GraphVar 2.0: A user-friendly toolbox for machine learning on functional connectivity measures

Exploring imitation of within hand prehensile object manipulation using fMRI and graph theory analysis

This study aims to establish an imitation task of multi-finger haptics in the context of regular grasping and regrasping processes during activities of daily living. A video guided the 26 healthy, right-handed volunteers through the three phases of the task: (1) fixation of a hand holding a cuboid, (2) observation of the sensori-motor manipulation, (3) imitation of that motor action. fMRI recorded the task; graph analysis of the acquisitions revealed the associated functional cerebral connectivity patterns. Inferred from four 60 ROI weighted graphs, the functional connectivities are consistent with a motor plan for observation and manipulation in the left hemisphere and with a network in the right hemisphere involving the inferior frontal gyrus, the site of intentional control of imitation. The networks exhibit (1) rich clubs which include sensori-motor hand, dorsal attention and cingulo-opercular communities for observation and motor execution in both hemispheres and (2) diversity clubs, significant only for manipulation and observation of the left hand, which include the dorsal visual association cortex, suggesting enhanced visual perception required for guiding the movement-limited left fingers. Short pathway analyses are consistent with these findings, confirming preferential involvement of ventral premotor cortices in the mirror network.

The pharmacodynamic modulation effect of oxytocin on resting state functional connectivity network topology

Introduction

Neuroimaging studies have demonstrated that intranasal oxytocin has extensive effects on the resting state functional connectivity of social and emotional processing networks and may have therapeutic potential. However, the extent to which intranasal oxytocin modulates functional connectivity network topology remains less explored, with inconsistent findings in the existing literature. To address this gap, we conducted an exploratory data-driven study.

Methods

We recruited 142 healthy males and administered 24 IU of intranasal oxytocin or placebo in a randomized controlled double-blind design. Resting-state functional MRI data were acquired for each subject. Network-based statistical analysis and graph theoretical approaches were employed to evaluate oxytocin's effects on whole-brain functional connectivity and graph topological measures.

Results

Our results revealed that oxytocin altered connectivity patterns within brain networks involved in sensory and motor processing, attention, memory, emotion and reward functions as well as social cognition, including the default mode, limbic, frontoparietal, cerebellar, and visual networks. Furthermore, oxytocin increased local efficiency, clustering coefficients, and small-world propensity in specific brain regions including the cerebellum, left thalamus, posterior cingulate cortex, right orbitofrontal cortex, right superior frontal gyrus, left inferior frontal gyrus, and right middle orbitofrontal cortex, while decreasing nodal path topological measures in the left and right caudate.

Discussion

These findings suggest that intranasal oxytocin may produce its functional effects through influencing the integration and segregation of information flow within small-world brain networks, particularly in regions closely associated with social cognition and motivation.

ACTION: Augmentation and computation toolbox for brain network analysis with functional MRI

Functional magnetic resonance imaging (fMRI) has been increasingly employed to investigate functional brain activity. Many fMRI-related software/toolboxes have been developed, providing specialized algorithms for fMRI analysis. However, existing toolboxes seldom consider fMRI data augmentation, which is quite useful, especially in studies with limited or imbalanced data. Moreover, current studies usually focus on analyzing fMRI using conventional machine learning models that rely on human-engineered fMRI features, without investigating deep learning models that can automatically learn data-driven fMRI representations. In this work, we develop an open-source toolbox, called Augmentation and Computation Toolbox for braIn netwOrk aNalysis (ACTION), offering comprehensive functions to streamline fMRI analysis. The ACTION is a Python-based and cross-platform toolbox with graphical user-friendly interfaces. It enables automatic fMRI augmentation, covering blood-oxygen-level-dependent (BOLD) signal augmentation and brain network augmentation. Many popular methods for brain network construction and network feature extraction are included. In particular, it supports constructing deep learning models, which leverage large-scale auxiliary unlabeled data (3,800+ resting-state fMRI scans) for model pretraining to enhance model performance for downstream tasks. To facilitate multi-site fMRI studies, it is also equipped with several popular federated learning strategies. Furthermore, it enables users to design and test custom algorithms through scripting, greatly improving its utility and extensibility. We demonstrate the effectiveness and user-friendliness of ACTION on real fMRI data and present the experimental results. The software, along with its source code and manual, can be accessed online.

Changes in Functional Connectivity Relate to Modulation of Cognitive Control by Subthalamic Stimulation

Subthalamic (STN) deep brain stimulation (DBS) in Parkinson's disease (PD) patients not only improves kinematic parameters of movement but also modulates cognitive control in the motor and non-motor domain, especially in situations of high conflict. The objective of this study was to investigate the relationship between DBS-induced changes in functional connectivity at rest and modulation of response- and movement inhibition by STN-DBS in a visuomotor task involving high conflict. During DBS ON and OFF conditions, we conducted a visuomotor task in 14 PD patients who previously underwent resting-state functional MRI (rs-fMRI) acquisitions DBS ON and OFF as part of a different study. In the task, participants had to move a cursor with a pen on a digital tablet either toward (automatic condition) or in the opposite direction (controlled condition) of a target. STN-DBS induced modulation of resting-state functional connectivity (RSFC) as a function of changes in behavior ON versus OFF DBS was estimated using link-wise network-based statistics. Behavioral results showed diminished reaction time adaptation and higher pen-to-target movement velocity under DBS. Reaction time reduction was associated with attenuated functional connectivity between cortical motor areas, basal ganglia, and thalamus. On the other hand, increased movement velocity ON DBS was associated with stronger pallido-thalamic connectivity. These findings suggest that decoupling of a motor cortico-basal ganglia network underlies impaired inhibitory control in PD patients undergoing subthalamic DBS and highlight the concept of functional network modulation through DBS.

Neuroplastic Responses to Chiropractic Care: Broad Impacts on Pain, Mood, Sleep, and Quality of Life

OBJECTIVES

This study aimed to elucidate the mechanisms of chiropractic care using resting electroencephalography (EEG), somatosensory evoked potentials (SEPs), clinical health assessments (Fitbit), and Patient-reported Outcomes Measurement Information System (PROMIS-29).

METHODS

Seventy-six people with chronic low back pain (mean age ± SD: 45 ± 11 years, 33 female) were randomised into control (n = 38) and chiropractic (n = 38) groups. EEG and SEPs were collected pre and post the first intervention and post 4 weeks of intervention. PROMIS-29 was measured pre and post 4 weeks. Fitbit data were recorded continuously.

RESULTS

Spectral analysis of resting EEG showed a significant increase in Theta, Alpha and Beta, and a significant decrease in Delta power in the chiropractic group post intervention. Source localisation revealed a significant increase in Alpha activity within the Default Mode Network (DMN) post intervention and post 4 weeks. A significant decrease in N30 SEP peak amplitude post intervention and post 4 weeks was found in the chiropractic group. Source localisation demonstrated significant changes in Alpha and Beta power within the DMN post-intervention and post 4 weeks. Significant improvements in light sleep stage were observed in the chiropractic group along with enhanced overall quality of life post 4 weeks, including significant reductions in anxiety, depression, fatigue, and pain.

CONCLUSIONS

These findings indicate that many health benefits of chiropractic care are due to altered brain activity.

Investigating Whether a Combination of Electro-Encephalography and Gene Expression Profiling Can Predict the Risk of Chronic Pain: A Protocol for an Observational Prospective Cohort Study

Despite most episodes of low back pain (LBP) being short-lasting, some transition into persistent long-lasting problems. Hence, the need for a deeper understanding of the physiological mechanisms of this is pertinent. Therefore, the aims of the present study are (1) to map pain-induced changes in brain activity and blood gene expression associated with persistent LBP, and (2) to explore whether these brain and gene expression signatures show promise as predictive biomarkers for the development of persistent LBP. The participants will be allocated into three different pain groups (no pain, mild short-lasting, or moderate long-term). One in-person visit, where two blood samples will be collected and sent for RNA sequencing, along with resting 64-channel electro-encephalography measurements before, during, and after a cold pressor test, will be conducted. Thereafter, follow-up questionnaires will be distributed at 2 weeks, 3 months, and 6 months. Recruitment will start during the second quarter of 2024, with expected completion by the last quarter of 2024. The results are expected to provide insight into the relationship between central nervous system activity, gene expression profiles, and LBP. If successful, this study has the potential to provide physiological indicators that are sensitive to the transition from mild, short-term LBP to more problematic, long-term LBP.

Spectrotemporal cues and attention jointly modulate fMRI network topology for sentence and melody perception

Speech and music are two fundamental modes of human communication. Lateralisation of key processes underlying their perception has been related both to the distinct sensitivity to low-level spectrotemporal acoustic features and to top-down attention. However, the interplay between bottom-up and top-down processes needs to be clarified. In the present study, we investigated the contribution of acoustics and attention to melodies or sentences to lateralisation in fMRI functional network topology. We used sung speech stimuli selectively filtered in temporal or spectral modulation domains with crossed and balanced verbal and melodic content. Perception of speech decreased with degradation of temporal information, whereas perception of melodies decreased with spectral degradation. Applying graph theoretical metrics on fMRI connectivity matrices, we found that local clustering, reflecting functional specialisation, linearly increased when spectral or temporal cues crucial for the task goal were incrementally degraded. These effects occurred in a bilateral fronto-temporo-parietal network for processing temporally degraded sentences and in right auditory regions for processing spectrally degraded melodies. In contrast, global topology remained stable across conditions. These findings suggest that lateralisation for speech and music partially depends on an interplay of acoustic cues and task goals under increased attentional demands.

Aberrant functional brain network organization is associated with relapse during 1-year follow-up in alcohol-dependent patients

Alcohol dependence (AD) is a debilitating disease associated with high relapse rates even after long periods of abstinence. Thus, elucidating neurobiological substrates of relapse risk is fundamental for the development of novel targeted interventions that could promote long-lasting abstinence. In the present study, we analysed resting-state functional magnetic resonance imaging (rsfMRI) data from a sample of recently detoxified patients with AD (n = 93) who were followed up for 12 months after rsfMRI assessment. Specifically, we employed graph theoretic analyses to compare functional brain network topology and functional connectivity between future relapsers (REL, n = 59), future abstainers (ABS, n = 28) and age- and gender-matched controls (CON, n = 83). Our results suggest increased whole-brain network segregation, decreased global network integration and overall blunted connectivity strength in REL compared with CON. Conversely, we found evidence for a comparable network architecture in ABS relative to CON. At the nodal level, REL exhibited decreased integration and decoupling between multiple brain systems compared with CON, encompassing regions associated with higher-order executive functions, sensory and reward processing. Among patients with AD, increased coupling between nodes implicated in reward valuation and salience attribution constitutes a particular risk factor for future relapse. Importantly, aberrant network organization in REL was consistently associated with shorter abstinence duration during follow-up, portending to a putative neural signature of relapse risk in AD. Future research should further evaluate the potential diagnostic value of the identified changes in network topology and functional connectivity for relapse prediction at the individual subject level.

Patients with Alzheimer's disease dementia show partially preserved parietal 'hubs' modeled from resting-state alpha electroencephalographic rhythms

Introduction

Graph theory models a network by its nodes (the fundamental unit by which graphs are formed) and connections. 'Degree' hubs reflect node centrality (the connection rate), while 'connector' hubs are those linked to several clusters of nodes (mainly long-range connections).

Methods

Here, we compared hubs modeled from measures of interdependencies of between-electrode resting-state eyes-closed electroencephalography (rsEEG) rhythms in normal elderly (Nold) and Alzheimer's disease dementia (ADD) participants. At least 5 min of rsEEG was recorded and analyzed. As ADD is considered a 'network disease' and is typically associated with abnormal rsEEG delta (<4 Hz) and alpha rhythms (8-12 Hz) over associative posterior areas, we tested the hypothesis of abnormal posterior hubs from measures of interdependencies of rsEEG rhythms from delta to gamma bands (2-40 Hz) using eLORETA bivariate and multivariate-directional techniques in ADD participants versus Nold participants. Three different definitions of 'connector' hub were used.

Results

Convergent results showed that in both the Nold and ADD groups there were significant parietal 'degree' and 'connector' hubs derived from alpha rhythms. These hubs had a prominent outward 'directionality' in the two groups, but that 'directionality' was lower in ADD participants than in Nold participants.

Discussion

In conclusion, independent methodologies and hub definitions suggest that ADD patients may be characterized by low outward 'directionality' of partially preserved parietal 'degree' and 'connector' hubs derived from rsEEG alpha rhythms.

Impact of Tai Chi as an adjunct treatment on brain connectivity in geriatric depression

BACKGROUND

As an adjunct to antidepressant treatment, Tai Chi Chih (TCC) is superior to health education and wellness (HEW) training in improving the general health of patients with geriatric depression (GD). This study investigated the brain connectivity changes associated with TCC and HEW in combination with antidepressant treatment in patients with GD.

METHODS

Forty patients with GD under stable antidepressant treatment underwent TCC training (n = 21) or HEW training (n = 19) for 12 weeks, and completed baseline and 3-month follow-up resting state magnetic resonance imaging scans. Within-group and between-group differences in parcel-to-parcel connectivity changes with intervention were evaluated by general linear modeling. Relationships between significant connectivity changes and symptom/resilience improvement were evaluated by partial least squares correlation analysis.

RESULTS

Significantly greater increases in connectivity with TCC than with HEW (FDR-corrected p < .05) were observed for 167 pairwise connections, most frequently involving the default mode network (DMN). In both groups, increased connectivity involving largely DMN regions was significantly and positively correlated with improvement in symptoms/resilience.

LIMITATIONS

The sample size was relatively small, mainly due to neuroimaging contraindications (e.g., implants). Additionally, the standard antidepressant treatment varied greatly among patients, adding heterogeneity.

CONCLUSIONS

Non-pharmacological adjuncts, such as TCC, may enhance DMN connectivity changes associated with improved depressive symptoms and psychological resilience in the treatment of GD.

Regional Disruption of White Matter Integrity and Network Connectivity Are Related to Cognition

BACKGROUND

Cognitive impairment is common in the elderly population. Exploring patterns of white matter damage at the microstructural level would give important indications for the underlying mechanisms.

OBJECTIVE

To investigate the spatial patterns of white matter microstructure and structural network alternations in relation to different cognition domainsMethods:Participants from the community-based Shunyi Study were included to investigate the association between white matter measurements and cognition cross-sectionally, via both global and local analysis. Cognitive functions were assessed using digit span, trail making test (TMT)-A/B, Fuld object Memory, and 12-Word Philadelphia Verbal Learning Test (PVLT). White matter measurements including fractional anisotropy (FA), mean diffusivity (MD), and structural network parameters were calculated based on diffusion tensor imaging.

RESULTS

Of the 943 participants included, the mean (SD) age was 55.8 (9.1) years, and the mean (SD) education level was 6.7 (3.2) years. We found the whole set of cognitive measurements was related to diffused white matter microstructural integrity damage and lower global efficiency. Poor executive functions (TMTA/B complete time) were related to lower FA and higher MD predominantly on the anterior white matter skeleton, while verbal memory loss (PVLT test scores) was related to sub-network dysconnectivity in the midline and the right temporal lobe.

CONCLUSION

The anterior brain is dominantly involved in executive dysfunction, while midline and right temporal brain disconnection are more prominent in verbal memory loss. Global and regional disruption of white matter integrity and network connectivity is the anatomical basis of the cognitive impairment in the aging population.

Machine learning approaches for parsing comorbidity/heterogeneity in antisociality and substance use disorders: A primer

By some accounts, as many as 93% of individuals diagnosed with antisocial personality disorder (ASPD) or psychopathy also meet criteria for some form of substance use disorder (SUD). This high level of comorbidity, combined with an overlapping biopsychosocial profile, and potentially interacting features, has made it difficult to delineate the shared/unique characteristics of each disorder. Moreover, while rarely acknowledged, both SUD and antisociality exist as highly heterogeneous disorders in need of more targeted parcellation. While emerging data-driven nosology for psychiatric disorders (e.g., Research Domain Criteria (RDoC), Hierarchical Taxonomy of Psychopathology (HiTOP)) offers the opportunity for a more systematic delineation of the externalizing spectrum, the interrogation of large, complex neuroimaging-based datasets may require data-driven approaches that are not yet widely employed in psychiatric neuroscience. With this in mind, the proposed article sets out to provide an introduction into machine learning methods for neuroimaging that can help parse comorbid, heterogeneous externalizing samples. The modest machine learning work conducted to date within the externalizing domain demonstrates the potential utility of the approach but remains highly nascent. Within the paper, we make suggestions for how future work can make use of machine learning methods, in combination with emerging psychiatric nosology systems, to further diagnostic and etiological understandings of the externalizing spectrum. Finally, we briefly consider some challenges that will need to be overcome to encourage further progress in the field.

Electrophysiological Activity and Brain Network During Recovery of Propofol Anesthesia: A Stereoelectroencephalography-Based Analysis in Patients With Intractable Epilepsy—An Exploratory Research

Background: The oscillations and interactions between different brain areas during recovery of consciousness (ROC) from anesthesia in humans are poorly understood. Reliable stereoelectroencephalography (SEEG) signatures for transitions between unconsciousness and consciousness under anesthesia have not yet been fully identified.

Objective: This study was designed to observe the change of electrophysiological activity during ROC and construct a ROC network based on SEEG data to describe the network property of cortical and deep areas during ROC from propofol-induced anesthetic epileptic patients.

Methods: We analyzed SEEG data recorded from sixteen right-handed epileptic patients during ROC from propofol anesthesia from March 1, 2019, to December 31, 2019. Power spectrum density (PSD), correlation, and coherence were used to describe different brain areas' electrophysiological activity. The clustering coefficient, characteristic path length, modularity, network efficiency, degrees, and betweenness centrality were used to describe the network changes during ROC from propofol anesthesia. Statistical analysis was performed using MATLAB 2016b. The power spectral data from different contacts were analyzed using a one-way analysis of variance (ANOVA) test with Tukey's post-hoc correction. One sample t-test was used for the analysis of network property. Kolmogorov-Smirnov test was used to judge data distribution. Non-normal distribution was analyzed using the signed rank-sum test.

Result: From the data of these 16 patients, 10 cortical, and 22 deep positions were observed. In this network, we observed that bilateral occipital areas are essential parts that have strong links with many regions. The recovery process is different in the bilateral cerebral cortex. Stage B (propofol 3.0-2.5 μg/ml) and E (propofol 1.5 μg/ml-ROC) play important roles during ROC exhibiting significant changes. The clustering coefficient gradually decreases with the recovery from anesthesia, and the changes mainly come from the cortical region. The characteristic path length and network efficiency do not change significantly during the recovery from anesthesia, and the changes of network modularity and clustering coefficient are similar. Deep areas tend to form functional modules. The left occipital lobe, the left temporal lobe, bilateral amygdala are essential nodes in the network. Some specific cortical regions (i.e., left angular gyrus, right angular gyrus, right temporal lobe, left temporal lobe, and right angular gyrus) and deep regions (i.e., right amygdala, left cingulate gyrus, right insular lobe, right amygdala) have more significant constraints on other regions.

Conclusion: We verified that the bilateral cortex's recovery process is the opposite, which is not found in the deep regions. Significant PSD changes were observed in many areas at the beginning of stop infusion and near recovery. Our study found that during the ROC process, the modularity and clustering coefficient of the deep area network is significantly improved. However, the changes of the bilateral cerebral cortex were different. Power spectrum analysis shows that low-frequency EEG in anesthesia recovery accounts for a large proportion. The changes of the bilateral brain in the process of anesthesia recovery are different. The clustering coefficient gradually decreased with the recovery from anesthesia, and the changes mainly came from the cortical region. The characteristic path length and network efficiency do not change significantly during the recovery from anesthesia, and the changes of network modularity and clustering coefficient were similar. During ROC, the left occipital lobe, the left temporal lobe, bilateral amygdala were essential nodes in the network. The findings of the current study suggest SEEG as an effective tool for providing direct evidence of the anesthesia recovery mechanism.

The integrated understanding of structural and functional connectomes in depression: A multimodal meta-analysis of graph metrics

BACKGROUND

From the perspective of information processing, an integrated understanding of the structural and functional connectomes in depression patients is important, a multimodal meta-analysis is required to detect the robust alterations in graph metrics across studies.

METHODS

Following a systematic search, 952 depression patients and 1447 controls in nine diffusion magnetic resonance imaging (dMRI) and twelve rest state functional MRI (rs-fMRI) studies with high methodological quality met the inclusion criteria and were included in the meta-analysis.

RESULTS

Regarding the dMRI results, no significant differences of meta-analytic metrics were found; regarding the rs-fMRI results, the modularity and local efficiency were found to be significantly lower in the depression group than in the controls (Hedge's g = -0.330 and -0.349, respectively).

CONCLUSION

Our findings suggested a lower modularity and network efficiency in the rs-fMRI network in depression patients, indicating that the pathological imbalances in brain connectomes needs further exploration.

LIMITATIONS

Included number of trials was low and heterogeneity should be noted.

Dyconnmap: Dynamic connectome mapping-A neuroimaging python module

Despite recent progress in the analysis of neuroimaging data sets, our comprehension of the main mechanisms and principles which govern human brain cognition and function remains incomplete. Network neuroscience makes substantial efforts to manipulate these challenges and provide real answers. For the last decade, researchers have been modelling brain structure and function via a graph or network that comprises brain regions that are either anatomically connected via tracts or functionally via a more extensive repertoire of functional associations. Network neuroscience is a relatively new multidisciplinary scientific avenue of the study of complex systems by pursuing novel ways to analyze, map, store and model the essential elements and their interactions in complex neurobiological systems, particularly the human brain, the most complex system in nature. Due to a rapid expansion of neuroimaging data sets' size and complexity, it is essential to propose and adopt new empirical tools to track dynamic patterns between neurons and brain areas and create comprehensive maps. In recent years, there is a rapid growth of scientific interest in moving functional neuroimaging analysis beyond simplified group or time‐averaged approaches and sophisticated algorithms that can capture the time‐varying properties of functional connectivity. We describe algorithms and network metrics that can capture the dynamic evolution of functional connectivity under this perspective. We adopt the word ‘chronnectome’ (integration of the Greek word ‘Chronos’, which means time, and connectome) to describe this specific branch of network neuroscience that explores how mutually informed brain activity correlates across time and brain space in a functional way. We also describe how good temporal mining of temporally evolved dynamic functional networks could give rise to the detection of specific brain states over which our brain evolved. This characteristic supports our complex human mind. The temporal evolution of these brain states and well‐known network metrics could give rise to new analytic trends. Functional brain networks could also increase the multi‐faced nature of the dynamic networks revealing complementary information. Finally, we describe a python module (https://github.com/makism/dyconnmap) which accompanies this article and contains a collection of dynamic complex network analytics and measures and demonstrates its great promise for the study of a healthy subject's repeated fMRI scans.

Brain Connectivity Studies on Structure-Function Relationships: A Short Survey with an Emphasis on Machine Learning

This short survey reviews the recent literature on the relationship between the brain structure and its functional dynamics. Imaging techniques such as diffusion tensor imaging (DTI) make it possible to reconstruct axonal fiber tracks and describe the structural connectivity (SC) between brain regions. By measuring fluctuations in neuronal activity, functional magnetic resonance imaging (fMRI) provides insights into the dynamics within this structural network. One key for a better understanding of brain mechanisms is to investigate how these fast dynamics emerge on a relatively stable structural backbone. So far, computational simulations and methods from graph theory have been mainly used for modeling this relationship. Machine learning techniques have already been established in neuroimaging for identifying functionally independent brain networks and classifying pathological brain states. This survey focuses on methods from machine learning, which contribute to our understanding of functional interactions between brain regions and their relation to the underlying anatomical substrate.

Linking Brain Biology to Intellectual Endowment: A Review on the Associations of Human Intelligence With Neuroimaging Data

Human intelligence has always been a fascinating subject for scientists. Since the inception of Spearman's general intelligence in the early 1900s, there has been significant progress towards characterizing different aspects of intelligence and its relationship with structural and functional features of the brain. In recent years, the invention of sophisticated brain imaging devices using Diffusion-Weighted Imaging (DWI) and functional Magnetic Resonance Imaging (fMRI) has allowed researchers to test hypotheses about neural correlates of intelligence in humans.This review summarizes recent findings on the associations of human intelligence with neuroimaging data. To this end, first, we review the literature that has related brain morphometry to intelligence. Next, we elaborate on the applications of DWI and restingstate fMRI on the investigation of intelligence. Then, we provide a survey of literature that has used multimodal DWI-fMRI to shed light on intelligence. Finally, we discuss the state-of-the-art of individualized prediction of intelligence from neuroimaging data and point out future strategies. Future studies hold promising outcomes for machine learning-based predictive frameworks using neuroimaging features to estimate human intelligence.

A Tensor-Based Framework for rs-fMRI Classification and Functional Connectivity Construction

Recently, machine learning methods have gained lots of attention from researchers seeking to analyze brain images such as Resting-State Functional Magnetic Resonance Imaging (rs-fMRI) to obtain a deeper understanding of the brain and such related diseases, for example, Alzheimer's disease. Finding the common patterns caused by a brain disorder through analysis of the functional connectivity (FC) network along with discriminating brain diseases from normal controls have long been the two principal goals in studying rs-fMRI data. The majority of FC extraction methods calculate the FC matrix for each subject and then use simple techniques to combine them and obtain a general FC matrix. In addition, the state-of-the-art classification techniques for finding subjects with brain disorders also rely on calculating an FC for each subject, vectorizing, and feeding them to the classifier. Considering these problems and based on multi-dimensional nature of the data, we have come up with a novel tensor framework in which a general FC matrix is obtained without the need to construct an FC matrix for each sample. This framework also allows us to reduce the dimensionality and create a novel discriminant function that rather than using FCs works directly with each sample, avoids vectorization in any step, and uses the test data in the training process without forcing any prior knowledge of its label into the classifier. Extensive experiments using the ADNI dataset demonstrate that our proposed framework effectively boosts the fMRI classification performance and reveals novel connectivity patterns in Alzheimer's disease at its early stages.

BrainNET: Inference of Brain Network Topology Using Machine Learning

Background: To develop a new functional magnetic resonance image (fMRI) network inference method, BrainNET, that utilizes an efficient machine learning algorithm to quantify contributions of various regions of interests (ROIs) in the brain to a specific ROI. Methods: BrainNET is based on extremely randomized trees to estimate network topology from fMRI data and modified to generate an adjacency matrix representing brain network topology, without reliance on arbitrary thresholds. Open-source simulated fMRI data of 50 subjects in 28 different simulations under various confounding conditions with known ground truth were used to validate the method. Performance was compared with correlation and partial correlation (PC). The real-world performance was then evaluated in a publicly available attention-deficit/hyperactivity disorder (ADHD) data set, including 134 typically developing children (mean age: 12.03, males: 83), 75 ADHD inattentive (mean age: 11.46, males: 56), and 93 ADHD combined (mean age: 11.86, males: 77) subjects. Network topologies in ADHD were inferred using BrainNET, correlation, and PC. Graph metrics were extracted to determine differences between the ADHD groups. Results: BrainNET demonstrated excellent performance across all simulations and varying confounders in identifying the true presence of connections. In the ADHD data set, BrainNET was able to identify significant changes (p < 0.05) in graph metrics between groups. No significant changes in graph metrics between ADHD groups were identified using correlation and PC. Conclusion: We describe BrainNET, a new network inference method to estimate fMRI connectivity that was adapted from gene regulatory methods. BrainNET out-performed Pearson correlation and PC in fMRI simulation data and real-world ADHD data. BrainNET can be used independently or combined with other existing methods as a useful tool to understand network changes and to determine the true network topology of the brain under various conditions and disease states. Impact statement Developed a new functional magnetic resonance image (fMRI) network inference method named as BrainNET using machine learning. BrainNET out-performed Pearson correlation and partial correlation in fMRI simulation data and real-world attention-deficit/hyperactivity disorder data. BrainNET does not need to be pretrained and can be applied to infer fMRI network topology independently on individual subjects and for varying number of nodes.

A toolbox for brain network construction and classification (BrainNetClass)

Brain functional network has been increasingly used in understanding brain functions and diseases. While many network construction methods have been proposed, the progress in the field still largely relies on static pairwise Pearson's correlation-based functional network and group-level comparisons. We introduce a "Brain Network Construction and Classification (BrainNetClass)" toolbox to promote more advanced brain network construction methods to the filed, including some state-of-the-art methods that were recently developed to capture complex and high-order interactions among brain regions. The toolbox also integrates a well-accepted and rigorous classification framework based on brain connectome features toward individualized disease diagnosis in a hope that the advanced network modeling could boost the subsequent classification. BrainNetClass is a MATLAB-based, open-source, cross-platform toolbox with both graphical user-friendly interfaces and a command line mode targeting cognitive neuroscientists and clinicians for promoting reliability, reproducibility, and interpretability of connectome-based, computer-aided diagnosis. It generates abundant classification-related results from network presentations to contributing features that have been largely ignored by most studies to grant users the ability of evaluating the disease diagnostic model and its robustness and generalizability. We demonstrate the effectiveness of the toolbox on real resting-state functional MRI datasets. BrainNetClass (v1.0) is available at https://github.com/zzstefan/BrainNetClass.

Kernel Granger Causality Based on Back Propagation Neural Network Fuzzy Inference System on fMRI Data

Granger causality (GC) is one of the most popular measures to investigate causality influence among brain regions and has been achieved significant results for exploring brain networks based on functional magnetic resonance imaging (fMRI). However, the predictors and order selection of conventional GC are based on linear models which result in such restrictions as poorly detection of nonlinearity and so on, in the application. This paper proposes a novel GC model called back propagation (BP) based kernel function Granger causality (BP_KFGC), in which symplectic geometry is used for embedding dimension and fuzzy inference system for predicting time series. The proposed method doesn't depend on the prediction of the vector auto-regression model, so that time series don't need to be wide-sense stationary as linear GC and kernel GC. In addition, it is a multivariate approach which is applicable to both linear and nonlinear systems and eliminates the effects of latent variables. The performance of the new method is evaluated and compared with linear GC, partial GC, neural network GC and kernel GC by simulated data with multiple adjustments to the nonlinearity. The results show that BP_KFGC outperforms the other four methods in detecting both linear and nonlinear causalities. Furthermore, we applied BP_KFGC to construct directed weight network (DWN) of Alzheimer's disease (AD) patients and health controls (HCs), and then nine graph-based features of DWN were used for classification by the classifier of support vector machine with radial basis kernel function. The accuracy of 95.89%, sensitivity of 93.31%, and specificity of 94.97% were achieved which may provide an auxiliary mean for the clinical diagnosis of AD.

Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review

Background: Analysis of the human connectome using functional magnetic resonance imaging (fMRI) started in the mid-1990s and attracted increasing attention in attempts to discover the neural underpinnings of human cognition and neurological disorders. In general, brain connectivity patterns from fMRI data are classified as statistical dependencies (functional connectivity) or causal interactions (effective connectivity) among various neural units. Computational methods, especially graph theory-based methods, have recently played a significant role in understanding brain connectivity architecture. Objectives: Thanks to the emergence of graph theoretical analysis, the main purpose of the current paper is to systematically review how brain properties can emerge through the interactions of distinct neuronal units in various cognitive and neurological applications using fMRI. Moreover, this article provides an overview of the existing functional and effective connectivity methods used to construct the brain network, along with their advantages and pitfalls. Methods: In this systematic review, the databases Science Direct, Scopus, arXiv, Google Scholar, IEEE Xplore, PsycINFO, PubMed, and SpringerLink are employed for exploring the evolution of computational methods in human brain connectivity from 1990 to the present, focusing on graph theory. The Cochrane Collaboration's tool was used to assess the risk of bias in individual studies. Results: Our results show that graph theory and its implications in cognitive neuroscience have attracted the attention of researchers since 2009 (as the Human Connectome Project launched), because of their prominent capability in characterizing the behavior of complex brain systems. Although graph theoretical approach can be generally applied to either functional or effective connectivity patterns during rest or task performance, to date, most articles have focused on the resting-state functional connectivity. Conclusions: This review provides an insight into how to utilize graph theoretical measures to make neurobiological inferences regarding the mechanisms underlying human cognition and behavior as well as different brain disorders.

Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review

Background: Analysis of the human connectome using functional magnetic resonance imaging (fMRI) started in the mid-1990s and attracted increasing attention in attempts to discover the neural underpinnings of human cognition and neurological disorders. In general, brain connectivity patterns from fMRI data are classified as statistical dependencies (functional connectivity) or causal interactions (effective connectivity) among various neural units. Computational methods, especially graph theory-based methods, have recently played a significant role in understanding brain connectivity architecture. Objectives: Thanks to the emergence of graph theoretical analysis, the main purpose of the current paper is to systematically review how brain properties can emerge through the interactions of distinct neuronal units in various cognitive and neurological applications using fMRI. Moreover, this article provides an overview of the existing functional and effective connectivity methods used to construct the brain network, along with their advantages and pitfalls. Methods: In this systematic review, the databases Science Direct, Scopus, arXiv, Google Scholar, IEEE Xplore, PsycINFO, PubMed, and SpringerLink are employed for exploring the evolution of computational methods in human brain connectivity from 1990 to the present, focusing on graph theory. The Cochrane Collaboration's tool was used to assess the risk of bias in individual studies. Results: Our results show that graph theory and its implications in cognitive neuroscience have attracted the attention of researchers since 2009 (as the Human Connectome Project launched), because of their prominent capability in characterizing the behavior of complex brain systems. Although graph theoretical approach can be generally applied to either functional or effective connectivity patterns during rest or task performance, to date, most articles have focused on the resting-state functional connectivity. Conclusions: This review provides an insight into how to utilize graph theoretical measures to make neurobiological inferences regarding the mechanisms underlying human cognition and behavior as well as different brain disorders.