation to the gut microbiota ecosystem, and we show that it produces a similar loss in criticality/antifragility as the one observed by internal perturbation due to parasitosis by the helminth A. lumbricoides. Finally, several general complexity-based guidelines to prevent or restore gut ecosystem antifragility are discussed.

Learning pyramidal multi-scale harmonic wavelets for identifying the neuropathology propagation patterns of Alzheimer's disease

Previous studies have established that neurodegenerative disease such as Alzheimer's disease (AD) is a disconnection syndrome, where the neuropathological burdens often propagate across the brain network to interfere with the structural and functional connections. In this context, identifying the propagation patterns of neuropathological burdens sheds new light on understanding the pathophysiological mechanism of AD progression. However, little attention has been paid to propagation pattern identification by fully considering the intrinsic properties of brain-network organization, which plays an important role in improving the interpretability of the identified propagation pathways. To this end, we propose a novel harmonic wavelet analysis approach to construct a set of region-specific pyramidal multi-scale harmonic wavelets, it allows us to characterize the propagation patterns of neuropathological burdens from multiple hierarchical modules across the brain network. Specifically, we first extract underlying hub nodes through a series of network centrality measurements on the common brain network reference generated from a population of minimum spanning tree (MST) brain networks. Then, we propose a manifold learning method to identify the region-specific pyramidal multi-scale harmonic wavelets corresponding to hub nodes by seamlessly integrating the hierarchically modular property of the brain network. We estimate the statistical power of our proposed harmonic wavelet analysis approach on synthetic data and large-scale neuroimaging data from ADNI. Compared with the other harmonic analysis techniques, our proposed method not only effectively predicts the early stage of AD but also provides a new window to capture the underlying hub nodes and the propagation pathways of neuropathological burdens in AD.

[Effect of electroconvulsive therapy on brain functional network in major depressive disorder]

Electroconvulsive therapy (ECT) is an interventional technique capable of highly effective neuromodulation in major depressive disorder (MDD), but its antidepressant mechanism remains unclear. By recording the resting-state electroencephalogram (RS-EEG) of 19 MDD patients before and after ECT, we analyzed the modulation effect of ECT on the resting-state brain functional network of MDD patients from multiple perspectives: estimating spontaneous EEG activity power spectral density (PSD) using Welch algorithm; constructing brain functional network based on imaginary part coherence (iCoh) and calculate functional connectivity; using minimum spanning tree theory to explore the topological characteristics of brain functional network. The results show that PSD, functional connectivity, and topology in multiple frequency bands were significantly changed after ECT in MDD patients. The results of this study reveal that ECT changes the brain activity of MDD patients, which provides an important reference in the clinical treatment and mechanism analysis of MDD.

Persistent homology-based functional connectivity and its association with cognitive ability: Life-span study

Brain-segregation attributes in resting-state functional networks have been widely investigated to understand cognition and cognitive aging using various approaches [e.g., average connectivity within/between networks and brain system segregation (BSS)]. While these approaches have assumed that resting-state functional networks operate in a modular structure, a complementary perspective assumes that a core-periphery or rich club structure accounts for brain functions where the hubs are tightly interconnected to each other to allow for integrated processing. In this article, we apply a novel method, persistent homology (PH), to develop an alternative to standard functional connectivity by quantifying the pattern of information during the integrated processing. We also investigate whether PH-based functional connectivity explains cognitive performance and compare the amount of variability in explaining cognitive performance for three sets of independent variables: (1) PH-based functional connectivity, (2) graph theory-based measures, and (3) BSS. Resting-state functional connectivity data were extracted from 279 healthy participants, and cognitive ability scores were generated in four domains (fluid reasoning, episodic memory, vocabulary, and processing speed). The results first highlight the pattern of brain-information flow over whole brain regions (i.e., integrated processing) accounts for more variance of cognitive abilities than other methods. The results also show that fluid reasoning and vocabulary performance significantly decrease as the strength of the additional information flow on functional connectivity with the shortest path increases. While PH has been applied to functional connectivity analysis in recent studies, our results demonstrate potential utility of PH-based functional connectivity in understanding cognitive function.

Statistical power in network neuroscience

Network neuroscience has emerged as a leading method to study brain connectivity. The success of these investigations is dependent not only on approaches to accurately map connectivity but also on the ability to detect real effects in the data - that is, statistical power. We review the state of statistical power in the field and discuss sample size, effect size, measurement error, and network topology as key factors that influence the power of brain connectivity investigations. We use the term 'differential power' to describe how power can vary between nodes, edges, and graph metrics, leaving traces in both positive and negative connectome findings. We conclude with strategies for working with, rather than around, power in connectivity studies.

‘Where there's smoke’: longitudinal cognitive disintegration after postoperative delirium?

Postoperative delirium is an important complication of surgery and is associated with poor long-term cognitive outcomes, although the neural basis underlying this relationship is poorly understood. Neuroimaging studies and network-based approaches play an important role in our understanding of the mechanism by which delirium relates to longitudinal cognitive decline. A recent resting state functional MRI study is reviewed, which shows reduced global connectivity up to 3 months after delirium, supporting recent models of delirium and opening the door for applying this approach to understanding the complex inter-relationship between delirium and dementia.

Classification of major depression disorder via using minimum spanning tree of individual high-order morphological brain network

BACKGROUND

Major depressive disorder (MDD) is an overbroad and heterogeneous diagnosis with no reliable or quantifiable markers. We aim to combine machine-learning techniques with the individual minimum spanning tree of the morphological brain network (MST-MBN) to determine whether the network properties can provide neuroimaging biomarkers to identify patients with MDD.

METHOD

Eight morphometric features of each region of interest (ROI) were extracted from 3D T1 structural images of 106 patients with MDD and 97 healthy controls. Six feature distances of the eight morphometric features were calculated to generate a feature distance matrix, which was defined as low-order MBN. Further linear correlations of feature distances between ROIs were calculated on the basis of low-order MBN to generate individual high-order MBN. The Kruskal's algorithm was used to generate the MST to obtain the core framework of individual low-order and high-order MBN. The regional and global properties of the individual MSTs were defined as the feature. The support vector machine and back-propagation neural network was used to diagnose MDD and assess its severity, respectively.

RESULT

The low-order and high-order MST-MBN constructed by cityblock distance had the excellent classification performance. The high-order MST-MBN significantly improved almost 20 % diagnostic accuracy compared with the low-order MST-MBN, and had a maximum R² value of 0.939 between the predictive and true Hamilton Depression Scale score. The different group-level connectivity strength mainly involves the central executive network and default mode network (no statistical significance after FDR correction).

CONCLUSION

We proposed an innovative individual high-order MST-MBN to capture the cortical high-order morphological correlation and make an excellent performance for individualized diagnosis and assessment of MDD.

How Functional Connectivity Measures Affect the Outcomes of Global Neuronal Network Characteristics in Patients with Schizophrenia Compared to Healthy Controls

Modern computational solutions used in the reconstruction of the global neuronal network arrangement seem to be particularly valuable for research on neuronal disconnection in schizophrenia. However, the vast number of algorithms used in these analyses may be an uncontrolled source of result inconsistency. Our study aimed to verify to what extent the characteristics of the global network organization in schizophrenia depend on the inclusion of a given type of functional connectivity measure. Resting-state EEG recordings from schizophrenia patients and healthy controls were collected. Based on these data, two identical procedures of graph-theory-based network arrangements were computed twice using two different functional connectivity measures (phase lag index, PLI, and phase locking value, PLV). Two series of between-group comparisons regarding global network parameters calculated on the basis of PLI or PLV gave contradictory results. In many cases, the values of a given network index based on PLI were higher in the patients, and the results based on PLV were lower in the patients than in the controls. Additionally, selected network measures were significantly different within the patient group when calculated from PLI or PLV. Our analysis shows that the selection of FC measures significantly affects the parameters of graph-theory-based neuronal network organization and might be an important source of disagreement in network studies on schizophrenia.

Hub structure in functional network of EEG signals supporting high cognitive functions in older individuals

Introduction

Maintaining high cognitive functions is desirable for "wellbeing" in old age and is particularly relevant to a super-aging society. According to their individual cognitive functions, optimal intervention for older individuals facilitates the maintenance of cognitive functions. Cognitive function is a result of whole-brain interactions. These interactions are reflected in several measures in graph theory analysis for the topological characteristics of functional connectivity. Betweenness centrality (BC), which can identify the "hub" node, i.e., the most important node affecting whole-brain network activity, may be appropriate for capturing whole-brain interactions. During the past decade, BC has been applied to capture changes in brain networks related to cognitive deficits arising from pathological conditions. In this study, we hypothesized that the hub structure of functional networks would reflect cognitive function, even in healthy elderly individuals.

Method

To test this hypothesis, based on the BC value of the functional connectivity obtained using the phase lag index from the electroencephalogram under the eyes closed resting state, we examined the relationship between the BC value and cognitive function measured using the Five Cognitive Functions test total score.

Results

We found a significant positive correlation of BC with cognitive functioning and a significant enhancement in the BC value of individuals with high cognitive functioning, particularly in the frontal theta network.

Discussion

The hub structure may reflect the sophisticated integration and transmission of information in whole-brain networks to support high-level cognitive function. Our findings may contribute to the development of biomarkers for assessing cognitive function, enabling optimal interventions for maintaining cognitive function in older individuals.

Effect of Levodopa Medication on Human Brain Connectome in Parkinson's Disease-A Combined Graph Theory and EEG Study

Background. Levodopa-based drugs are widely used for mitigating the complications induced by Parkinson's disease (PD). Despite the positive effects, several issues regarding the way that levodopa changes brain activities have remained unclear. Methods. A combined strategy using EEG data and graph theory was used for investigating how levodopa changed connectome and processing hubs of the brain during resting-state. Obtained results were subjected to ANOVA test and multiple-comparison post-hoc correction procedure. Results. Outcomes showed that graph topology was not significantly different between PD and healthy groups during the eyes-closed condition, while in the eyes-open condition, statistically significant differences were found. The main effect of levodopa medication was observed for gamma-band activity in which levodopa changed the brain connectome toward a star-like topology. Considering the beta subband of EEG data, graph leaf number increased following levodopa medication in PD patients. Enhanced brain connectivity in the gamma band and reduced beta band connections in the basal ganglia were also observed after levodopa medication. Furthermore, source localization using dipole fitting showed that levodopa suppressed the activity of collateral trigone. Conclusion. Our combined EEG and graph analysis showed that levodopa medication changed the brain connectome, especially in the high-frequency range of brain electrical activities (beta and gamma).

State Changes During Resting-State (Magneto)encephalographic Studies: The Effect of Drowsiness on Spectral, Connectivity, and Network Analyses

Background

A common problem in resting-state neuroimaging studies is that subjects become drowsy or fall asleep. Although this could drastically affect neurophysiological measurements, such as magnetoencephalography (MEG), its specific impact remains understudied. We aimed to systematically investigate how often drowsiness is present during resting-state MEG recordings, and how the state changes alter quantitative estimates of oscillatory activity, functional connectivity, and network topology.

Methods

About 8-min MEG recordings of 19 healthy subjects, split into ~13-s epochs, were scored for the presence of eyes-open (EO), alert eyes-closed (A-EC), or drowsy eyes-closed (D-EC) states. After projection to source-space, results of spectral, functional connectivity, and network analyses in 6 canonical frequency bands were compared between these states on a global and regional levels. Functional connectivity was analyzed using the phase lag index (PLI) and corrected amplitude envelope correlation (AECc), and network topology was analyzed using the minimum spanning tree (MST).

Results

Drowsiness was present in >55% of all epochs that did not fulfill the AASM criteria for sleep. There were clear differences in spectral results between the states (A-EC vs. D-EC) and conditions (EO vs. A-EC). The influence of state and condition was far less pronounced for connectivity analyses, with only minimal differences between D-EC and EO in the AECc in the delta band. There were no effects of drowsiness on any of the MST measures.

Conclusions

Drowsiness during eyes-closed resting-state MEG recordings is present in the majority of epochs, despite the instructions to stay awake. This has considerable influence on spectral properties, but much less so on functional connectivity and network topology. These findings are important for interpreting the results of EEG/MEG studies using spectral analyses in neurological disease, where recordings should be evaluated for the presence of drowsiness. For connectivity analyses or studies on network topology, this seems of far less importance.

Depression Classification Using Frequent Subgraph Mining Based on Pattern Growth of Frequent Edge in Functional Magnetic Resonance Imaging Uncertain Network

The brain network structure is highly uncertain due to the noise in imaging signals and evaluation methods. Recent works have shown that uncertain brain networks could capture uncertain information with regards to functional connections. Most of the existing research studies covering uncertain brain networks used graph mining methods for analysis; for example, the mining uncertain subgraph patterns (MUSE) method was used to mine frequent subgraphs and the discriminative feature selection for uncertain graph classification (DUG) method was used to select discriminant subgraphs. However, these methods led to a lack of effective discriminative information; this reduced the classification accuracy for brain diseases. Therefore, considering these problems, we propose an approximate frequent subgraph mining algorithm based on pattern growth of frequent edge (unFEPG) for uncertain brain networks and a novel discriminative feature selection method based on statistical index (dfsSI) to perform graph mining and selection. Results showed that compared with the conventional methods, the unFEPG and dfsSI methods achieved a higher classification accuracy. Furthermore, to demonstrate the efficacy of the proposed method, we used consistent discriminative subgraph patterns based on thresholding and weighting approaches to compare the classification performance of uncertain networks and certain networks in a bidirectional manner. Results showed that classification performance of the uncertain network was superior to that of the certain network within a defined sparsity range. This indicated that if a better classification performance is to be achieved, it is necessary to select a certain brain network with a higher threshold or an uncertain brain network model. Moreover, if the uncertain brain network model was selected, it is necessary to make full use of the uncertain information of its functional connection.

Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: A review

Diffusion magnetic resonance imaging (dMRI) tractography is an advanced imaging technique that enables in vivo reconstruction of the brain's white matter connections at macro scale. It provides an important tool for quantitative mapping of the brain's structural connectivity using measures of connectivity or tissue microstructure. Over the last two decades, the study of brain connectivity using dMRI tractography has played a prominent role in the neuroimaging research landscape. In this paper, we provide a high-level overview of how tractography is used to enable quantitative analysis of the brain's structural connectivity in health and disease. We focus on two types of quantitative analyses of tractography, including: 1) tract-specific analysis that refers to research that is typically hypothesis-driven and studies particular anatomical fiber tracts, and 2) connectome-based analysis that refers to research that is more data-driven and generally studies the structural connectivity of the entire brain. We first provide a review of methodology involved in three main processing steps that are common across most approaches for quantitative analysis of tractography, including methods for tractography correction, segmentation and quantification. For each step, we aim to describe methodological choices, their popularity, and potential pros and cons. We then review studies that have used quantitative tractography approaches to study the brain's white matter, focusing on applications in neurodevelopment, aging, neurological disorders, mental disorders, and neurosurgery. We conclude that, while there have been considerable advancements in methodological technologies and breadth of applications, there nevertheless remains no consensus about the "best" methodology in quantitative analysis of tractography, and researchers should remain cautious when interpreting results in research and clinical applications.

A hands-on tutorial on network and topological neuroscience

The brain is an extraordinarily complex system that facilitates the optimal 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 pairwise 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 the 1000 Functional Connectomes Project dataset. Moreover, we would like to highlight one part of our notebook dedicated to the realistic visualisation of high order interactions in brain networks. This pipeline provides three-dimensional (3-D) plots of pairwise and higher-order interactions projected in a brain atlas, a new feature tailor-made for network neuroscience.

Minimum spanning tree analysis of brain networks: A systematic review of network size effects, sensitivity for neuropsychiatric pathology and disorder specificity

Brain network characteristics’ potential to serve as a neurological and psychiatric pathology biomarker has been hampered by the so-called thresholding problem. The minimum spanning tree (MST) is increasingly applied to overcome this problem. It is yet unknown whether this approach leads to more consistent findings across studies and converging outcomes of either disease-specific biomarkers or transdiagnostic effects. We performed a systematic review on MST analysis in neurophysiological and neuroimaging studies (N = 43) to study consistency of MST metrics between different network sizes and assessed disease specificity and transdiagnostic sensitivity of MST metrics for neurological and psychiatric conditions. Analysis of data from control groups (12 studies) showed that MST leaf fraction but not diameter decreased with increasing network size. Studies showed a broad range in metric values, suggesting that specific processing pipelines affect MST topology. Contradicting findings remain in the inconclusive literature of MST brain network studies, but some trends were seen: (1) a more linelike organization characterizes neurodegenerative disorders across pathologies, and is associated with symptom severity and disease progression; (2) neurophysiological studies in epilepsy show frequency band specific MST alterations that normalize after successful treatment; and (3) less efficient MST topology in alpha band is found across disorders associated with attention impairments.

The potential of brain network characteristics to serve as biomarker of neurological and psychiatric pathology has been hampered by the so-called thresholding problem. The minimum spanning tree (MST) is increasingly applied to overcome this problem. We performed a systematic review on MST analysis in neurophysiological and neuroimaging studies and assessed disease specificity and transdiagnostic sensitivity of MST metrics for neurological and psychiatric conditions. MST leaf fraction but not diameter decreased with increasing network size. Contradicting findings remain in the literature on MST brain network studies, but some trends were seen: (1) a more linelike organization characterizes neurodegenerative disorders; (2) in epilepsy there are frequency band specific MST alterations that normalize after successful treatment; and (3) less efficient MST topology is found across disorders associated with attention impairments.

Global and localized network characteristics of the resting brain predict and adapt to foreign language learning in older adults

Resting brain (rs) activity has been shown to be a reliable predictor of the level of foreign language (L2) proficiency younger adults can achieve in a given time-period. Since rs properties change over the lifespan, we investigated whether L2 attainment in older adults (aged 64-74 years) is also predicted by individual differences in rs activity, and to what extent rs activity itself changes as a function of L2 proficiency. To assess how neuronal assemblies communicate at specific frequencies to facilitate L2 development, we examined localized and global measures (Minimum Spanning Trees) of connectivity. Results showed that central organization within the beta band (~ 13-29.5 Hz) predicted measures of L2 complexity, fluency and accuracy, with the latter additionally predicted by a left-lateralized centro-parietal beta network. In contrast, reduced connectivity in a right-lateralized alpha (~ 7.5-12.5 Hz) network predicted development of L2 complexity. As accuracy improved, so did central organization in beta, whereas fluency improvements were reflected in localized changes within an interhemispheric beta network. Our findings highlight the importance of global and localized network efficiency and the role of beta oscillations for L2 learning and suggest plasticity even in the ageing brain. We interpret the findings against the background of networks identified in socio-cognitive processes.

Aberrant dynamic minimal spanning tree parameters within default mode network in patients with autism spectrum disorder

The altered functional connectivity (FC) level and its temporal characteristics within certain cortical networks, such as the default mode network (DMN), could provide a possible explanatory framework for Autism spectrum disorder (ASD). In the current study, we hypothesized that the topographical organization along with its temporal dynamics of the autistic brain measured by temporal mean and variance of complex network measures, respectively, were significantly altered, which may further explain the autistic symptom severity in patients with ASD. To validate these hypotheses, the precise FCs between DMN regions at each time point were calculated using the resting-state functional magnetic resonance imaging (fMRI) datasets from the Autism Brain Imaging Data Exchange (ABIDE) project. Then, the minimal spanning tree (MST) technique was applied to construct a time-varying complex network of DMN. By analyzing the temporal mean and variance of MST parameters and their relationship with autistic symptom severity, we found that in persons with ASD, the information exchange efficiencies between cortical regions within DMN were significantly lower and more volatile compared with those in typical developing participants. Moreover, these alterations within DMN were closely associated with the autistic symptom severity of the ASD group.

Visual Effect on Brain Connectome That Scales Feedforward and Feedback Processes of Aged Postural System During Unstable Stance

Older adults with degenerative declines in sensory systems depend strongly on visual input for postural control. By connecting advanced neural imaging and a postural control model, this study investigated the visual effect on the brain functional network that regulates feedback and feedforward processes of the postural system in older adults under somatosensory perturbations. Thirty-six older adults conducted bilateral stance on a foam surface in the eyes-open (EO) and eyes-closed (EC) conditions while their center of pressure (COP) and scalp EEG were recorded. The stochastic COP trajectory was modeled with non-linear stabilogram diffusion analysis (SDA) to characterize shifts in postural control in a continuum of feedback and feedforward processes. The EEG network was analyzed with the phase-lag index (PLI) and minimum spanning tree (MST). The results indicated that visual input rebalanced feedforward and feedback processes for postural sway, resulting in a greater critical point of displacement (CD), short-term effective diffusion coefficients (D_s) and short-term exponent (H_s), but the smaller critical point of time (CT) and long-term exponent (H_l) for the EC state. The EC network demonstrated stronger frontoparietal-occipital connectivity but weaker fronto-tempo-motor connectivity of the theta (4–7 Hz), alpha (8–12 Hz), and beta (13–35 Hz) bands than did the EO network. MST analysis revealed generally greater leaf fraction and maximal betweenness centrality (BC_max) and kappa of the EC network, as compared with those of the EO network. In contrast, the EC network exhibited a smaller diameter and average eccentricity than those of the EO network. The modulation of long-term negative feedback gain of the aged postural system with visual occlusion was positively correlated with leaf fraction, BC_max, and kappa, but negatively correlated with the diameter and average eccentricity for all EEG sub-bands. In conclusion, the aged brain functional network in older adults is tuned to visual information for modulating long-term negative feedback of the postural system under somatosensory perturbations.

Predicted disconnectome associated with progressive periventricular white matter ischemia

We used a virtual lesion DTI fiber tracking approach with healthy subject DTI data and simulated periventricular white matter (PVWM) lesion masks to predict the sequence of connectivity changes associated with progressive PVWM ischemia. We found that the optic radiations, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, corpus callosum, temporopontine tract and fornix were affected in early simulated ischemic injury, and that the connectivity of subcortical, cerebellar, and visual regions were significantly disrupted with increasing simulated lesion severity. The results of this study provide insights into the spatial-temporal changes of the brain structural connectome under progressive PVWM ischemia. The virtual lesion approach provides a meaningful proxy to the spatial-temporal changes of the brain's structural connectome and can be used to further characterize the cognitive sequelae of progressive PVWM ischemia in both normal aging and dementia.

Special Patterns of Dynamic Brain Networks Discriminate Between Face and Non-face Processing: A Single-Trial EEG Study

Face processing is a spatiotemporal dynamic process involving widely distributed and closely connected brain regions. Although previous studies have examined the topological differences in brain networks between face and non-face processing, the time-varying patterns at different processing stages have not been fully characterized. In this study, dynamic brain networks were used to explore the mechanism of face processing in human brain. We constructed a set of brain networks based on consecutive short EEG segments recorded during face and non-face (ketch) processing respectively, and analyzed the topological characteristic of these brain networks by graph theory. We found that the topological differences of the backbone of original brain networks (the minimum spanning tree, MST) between face and ketch processing changed dynamically. Specifically, during face processing, the MST was more line-like over alpha band in 0-100 ms time window after stimuli onset, and more star-like over theta and alpha bands in 100-200 and 200-300 ms time windows. The results indicated that the brain network was more efficient for information transfer and exchange during face processing compared with non-face processing. In the MST, the nodes with significant differences of betweenness centrality and degree were mainly located in the left frontal area and ventral visual pathway, which were involved in the face-related regions. In addition, the special MST patterns can discriminate between face and ketch processing by an accuracy of 93.39%. Our results suggested that special MST structures of dynamic brain networks reflected the potential mechanism of face processing in human brain.

Assessing a transmission network of Mycobacterium tuberculosis in an African city using single nucleotide polymorphism threshold analysis

Tuberculosis (TB) is the leading cause of death in humans by a single infectious agent worldwide with approximately two billion humans latently infected with the bacterium Mycobacterium tuberculosis. Currently, the accepted method for controlling the disease is Tuberculosis Directly Observed Treatment Shortcourse (TB-DOTS). This program is not preventative and individuals may transmit disease before diagnosis, thus better understanding of disease transmission is essential. Using whole-genome sequencing and single nucleotide polymorphism analysis, we analyzed genomes of 145 M. tuberculosis clinical isolates from active TB cases from the Rubaga Division of Kampala, Uganda. We established that these isolates grouped into M. tuberculosis complex (MTBC) lineages 1, 2, 3, and 4, with the most isolates grouping into lineage 4. Possible transmission pairs containing ≤12 SNPs were identified in lineages 1, 3, and 4 with the prevailing transmission in lineages 3 and 4. Furthermore, investigating DNA codon changes as a result of specific SNPs in prominent virulence genes including plcA and plcB could indicate potentially important modifications in protein function. Incorporating this analysis with corresponding epidemiological data may provide a blueprint for the integration of public health interventions to decrease TB transmission in a region.

Disentangling age- and disease-related alterations in schizophrenia brain network using structural equation modeling: A graph theoretical study based on minimum spanning tree

Functional brain networks have been shown to undergo fundamental changes associated with aging or schizophrenia. However, the mechanism of how these factors exert influences jointly or interactively on brain networks remains elusive. A unified recognition of connectomic alteration patterns was also hampered by heterogeneities in network construction and thresholding methods. Recently, an unbiased network representation method regardless of network thresholding, so called minimal spanning tree algorithm, has been applied to study the critical skeleton of the brain network. In this study, we aimed to use minimum spanning tree (MST) as an unbiased network reconstruction and employed structural equation modeling (SEM) to unravel intertwined relationships among multiple phenotypic and connectomic variables in schizophrenia. First, we examined global and local brain network properties in 40 healthy subjects and 40 schizophrenic patients aged 21–55 using resting‐state functional magnetic resonance imaging (rs‐fMRI). Global network alterations are measured by graph theoretical metrics of MSTs and a connectivity‐transitivity two‐dimensional approach was proposed to characterize nodal roles. We found that networks of schizophrenic patients exhibited a more star‐like global structure compared to controls, indicating excessive integration, and a loss of regional transitivity in the dorsal frontal cortex (corrected p <.05). Regional analysis of MST network topology revealed that schizophrenia patients had more network hubs in frontal regions, which may be linked to the “overloading” hypothesis. Furthermore, using SEM, we found that the level of MST integration mediated the influence of age on negative symptom severity (indirect effect 95% CI [0.026, 0.449]). These findings highlighted an altered network skeleton in schizophrenia and suggested that aging‐related enhancement of network integration may undermine functional specialization of distinct neural systems and result in aggravated schizophrenic symptoms.

Aberrant Structural Network Architecture in Leber's Hereditary Optic Neuropathy. Minimum Spanning Tree Graph Analysis Application into Diffusion 7T MRI

Examining individuals with Leber's hereditary optic neuropathy (LHON) provides a rare opportunity to understand how changes in mitochondrial DNA and loss of vision can be related to changes in organization of the whole-brain structural network architecture. In comparison with the previous neuroimaging studies with LHON participants, which were focused mainly on analyzing changes which occur in different areas of the patient's brain, network analysis not only makes it possible to observe single white matter fibers' aberrations but also the whole-brain nature of these changes. The purpose of our study was to better understand whole-brain neural network changes in LHON participants and see the correlation between the clinical data and the changes. To achieve this, we examined fifteen LHON patients and seventeen age-matched healthy subjects with the usage of ultra-high filed 7T magnetic resonance imaging (MRI). Basing on the analysis on MRI diffusion tensor imaging (DTI) data, whole-brain structural neural networks were reconstructed with the use of the minimum spanning tree algorithm (MST) for every participant. Our results revealed that the structural network in LHON participants was altered at both the local and the global level. The global network structures of LHON subjects were less centralized with path-like organization and there was an imbalance in the main hub centrality. Moreover, the inspection of nodes and hubs in terms of their anatomical placement revealed that in the LHON participants the prominent hubs were located within the basal ganglia (i.e. bilateral caudate, left pallidum), which differed them from healthy controls. An analysis of the relationships between the global MST metrics and LHON participants' clinical characteristics revealed significant correlations between the global network metrics and the duration of illness. Furthermore, the nodal parameters of the optic chiasm were significantly correlated with the duration of illness and the averaged thickness of the right retinal nerve fiber layer (RNFL). These findings clearly showed that the progression of the disease is accompanied by alterations within the brain network structure and its efficiency.

Frontal Functional Network Disruption Associated with Amyotrophic Lateral Sclerosis: An fNIRS-Based Minimum Spanning Tree Analysis

Recent evidence increasingly associates network disruption in brain organization with multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), a rare terminal disease. However, the comparability of brain network characteristics across different studies remains a challenge for conventional graph theoretical methods. One suggested method to address this issue is minimum spanning tree (MST) analysis, which provides a less biased comparison. Here, we assessed the novel application of MST network analysis to hemodynamic responses recorded by functional near-infrared spectroscopy (fNIRS) neuroimaging modality, during an activity-based paradigm to investigate hypothetical disruptions in frontal functional brain network topology as a marker of the executive dysfunction, one of the most prevalent cognitive deficit reported across ALS studies. We analyzed data recorded from nine participants with ALS and ten age-matched healthy controls by first estimating functional connectivity, using phase-locking value (PLV) analysis, and then constructing the corresponding individual and group MSTs. Our results showed significant between-group differences in several MST topological properties, including leaf fraction, maximum degree, diameter, eccentricity, and degree divergence. We further observed a global shift toward more centralized frontal network organizations in the ALS group, interpreted as a more random or dysregulated network in this cohort. Moreover, the similarity analysis demonstrated marginally significantly increased overlap in the individual MSTs from the control group, implying a reference network with lower topological variation in the healthy cohort. Our nodal analysis characterized the main local hubs in healthy controls as distributed more evenly over the frontal cortex, with slightly higher occurrence in the left prefrontal cortex (PFC), while in the ALS group, the most frequent hubs were asymmetrical, observed primarily in the right prefrontal cortex. Furthermore, it was demonstrated that the global PLV (gPLV) synchronization metric is associated with disease progression, and a few topological properties, including leaf fraction and tree hierarchy, are linked to disease duration. These results suggest that dysregulation, centralization, and asymmetry of the hemodynamic-based frontal functional network during activity are potential neuro-topological markers of ALS pathogenesis. Our findings can possibly support new bedside assessments of the functional status of ALS' brain network and could hypothetically extend to applications in other neurodegenerative diseases.

Functional brain network organization measured with magnetoencephalography predicts cognitive decline in multiple sclerosis

BACKGROUND

Cognitive decline remains difficult to predict as structural brain damage cannot fully explain the extensive heterogeneity found between MS patients.

OBJECTIVE

To investigate whether functional brain network organization measured with magnetoencephalography (MEG) predicts cognitive decline in MS patients after 5 years and to explore its value beyond structural pathology.

METHODS

Resting-state MEG recordings, structural MRI, and neuropsychological assessments were analyzed of 146 MS patients, and 100 patients had a 5-year follow-up neuropsychological assessment. Network properties of the minimum spanning tree (i.e. backbone of the functional brain network) indicating network integration and overload were related to baseline and longitudinal cognition, correcting for structural damage.

RESULTS

A more integrated beta band network (i.e. smaller diameter) and a less integrated delta band network (i.e. lower leaf fraction) predicted cognitive decline after 5 years (Radj2=15%), independent of structural damage. Cross-sectional analyses showed that a less integrated network (e.g. lower tree hierarchy) related to worse cognition, independent of frequency band.

CONCLUSIONS

The level of functional brain network integration was an independent predictive marker of cognitive decline, in addition to the severity of structural damage. This work thereby indicates the promise of MEG-derived network measures in predicting disease progression in MS.

Motion-Dependent Effects of Functional Magnetic Resonance Imaging Preprocessing Methodology on Global Functional Connectivity

Background: While functional magnetic resonance imaging (fMRI) has become an established noninvasive tool for studying brain activity in both healthy and diseased states, no broad consensus has been reached regarding preprocessing methodology. Furthermore, the relationship between variations in preprocessing and functional connectivity (FC) networks remains incompletely understood. Purpose: The aim of this study was to relate FC to (1) choices in preprocessing methodology and (2) subject motion. Methods: Clinical and MRI data were analyzed from healthy subjects acquired as part of the Autism Brain Imaging Data Exchange (ABIDE). Data were obtained from 508 healthy subjects. Data from subjects in the highest and lowest quartiles for motion were used to calculate the interaction between motion and preprocessing. Data were analyzed across four domains of fMRI preprocessing: (1) pipeline, (2) global signal regression (GSR), (3) bandpass filtering, and (4) anatomic atlas. For the FC network calculated from each preprocessing scheme, overall FC using Pearson correlation, as well as leaf fraction and diameter, was calculated for each subject, and statistical comparison was made across schemes using generalized estimating equations. Results: FC and global network properties were significantly affected by each preprocessing step, and each preprocessing step significantly interacted with subject motion to differentially affect global functional network properties, with GSR having the strongest effect. Conclusion: Preprocessing choices in fMRI studies influence overall FC and global network properties and can have motion-dependent effects. Impact statement Different parameter choices across the four domains of functional magnetic resonance imaging (fMRI) preprocessing analyzed in this study (global signal regression, bandpass filtering, anatomic atlas, and pipeline) were associated with differences in functional connectivity (FC) as well as global network properties in healthy subjects. Some fMRI preprocessing parameter choices resulted in motion-dependent effects on FC and global network properties.

Functional brain networks in the schizophrenia spectrum and bipolar disorder with psychosis

Psychotic experiences have been proposed to lie on a spectrum, ranging from subclinical experiences to treatment-resistant schizophrenia. We aimed to characterize functional connectivity and brain network characteristics in relation to the schizophrenia spectrum and bipolar disorder with psychosis to disentangle neural correlates to psychosis. Additionally, we studied antipsychotic medication and lithium effects on network characteristics. We analyzed functional connectivity strength and network topology in 487 resting-state functional MRI scans of individuals with schizophrenia spectrum disorder (SCZ), bipolar disorder with a history of psychotic experiences (BD), treatment-naïve subclinical psychosis (SCP), and healthy controls (HC). Since differences in connectivity strength may confound group comparisons of brain network topology, we analyzed characteristics of the minimum spanning tree (MST), a relatively unbiased backbone of the network. SCZ and SCP subjects had a lower connectivity strength than BD and HC individuals but showed no differences in network topology. In contrast, BD patients showed a less integrated network topology but no disturbances in connectivity strength. No differences in outcome measures were found between SCP and SCZ, or between BD patients that used antipsychotic medication or lithium and those that did not. We conclude that functional networks in patients prone to psychosis have different signatures for chronic SCZ patients and SCP compared to euthymic BD patients, with a limited role for medication. Connectivity strength effects may have confounded previous studies, as no functional network alterations were found in SCZ after strict correction for connectivity strength.

fMRI network correlates of predisposing risk factors for delirium: A cross-sectional study

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Predisposing risk is not associated with delirium-related fMRI characteristics.

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Older age within an elderly cohort is related to higher functional connectivity strength.

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This relation is in opposite direction than hypothesized.

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The onset of delirium may reflect new functional network impairments.

Delirium, the clinical expression of acute encephalopathy, is a common neuropsychiatric syndrome that is related to poor outcomes, such as long-term cognitive impairment. Disturbances of functional brain networks are hypothesized to predispose for delirium. The aim of this study in non-delirious elderly individuals was to investigate whether predisposing risk factors for delirium are associated with fMRI network characteristics that have been observed during delirium. As predisposing risk factors, we studied age, alcohol misuse, cognitive impairment, depression, functional impairment, history of transient ischemic attack or stroke, and physical status. In this multicenter study, we included 554 subjects and analyzed resting-state fMRI data from 222 elderly subjects (63% male, age range: 65–85 year) after rigorous motion correction. Functional network characteristics were analyzed and based on the minimum spanning tree (MST). Global functional connectivity strength, network efficiency (MST diameter) and network integration (MST leaf fraction) were analyzed, as these measures were altered during delirium in previous studies. Linear regression analyses were used to investigate the relation between predisposing delirium risk factors and delirium-related fMRI characteristics, adjusted for confounding and multiple testing. Predisposing risk factors for delirium were not associated with delirium-related fMRI network characteristics. Older age within our elderly cohort was related to global functional connectivity strength (β = 0.182, p < 0.05), but in the opposite direction than hypothesized. Delirium-related functional network impairments can therefore not be considered as the common mechanism for predisposition for delirium.

The compensatory phenomenon of the functional connectome related to pathological biomarkers in individuals with subjective cognitive decline

Background

Subjective cognitive decline (SCD) is a preclinical stage along the Alzheimer’s disease (AD) continuum. However, little is known about the aberrant patterns of connectivity and topological alterations of the brain functional connectome and their diagnostic value in SCD.

Methods

Resting-state functional magnetic resonance imaging and graph theory analyses were used to investigate the alterations of the functional connectome in 66 SCD individuals and 64 healthy controls (HC). Pearson correlation analysis was computed to assess the relationships among network metrics, neuropsychological performance and pathological biomarkers. Finally, we used the multiple kernel learning-support vector machine (MKL-SVM) to differentiate the SCD and HC individuals.

Results

SCD individuals showed higher nodal topological properties (including nodal strength, nodal global efficiency and nodal local efficiency) associated with amyloid-β levels and memory function than the HC, and these regions were mainly located in the default mode network (DMN). Moreover, increased local and medium-range connectivity mainly between the bilateral parahippocampal gyrus (PHG) and other DMN-related regions was found in SCD individuals compared with HC individuals. These aberrant functional network measures exhibited good classification performance in the differentiation of SCD individuals from HC individuals at an accuracy up to 79.23%.

Conclusion

The findings of this study provide insight into the compensatory mechanism of the functional connectome underlying SCD. The proposed classification method highlights the potential of connectome-based metrics for the identification of the preclinical stage of AD.

Effect of Fixed-Density Thresholding on Structural Brain Networks: A Demonstration in Cerebral Small Vessel Disease

A popular solution to control for edge density variability in structural brain network analysis is to threshold the networks to a fixed density across all subjects. However, it remains unclear how this type of thresholding affects the basic network architecture in terms of edge weights, hub location, and hub connectivity and, especially, how it affects the sensitivity to detect disease-related abnormalities. We investigated these two questions in a cohort of patients with cerebral small vessel disease and age-matched controls. Brain networks were reconstructed from diffusion magnetic resonance imaging data using deterministic fiber tractography. Networks were thresholded to a fixed density by removing edges with the lowest number of streamlines. We compared edge length (mm), fractional anisotropy (FA), proportion of hub connections, and hub location between the unthresholded and the thresholded networks of each subject. Moreover, we compared weighted graph measures of global and local connectivity obtained from the (un)thresholded networks between patients and controls. We performed these analyses over a range of densities (2-20%). Results indicate that fixed-density thresholding disproportionally removes edges composed of long streamlines, but is independent of FA. The edges removed were not preferentially connected to hub or nonhub nodes. Over half of the original hubs were reproducible when networks were thresholded to a density ≥10%. Furthermore, the between-group differences in graph measures observed in the unthresholded network remained present after thresholding, irrespective of the chosen density. We therefore conclude that moderate fixed-density thresholds can successfully be applied to control for the effects of density in structural brain network analysis.

Clustering of Brain Function Network Based on Attribute and Structural Information and Its Application in Brain Diseases

At present, the diagnosis of brain disease is mainly based on the self-reported symptoms and clinical signs of the patient, which can easily lead to psychiatrists' bias. The purpose of this study is to develop a brain network clustering model to accurately identify brain diseases based on resting state functional magnetic resonance imaging (fMRI) in the absence of clinical information. We use cosine similarity and sub-network kernels to measure attribute similarity and structure similarity, respectively. By integrating the structure similarity and attribute similarity into one matrix, spectral clustering is used to achieve brain network clustering. Finally, we evaluate this method on three diseases: Alzheimer's disease, Bipolar disorder patients, and Schizophrenia. The performance of methods is evaluated by measuring clustering consistency. Clustering consistency is similar to clustering accuracy, which is used to evaluate the consistency between the clustering labels and clinical diagnostic labels of the subjects. The experimental results show that our proposed method can significantly improve clustering performance, with a consistency of 60.6% for Alzheimer's disease, with a consistency of 100% for Schizophrenia, with a consistency of 100% for Bipolar disorder patients.

The road ahead in clinical network neuroscience

Clinical network neuroscience, the study of brain network topology in neurological and psychiatric diseases, has become a mainstay field within clinical neuroscience. Being a multidisciplinary group of clinical network neuroscience experts based in The Netherlands, we often discuss the current state of the art and possible avenues for future investigations. These discussions revolve around questions like "How do dynamic processes alter the underlying structural network?" and "Can we use network neuroscience for disease classification?" This opinion paper is an incomplete overview of these discussions and expands on ten questions that may potentially advance the field. By no means intended as a review of the current state of the field, it is instead meant as a conversation starter and source of inspiration to others.

Abnormalities in hubs location and nodes centrality predict cognitive slowing and increased performance variability in first-episode schizophrenia patients

Introducing the Minimum Spanning Tree (MST) algorithms to neural networks science eliminated the problem of arbitrary setting of the threshold for connectivity strength. Despite these advantages, MST has been rarely used to study network abnormalities in schizophrenia. An MST graph mapping a network structure is its simplification, therefore, it is important to verify whether the reconfigured network is significantly related to the behavioural dimensions of the clinical picture of schizophrenia. 35 first-episode schizophrenia patients and 35 matched healthy controls underwent an assessment of information processing speed, cognitive inter-trial variability modelled with ex-Gaussian distributional analysis of reaction times and resting-state EEG recordings to obtain frequency-specific functional connectivity matrices from which MST graphs were computed. The patients’ network had a more random structure and star-like arrangement with overloaded hubs positioned more posteriorly than it was in the case of the control group. Deficient processing speed in the group of patients was predicted by increased maximal betweenness centrality in beta and gamma bands, while decreased consistency in cognitive processing was predicted by the betweenness centrality of posterior nodes in the gamma band, together with duration of illness. The betweenness centrality of posterior nodes in the gamma band was also significantly correlated with positive psychotic symptoms in the clinical group.

Increased segregation of functional networks in developing brains

A growing literature conceptualises typical brain development from a network perspective. However, largely due to technical and methodological challenges inherent in paediatric functional neuroimaging, there remains an important gap in our knowledge regarding the typical development of functional brain networks in "preschool" childhood (i.e., children younger than 6 years of age). In this study, we recorded brain oscillatory activity using age-appropriate magnetoencephalography in 24 children, including 14 preschool children aged from 4 to 6 years and 10 school children aged from 7 to 12 years. We compared the topology of the resting-state brain networks in these children, estimated using minimum spanning tree (MST) constructed from phase synchrony between beamformer-reconstructed time-series, with that of 24 adults. Our results show that during childhood the MST topology shifts from a star-like (centralised) toward a more line-like (de-centralised) configuration, indicating the functional brain networks become increasingly segregated. In addition, the increasing global network segregation is frequency-independent and accompanied by decreases in centrality (or connectedness) of cortical regions with age, especially in areas of the default mode network. We propose a heuristic MST model of "network space", which posits a clear developmental trajectory for the emergence of complex brain networks. Our results not only revealed topological reorganisation of functional networks across multiple temporal and spatial scales in childhood, but also fill a gap in the literature regarding neurophysiological mechanisms of functional brain maturation during the preschool years of childhood.

A concise and persistent feature to study brain resting-state network dynamics: Findings from the Alzheimer's Disease Neuroimaging Initiative

Alzheimer's disease (AD) is the most common type of dementia in the elderly with no effective treatment currently. Recent studies of noninvasive neuroimaging, resting-state functional magnetic resonance imaging (rs-fMRI) with graph theoretical analysis have shown that patients with AD and mild cognitive impairment (MCI) exhibit disrupted topological organization in large-scale brain networks. In previous work, it is a common practice to threshold such networks. However, it is not only difficult to make a principled choice of threshold values, but also worse is the discard of potential important information. To address this issue, we propose a threshold-free feature by integrating a prior persistent homology-based topological feature (the zeroth Betti number) and a newly defined connected component aggregation cost feature to model brain networks over all possible scales. We show that the induced topological feature (Integrated Persistent Feature) follows a monotonically decreasing convergence function and further propose to use its slope as a concise and persistent brain network topological measure. We apply this measure to study rs-fMRI data from the Alzheimer's Disease Neuroimaging Initiative and compare our approach with five other widely used graph measures across five parcellation schemes ranging from 90 to 1,024 region-of-interests. The experimental results demonstrate that the proposed network measure shows more statistical power and stronger robustness in group difference studies in that the absolute values of the proposed measure of AD are lower than MCI and much lower than normal controls, providing empirical evidence for decreased functional integration in AD dementia and MCI.

Brain functional networks become more connected as amyotrophic lateral sclerosis progresses: a source level magnetoencephalographic study

This study hypothesizes that the brain shows hyper connectedness as amyotrophic lateral sclerosis (ALS) progresses. 54 patients (classified as "early stage" or "advanced stage") and 25 controls underwent magnetoencephalography and MRI recordings. The activity of the brain areas was reconstructed, and the synchronization between them was estimated in the classical frequency bands using the phase lag index. Brain topological metrics such as the leaf fraction (number of nodes with degree of 1), the degree divergence (a measure of the scale-freeness) and the degree correlation (a measure of disassortativity) were estimated. Betweenness centrality was used to estimate the centrality of the brain areas. In all frequency bands, it was evident that, the more advanced the disease, the more connected, scale-free and disassortative the brain networks. No differences were evident in specific brain areas. Such modified brain topology is sub-optimal as compared to controls. Within this framework, our study shows that brain networks become more connected according to disease staging in ALS patients.

Minimum spanning tree analysis of the human connectome

One of the challenges of brain network analysis is to directly compare network organization between subjects, irrespective of the number or strength of connections. In this study, we used minimum spanning tree (MST; a unique, acyclic subnetwork with a fixed number of connections) analysis to characterize the human brain network to create an empirical reference network. Such a reference network could be used as a null model of connections that form the backbone structure of the human brain. We analyzed the MST in three diffusion‐weighted imaging datasets of healthy adults. The MST of the group mean connectivity matrix was used as the empirical null‐model. The MST of individual subjects matched this reference MST for a mean 58%–88% of connections, depending on the analysis pipeline. Hub nodes in the MST matched with previously reported locations of hub regions, including the so‐called rich club nodes (a subset of high‐degree, highly interconnected nodes). Although most brain network studies have focused primarily on cortical connections, cortical–subcortical connections were consistently present in the MST across subjects. Brain network efficiency was higher when these connections were included in the analysis, suggesting that these tracts may be utilized as the major neural communication routes. Finally, we confirmed that MST characteristics index the effects of brain aging. We conclude that the MST provides an elegant and straightforward approach to analyze structural brain networks, and to test network topological features of individual subjects in comparison to empirical null models.