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

Topological Properties of the Structural Brain Network in Autism via ϵ-Neighbor Method

OBJECTIVE

Topological characteristics of the brain can be analyzed using structural brain networks constructed by diffusion tensor imaging (DTI). When a brain network is constructed by the existing parcellation method, the structure of the network changes depending on the scale of parcellation and arbitrary thresholding. To overcome these issues, we propose to construct brain networks using the improved $\varepsilon $-neighbor construction, which is a parcellation free network construction technique.

METHODS

We acquired DTI from 14 control subjects and 15 subjects with autism. We examined the differences in topological properties of the brain networks constructed using the proposed method and the existing parcellation between the two groups.

RESULTS

As the number of nodes increased, the connectedness of the network decreased in the parcellation method. However, for brain networks constructed using the proposed method, connectedness remained at a high level even with an increase in the number of nodes. We found significant differences in several topological properties of brain networks constructed using the proposed method, whereas topological properties were not significantly different for the parcellation method.

CONCLUSION

The brain networks constructed using the proposed method are considered as more realistic than a parcellation method with respect to the stability of connectedness. We found that subjects with autism showed the abnormal characteristics in the brain networks. These results demonstrate that the proposed method may provide new insights to analysis in the structural brain network.

SIGNIFICANCE

We proposed the novel brain network construction method to overcome the shortcoming in the existing parcellation method.

Mining EEG with SVM for Understanding Cognitive Underpinnings of Math Problem Solving Strategies

We have developed a new methodology for examining and extracting patterns from brain electric activity by using data mining and machine learning techniques. Data was collected from experiments focused on the study of cognitive processes that might evoke different specific strategies in the resolution of math problems. A binary classification problem was constructed using correlations and phase synchronization between different electroencephalographic channels as characteristics and, as labels or classes, the math performances of individuals participating in specially designed experiments. The proposed methodology is based on using well-established procedures of feature selection, which were used to determine a suitable brain functional network size related to math problem solving strategies and also to discover the most relevant links in this network without including noisy connections or excluding significant connections.

Diffusion Tensor Imaging Tractography Reveals Disrupted White Matter Structural Connectivity Network in Healthy Adults with Insomnia Symptoms

Neuroimaging studies have revealed that insomnia is characterized by aberrant neuronal connectivity in specific brain regions, but the topological disruptions in the white matter (WM) structural connectivity networks remain largely unknown in insomnia. The current study uses diffusion tensor imaging (DTI) tractography to construct the WM structural networks and graph theory analysis to detect alterations of the brain structural networks. The study participants comprised 30 healthy subjects with insomnia symptoms (IS) and 62 healthy subjects without IS. Both the two groups showed small-world properties regarding their WM structural connectivity networks. By contrast, increased local efficiency and decreased global efficiency were identified in the IS group, indicating an insomnia-related shift in topology away from regular networks. In addition, the IS group exhibited disrupted nodal topological characteristics in regions involving the fronto-limbic and the default-mode systems. To our knowledge, this is the first study to explore the topological organization of WM structural network connectivity in insomnia. More importantly, the dysfunctions of large-scale brain systems including the fronto-limbic pathways, salience network and default-mode network in insomnia were identified, which provides new insights into the insomnia connectome. Topology-based brain network analysis thus could be a potential biomarker for IS.

Linking functional connectivity and dynamic properties of resting-state networks

Spontaneous brain activity is organized into resting-state networks (RSNs) involved in internally-guided, higher-order mental functions (default mode, central executive and salience networks) and externally-driven, specialized sensory and motor processing (auditory, visual and sensorimotor networks). RSNs are characterized by their functional connectivity in terms of within-network cohesion and between-network integration, and by their dynamic properties in terms of synchrony and metastability. We examined the relationship between functional connectivity and dynamic network features using fMRI data and an anatomically constrained Kuramoto model. Extrapolating from simulated data, synchrony and metastability across the RSNs emerged at coupling strengths of 5 ≤ k ≤ 12. In the empirical RSNs, higher metastability and synchrony were respectively associated with greater cohesion and lower integration. Consistent with their dual role in supporting both sustained and diverse mental operations, higher-order RSNs had lower metastability and synchrony. Sensory and motor RSNs showed greater cohesion and metastability, likely to respectively reflect their functional specialization and their greater capacity for altering network states in response to multiple and diverse external demands. Our findings suggest that functional and dynamic RSN properties are closely linked and expand our understanding of the neural architectures that support optimal brain function.

Mapping Language Networks Using the Structural and Dynamic Brain Connectomes

Lesion-symptom mapping is often employed to define brain structures that are crucial for human behavior. Even though poststroke deficits result from gray matter damage as well as secondary white matter loss, the impact of structural disconnection is overlooked by conventional lesion-symptom mapping because it does not measure loss of connectivity beyond the stroke lesion. This study describes how traditional lesion mapping can be combined with structural connectome lesion symptom mapping (CLSM) and connectome dynamics lesion symptom mapping (CDLSM) to relate residual white matter networks to behavior. Using data from a large cohort of stroke survivors with aphasia, we observed improved prediction of aphasia severity when traditional lesion symptom mapping was combined with CLSM and CDLSM. Moreover, only CLSM and CDLSM disclosed the importance of temporal-parietal junction connections in aphasia severity. In summary, connectome measures can uniquely reveal brain networks that are necessary for function, improving the traditional lesion symptom mapping approach.

Development of large-scale functional networks from birth to adulthood: A guide to the neuroimaging literature

The development of human cognition results from the emergence of coordinated activity between distant brain areas. Network science, combined with non-invasive functional imaging, has generated unprecedented insights regarding the adult brain's functional organization, and promises to help elucidate the development of functional architectures supporting complex behavior. Here we review what is known about functional network development from birth until adulthood, particularly as understood through the use of resting-state functional connectivity MRI (rs-fcMRI). We attempt to synthesize rs-fcMRI findings with other functional imaging techniques, with macro-scale structural connectivity, and with knowledge regarding the development of micro-scale structure. We highlight a number of outstanding conceptual and technical barriers that need to be addressed, as well as previous developmental findings that may need to be revisited. Finally, we discuss key areas ripe for future research in order to (1) better characterize normative developmental trajectories, (2) link these trajectories to biologic mechanistic events, as well as component behaviors and (3) better understand the clinical implications and pathophysiological basis of aberrant network development.

Brain network connectivity differs in early-onset neurodegenerative dementia

OBJECTIVE

To investigate functional brain network architecture in early-onset Alzheimer disease (EOAD) and behavioral variant frontotemporal dementia (bvFTD).

METHODS

Thirty-eight patients with bvFTD, 37 patients with EOAD, and 32 age-matched healthy controls underwent 3D T1-weighted and resting-state fMRI. Graph analysis and connectomics assessed global and local functional topologic network properties, regional functional connectivity, and intrahemispheric and interhemispheric between-lobe connectivity.

RESULTS

Despite similarly extensive cognitive impairment relative to controls, patients with EOAD showed severe global functional network alterations (lower mean nodal strength, local efficiency, clustering coefficient, and longer path length), while patients with bvFTD showed relatively preserved global functional brain architecture. Patients with bvFTD demonstrated reduced nodal strength in the frontoinsular lobe and a relatively focal altered functional connectivity of frontoinsular and temporal regions. Functional connectivity breakdown in the posterior brain nodes, particularly in the parietal lobe, differentiated patients with EOAD from those with bvFTD. While EOAD was associated with widespread loss of both intrahemispheric and interhemispheric functional correlations, bvFTD showed a preferential disruption of the intrahemispheric connectivity.

CONCLUSIONS

Disease-specific patterns of functional network topology and connectivity alterations were observed in patients with EOAD and bvFTD. Graph analysis and connectomics may aid clinical diagnosis and help elucidate pathophysiologic differences between neurodegenerative dementias.

A Single Session of rTMS Enhances Small-Worldness in Writer's Cramp: Evidence from Simultaneous EEG-fMRI Multi-Modal Brain Graph

Background and Purpose: Repetitive transcranial magnetic stimulation (rTMS) induces widespread changes in brain connectivity. As the network topology differences induced by a single session of rTMS are less known we undertook this study to ascertain whether the network alterations had a small-world morphology using multi-modal graph theory analysis of simultaneous EEG-fMRI.

Method: Simultaneous EEG-fMRI was acquired in duplicate before (R1) and after (R2) a single session of rTMS in 14 patients with Writer’s Cramp (WC). Whole brain neuronal and hemodynamic network connectivity were explored using the graph theory measures and clustering coefficient, path length and small-world index were calculated for EEG and resting state fMRI (rsfMRI). Multi-modal graph theory analysis was used to evaluate the correlation of EEG and fMRI clustering coefficients.

Result: A single session of rTMS was found to increase the clustering coefficient and small-worldness significantly in both EEG and fMRI (p < 0.05). Multi-modal graph theory analysis revealed significant modulations in the fronto-parietal regions immediately after rTMS. The rsfMRI revealed additional modulations in several deep brain regions including cerebellum, insula and medial frontal lobe.

Conclusion: Multi-modal graph theory analysis of simultaneous EEG-fMRI can supplement motor physiology methods in understanding the neurobiology of rTMS in vivo. Coinciding evidence from EEG and rsfMRI reports small-world morphology for the acute phase network hyper-connectivity indicating changes ensuing low-frequency rTMS is probably not “noise”.

Weight Rich-Club Analysis in the White Matter Network of Late-Life Depression with Memory Deficits

Patients with late-life depression (LLD) have a higher incident of developing dementia, especially individuals with memory deficits. However, little is known about the white matter characteristics of LLD with memory deficits (LLD-MD) in the human connectome, especially for the rich-club coefficient, which is an indicator that describes the organization pattern of hub in the network. To address this question, diffusion tensor imaging of 69 participants [15 LLD-MD patients; 24 patients with LLD with intact memory (LLD-IM); and 30 healthy controls (HC)] was applied to construct a brain network for each individual. A full-scale battery of neuropsychological tests were used for grouping, and evaluating executive function, processing speed and memory. Rich-club analysis and global network properties were utilized to describe the topological features in each group. Network-based statistics (NBS) were calculated to identify the impaired subnetwork in the LLD-MD group relative to that in the LLD-IM group. We found that compared with HC participants, patients with LLD (LLD-MD and LLD-IM) had relatively impaired rich-club organizations and rich-club connectivity. In addition, LLD-MD group exhibited lower feeder and local connective average strength than LLD-IM group. Furthermore, global network properties, such as the shortest path length, connective strength, efficiency and fault tolerant efficiency, were significantly decreased in the LLD-MD group relative to those in the LLD-IM and HC groups. According to NBS analysis, a subnetwork, including right cognitive control network (CCN) and corticostriatal circuits, were disrupted in LLD-MD patients. In conclusion, the disease effects of LLD were prevalent in rich-club organization. Feeder and local connections, especially in the subnetwork including right CCN and corticostriatal circuits, were further impaired in those with memory deficits. Global network properties were disrupted in LLD-MD patients relative to those in LLD-IM patients.

Altered brain network measures in patients with primary writing tremor

PURPOSE

Primary writing tremor (PWT) is a rare task-specific tremor, which occurs only while writing or while adopting the hand in the writing position. The basic pathophysiology of PWT has not been fully understood. The objective of this study is to explore the alterations in the resting state functional brain connectivity, if any, in patients with PWT using graph theory-based analysis.

METHODS

This prospective case-control study included 10 patients with PWT and 10 age and gender matched healthy controls. All subjects underwent MRI in a 3-Tesla scanner. Several parameters of small-world functional connectivity were compared between patients and healthy controls by using graph theory-based analysis.

RESULTS

There were no significant differences in age, handedness (all right handed), gender distribution (all were males), and MMSE scores between the patients and controls. The mean age at presentation of tremor in the patient group was 51.7 ± 8.6 years, and the mean duration of tremor was 3.5 ± 1.9 years. Graph theory-based analysis revealed that patients with PWT had significantly lower clustering coefficient and higher path length compared to healthy controls suggesting alterations in small-world architecture of the brain. The clustering coefficients were lower in PWT patients in left and right medial cerebellum, right dorsolateral prefrontal cortex (DLPFC), and left posterior parietal cortex (PPC).

CONCLUSION

Patients with PWT have significantly altered small-world brain connectivity in bilateral medial cerebellum, right DLPFC, and left PPC. Further studies with larger sample size are required to confirm our results.

Computational approaches to fMRI analysis

Analysis methods in cognitive neuroscience have not always matched the richness of fMRI data. Early methods focused on estimating neural activity within individual voxels or regions, averaged over trials or blocks and modeled separately in each participant. This approach mostly neglected the distributed nature of neural representations over voxels, the continuous dynamics of neural activity during tasks, the statistical benefits of performing joint inference over multiple participants and the value of using predictive models to constrain analysis. Several recent exploratory and theory-driven methods have begun to pursue these opportunities. These methods highlight the importance of computational techniques in fMRI analysis, especially machine learning, algorithmic optimization and parallel computing. Adoption of these techniques is enabling a new generation of experiments and analyses that could transform our understanding of some of the most complex-and distinctly human-signals in the brain: acts of cognition such as thoughts, intentions and memories.

Identifying current and remitted major depressive disorder with the Hurst exponent: a comparative study on two automated anatomical labeling atlases

Major depressive disorder (MDD) is a leading world-wide psychiatric disorder with high recurrence rate, therefore, it is desirable to identify current MDD (cMDD) and remitted MDD (rMDD) for their appropriate therapeutic interventions. In the study, 19 cMDD, 19 rMDD and 19 well-matched healthy controls (HC) were enrolled and scanned with the resting-state functional magnetic resonance imaging (rs-fMRI). The Hurst exponent (HE) of rs-fMRI in AAL-90 and AAL-1024 atlases were calculated and compared between groups. Then, a radial basis function (RBF) based support vector machine was proposed to identify every pair of the cMDD, rMDD and HC groups using the abnormal HE features, and a leave-one-out cross-validation was used to evaluate the classification performance. Applying the proposed method with AAL-1024 and AAL-90 atlas respectively, 87% and 84% subjects were correctly identified between cMDD and HC, 84% and 71% between rMDD and HC, and 89% and 74% between cMDD and rMDD. Our results indicated that the HE was an effective feature to distinguish cMDD and rMDD from HC, and the recognition performances with AAL-1024 parcellation were better than that with the conventional AAL-90 parcellation.

Structural and functional, empirical and modeled connectivity in the cerebral cortex of the rat

Connectomics data from animal models provide an invaluable opportunity to reveal the complex interplay between structure and function in the mammalian brain. In this work, we investigate the relationship between structural and functional connectivity in the rat brain cortex using a directed anatomical network generated from a carefully curated meta-analysis of published tracing data, along with resting-state functional MRI data obtained from a group of 14 anesthetized Wistar rats. We found a high correspondence between the strength of functional connections, measured as blood oxygen level dependent (BOLD) signal correlations between cortical regions, and the weight of the corresponding anatomical links in the connectome graph (maximum Spearman rank-order correlation ρ=0.48). At the network-level, regions belonging to the same functionally defined community tend to form more mutual weighted connections between each other compared to regions located in different communities. We further found that functional communities in resting-state networks are enriched in densely connected anatomical motifs. Importantly, these higher-order structural subgraphs cannot be explained by lower-order topological properties, suggesting that dense structural patterns support functional associations in the resting brain. Simulations of brain-wide resting-state activity based on neural mass models implemented on the empirical rat anatomical connectome demonstrated high correlation between the simulated and the measured functional connectivity (maximum Pearson correlation ρ=0.53), further suggesting that the topology of structural connections plays an important role in shaping functional cortical networks.

Pseudo-Bootstrap Network Analysis-an Application in Functional Connectivity Fingerprinting

Brain parcellation divides the brain's spatial domain into small regions, which are represented by nodes within the network analysis framework. While template-based parcellations are widely used, the parcels on the template do not necessarily match individual's functional nodes. A new method is developed to overcome the inconsistent network analysis results by by-passing the difficulties of parcellating the brain into functionally meaningful areas. First, roughly equal-sized parcellations are obtained. Second, these random parcellations are applied to individual subjects multiple times and a pseudo-bootstrap (PBS) of the network is obtained for statistical inferences. It was found that the variation of mean global network metrics from PBS sampling is smaller compared with inter-subject variation or within-subject variation between two diffusion MRI scans. Using the mean global network metrics from PBS sampling, the intra-class correlation is always higher than the average obtained from using a single random parcellation. As one application, the PBS method was tested on the Human Connectome Project resting state dataset to identify individuals across scan sessions based on the mean functional connectivity (FC)-a trivial network property that has little information about the connectivity between nodes. An accuracy rate of ∼90% was achieved by simply finding the maximum correlation of mean FC of PBS samples between two scan sessions.

Organization and hierarchy of the human functional brain network lead to a chain-like core

The brain is a paradigmatic example of a complex system: its functionality emerges as a global property of local mesoscopic and microscopic interactions. Complex network theory allows to elicit the functional architecture of the brain in terms of links (correlations) between nodes (grey matter regions) and to extract information out of the noise. Here we present the analysis of functional magnetic resonance imaging data from forty healthy humans at rest for the investigation of the basal scaffold of the functional brain network organization. We show how brain regions tend to coordinate by forming a highly hierarchical chain-like structure of homogeneously clustered anatomical areas. A maximum spanning tree approach revealed the centrality of the occipital cortex and the peculiar aggregation of cerebellar regions to form a closed core. We also report the hierarchy of network segregation and the level of clusters integration as a function of the connectivity strength between brain regions.

Gender differences in the structural connectome of the teenage brain revealed by generalized q-sampling MRI

The question of whether there are biological differences between male and female brains is a fraught one, and political positions and prior expectations seem to have a strong influence on the interpretation of scientific data in this field. This question is relevant to issues of gender differences in the prevalence of psychiatric conditions, including autism, attention deficit hyperactivity disorder (ADHD), Tourette's syndrome, schizophrenia, dyslexia, depression, and eating disorders. Understanding how gender influences vulnerability to these conditions is significant. Diffusion magnetic resonance imaging (dMRI) provides a non-invasive method to investigate brain microstructure and the integrity of anatomical connectivity. Generalized q-sampling imaging (GQI) has been proposed to characterize complicated fiber patterns and distinguish fiber orientations, providing an opportunity for more accurate, higher-order descriptions through the water diffusion process. Therefore, we aimed to investigate differences in the brain's structural network between teenage males and females using GQI. This study included 59 (i.e., 33 males and 26 females) age- and education-matched subjects (age range: 13 to 14 years). The structural connectome was obtained by graph theoretical and network-based statistical (NBS) analyses. Our findings show that teenage male brains exhibit better intrahemispheric communication, and teenage female brains exhibit better interhemispheric communication. Our results also suggest that the network organization of teenage male brains is more local, more segregated, and more similar to small-world networks than teenage female brains. We conclude that the use of an MRI study with a GQI-based structural connectomic approach like ours presents novel insights into network-based systems of the brain and provides a new piece of the puzzle regarding gender differences.

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The GQI-based structural connectomic study provides a new piece of the puzzle regarding gender differences.

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Male brains exhibit better intrahemispheric communication, and female exhibit better interhemispheric communication.

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The network organization of teenage male brains is more local and more segregated than teenage female brains.

Tackling variability: A multicenter study to provide a gold-standard network approach for frontotemporal dementia

Biomarkers represent a critical research area in neurodegeneration disease as they can contribute to studying potential disease-modifying agents, fostering timely therapeutic interventions, and alleviating associated financial costs. Functional connectivity (FC) analysis represents a promising approach to identify early biomarkers in specific diseases. Yet, virtually no study has tested whether potential FC biomarkers prove to be reliable and reproducible across different centers. As such, their implementation remains uncertain due to multiple sources of variability across studies: the numerous international centers capable conducting FC research vary in their scanning equipment and their samples' socio-cultural background, and, more troublingly still, no gold-standard method exists to analyze FC. In this unprecedented study, we aim to address both issues by performing the first multicenter FC research in the behavioral-variant frontotemporal dementia (bvFTD), and by assessing multiple FC approaches to propose a gold-standard method for analysis. We enrolled 52 bvFTD patients and 60 controls from three international clinics (with different fMRI recording parameters), and three additional neurological patient groups. To evaluate FC, we focused on seed analysis, inter-regional connectivity, and several graph-theory approaches. Only graph-theory analysis, based on weighted-matrices, yielded consistent differences between bvFTD and controls across centers. Also, graph metrics robustly discriminated bvFTD from the other neurological conditions. The consistency of our findings across heterogeneous contexts highlights graph-theory as a potential gold-standard approach for brain network analysis in bvFTD. Hum Brain Mapp 38:3804-3822, 2017. © 2017 Wiley Periodicals, Inc.

Disrupted Structural and Functional Networks and Their Correlation with Alertness in Right Temporal Lobe Epilepsy: A Graph Theory Study

Previous studies have shown that temporal lobe epilepsy (TLE) involves abnormal structural or functional connectivity in specific brain areas. However, limited comprehensive studies have been conducted on TLE associated changes in the topological organization of structural and functional networks. Additionally, epilepsy is associated with impairment in alertness, a fundamental component of attention. In this study, structural networks were constructed using diffusion tensor imaging tractography, and functional networks were obtained from resting-state functional MRI temporal series correlations in 20 right temporal lobe epilepsy (rTLE) patients and 19 healthy controls. Global network properties were computed by graph theoretical analysis, and correlations were assessed between global network properties and alertness. The results from these analyses showed that rTLE patients exhibit abnormal small-world attributes in structural and functional networks. Structural networks shifted toward more regular attributes, but functional networks trended toward more random attributes. After controlling for the influence of the disease duration, negative correlations were found between alertness, small-worldness, and the cluster coefficient. However, alertness did not correlate with either the characteristic path length or global efficiency in rTLE patients. Our findings show that disruptions of the topological construction of brain structural and functional networks as well as small-world property bias are associated with deficits in alertness in rTLE patients. These data suggest that reorganization of brain networks develops as a mechanism to compensate for altered structural and functional brain function during disease progression.

Transition of the functional brain network related to increasing cognitive demands

Network neuroscience provides tools that can easily be used to verify main assumptions of the global workspace theory (GWT), such as the existence of highly segregated information processing during effortless tasks performance, engagement of multiple distributed networks during effortful tasks and the critical role of long-range connections in workspace formation. A number of studies support the assumptions of GWT by showing the reorganization of the whole-brain functional network during cognitive task performance; however, the involvement of specific large scale networks in the formation of workspace is still not well-understood. The aims of our study were: (1) to examine changes in the whole-brain functional network under increased cognitive demands of working memory during an n-back task, and their relationship with behavioral outcomes; and (2) to provide a comprehensive description of local changes that may be involved in the formation of the global workspace, using hub detection and network-based statistic. Our results show that network modularity decreased with increasing cognitive demands, and this change allowed us to predict behavioral performance. The number of connector hubs increased, whereas the number of provincial hubs decreased when the task became more demanding. We also found that the default mode network (DMN) increased its connectivity to other networks while decreasing connectivity between its own regions. These results, apart from replicating previous findings, provide a valuable insight into the mechanisms of the formation of the global workspace, highlighting the role of the DMN in the processes of network integration. Hum Brain Mapp 38:3659-3674, 2017. © 2017 Wiley Periodicals, Inc.

Identifying topological motif patterns of human brain functional networks

Recent imaging connectome studies demonstrated that the human functional brain network follows an efficient small-world topology with cohesive functional modules and highly connected hubs. However, the functional motif patterns that represent the underlying information flow remain largely unknown. Here, we investigated motif patterns within directed human functional brain networks, which were derived from resting-state functional magnetic resonance imaging data with controlled confounding hemodynamic latencies. We found several significantly recurring motifs within the network, including the two-node reciprocal motif and five classes of three-node motifs. These recurring motifs were distributed in distinct patterns to support intra- and inter-module functional connectivity, which also promoted integration and segregation in network organization. Moreover, the significant participation of several functional hubs in the recurring motifs exhibited their critical role in global integration. Collectively, our findings highlight the basic architecture governing brain network organization and provide insight into the information flow mechanism underlying intrinsic brain activities. Hum Brain Mapp 38:2734-2750, 2017. © 2017 Wiley Periodicals, Inc.

Predicting individual brain functional connectivity using a Bayesian hierarchical model

Network-oriented analysis of functional magnetic resonance imaging (fMRI), especially resting-state fMRI, has revealed important association between abnormal connectivity and brain disorders such as schizophrenia, major depression and Alzheimer's disease. Imaging-based brain connectivity measures have become a useful tool for investigating the pathophysiology, progression and treatment response of psychiatric disorders and neurodegenerative diseases. Recent studies have started to explore the possibility of using functional neuroimaging to help predict disease progression and guide treatment selection for individual patients. These studies provide the impetus to develop statistical methodology that would help provide predictive information on disease progression-related or treatment-related changes in neural connectivity. To this end, we propose a prediction method based on Bayesian hierarchical model that uses individual's baseline fMRI scans, coupled with relevant subject characteristics, to predict the individual's future functional connectivity. A key advantage of the proposed method is that it can improve the accuracy of individualized prediction of connectivity by combining information from both group-level connectivity patterns that are common to subjects with similar characteristics as well as individual-level connectivity features that are particular to the specific subject. Furthermore, our method also offers statistical inference tools such as predictive intervals that help quantify the uncertainty or variability of the predicted outcomes. The proposed prediction method could be a useful approach to predict the changes in individual patient's brain connectivity with the progression of a disease. It can also be used to predict a patient's post-treatment brain connectivity after a specified treatment regimen. Another utility of the proposed method is that it can be applied to test-retest imaging data to develop a more reliable estimator for individual functional connectivity. We show there exists a nice connection between our proposed estimator and a recently developed shrinkage estimator of connectivity measures in the neuroimaging community. We develop an expectation-maximization (EM) algorithm for estimation of the proposed Bayesian hierarchical model. Simulations studies are performed to evaluate the accuracy of our proposed prediction methods. We illustrate the application of the methods with two data examples: the longitudinal resting-state fMRI from ADNI2 study and the test-retest fMRI data from Kirby21 study. In both the simulation studies and the fMRI data applications, we demonstrate that the proposed methods provide more accurate prediction and more reliable estimation of individual functional connectivity as compared with alternative methods.

Community detection in weighted brain connectivity networks beyond the resolution limit

Graph theory provides a powerful framework to investigate brain functional connectivity networks and their modular organization. However, most graph-based methods suffer from a fundamental resolution limit that may have affected previous studies and prevented detection of modules, or "communities", that are smaller than a specific scale. Surprise, a resolution-limit-free function rooted in discrete probability theory, has been recently introduced and applied to brain networks, revealing a wide size-distribution of functional modules (Nicolini and Bifone, 2016), in contrast with many previous reports. However, the use of Surprise is limited to binary networks, while brain networks are intrinsically weighted, reflecting a continuous distribution of connectivity strengths between different brain regions. Here, we propose Asymptotical Surprise, a continuous version of Surprise, for the study of weighted brain connectivity networks, and validate this approach in synthetic networks endowed with a ground-truth modular structure. We compare Asymptotical Surprise with leading community detection methods currently in use and show its superior sensitivity in the detection of small modules even in the presence of noise and intersubject variability such as those observed in fMRI data. We apply our novel approach to functional connectivity networks from resting state fMRI experiments, and demonstrate a heterogeneous modular organization, with a wide distribution of clusters spanning multiple scales. Finally, we discuss the implications of these findings for the identification of connector hubs, the brain regions responsible for the integration of the different network elements, showing that the improved resolution afforded by Asymptotical Surprise leads to a different classification compared to current methods.

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Methods to study modularity of brain connectivity networks have a resolution limit.

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Asymptotical Surprise, a nearly resolution-limit-free method for weighted graphs, is proposed.

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Improved sensitivity and specificity are demonstrated in model networks.

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Resting state functional connectivity networks consist of heterogeneous modules.

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Classification of hubs in function connectivity networks should be revised.

Global disruption of degree rank order: a hallmark of chronic pain

Chronic pain remains poorly understood; yet it is associated with the reorganization of the nervous system. Here, we demonstrate that a unitary global measure of functional connectivity, defined as the extent of degree rank order disruption, kD, identifies the chronic pain state. In contrast, local degree disruption differentiates between chronic pain conditions. We used resting-state functional MRI data to analyze the brain connectome at varying scales and densities. In three chronic pain conditions, we observe disrupted kD, in proportion to individuals' pain intensity, and associated with community membership disruption. Additionally, we observe regional degree changes, some of which were unique to each type of chronic pain. Subjects with recent onset of back pain exhibited emergence of kD only when the pain became chronic. Similarly, in neuropathic rats kD emerged weeks after injury, in proportion to pain-like behavior. Thus, we found comprehensive cross-species evidence for chronic pain being a state of global randomization of functional connectivity.

Altered whole-brain connectivity in albinism

Albinism is a group of congenital disorders of the melanin synthesis pathway. Multiple ocular, white matter and cortical abnormalities occur in albinism, including a greater decussation of nerve fibres at the optic chiasm, foveal hypoplasia and nystagmus. Despite this, visual perception is largely preserved. It was proposed that this may be attributable to reorganisation among cerebral networks, including an increased interhemispheric connectivity of the primary visual areas. A graph-theoretic model was applied to explore brain connectivity networks derived from resting-state functional and diffusion-tensor magnetic resonance imaging data in 23 people with albinism and 20 controls. They tested for group differences in connectivity between primary visual areas and in summary network organisation descriptors. Main findings were supplemented with analyses of control regions, brain volumes and white matter microstructure. Significant functional interhemispheric hyperconnectivity of the primary visual areas in the albinism group were found (P = 0.012). Tests of interhemispheric connectivity based on the diffusion-tensor data showed no significant group difference (P = 0.713). Second, it was found that a range of functional whole-brain network metrics were abnormal in people with albinism, including the clustering coefficient (P = 0.005), although this may have been driven partly by overall differences in connectivity, rather than reorganisation. Based on the results, it was suggested that changes occur in albinism at the whole-brain level, and not just within the visual processing pathways. It was proposed that their findings may reflect compensatory adaptations to increased chiasmic decussation, foveal hypoplasia and nystagmus. Hum Brain Mapp 38:740-752, 2017. © 2016 Wiley Periodicals, Inc.

Building an EEG-fMRI Multi-Modal Brain Graph: A Concurrent EEG-fMRI Study

The topological architecture of brain connectivity has been well-characterized by graph theory based analysis. However, previous studies have primarily built brain graphs based on a single modality of brain imaging data. Here we develop a framework to construct multi-modal brain graphs using concurrent EEG-fMRI data which are simultaneously collected during eyes open (EO) and eyes closed (EC) resting states. FMRI data are decomposed into independent components with associated time courses by group independent component analysis (ICA). EEG time series are segmented, and then spectral power time courses are computed and averaged within 5 frequency bands (delta; theta; alpha; beta; low gamma). EEG-fMRI brain graphs, with EEG electrodes and fMRI brain components serving as nodes, are built by computing correlations within and between fMRI ICA time courses and EEG spectral power time courses. Dynamic EEG-fMRI graphs are built using a sliding window method, versus static ones treating the entire time course as stationary. In global level, static graph measures and properties of dynamic graph measures are different across frequency bands and are mainly showing higher values in eyes closed than eyes open. Nodal level graph measures of a few brain components are also showing higher values during eyes closed in specific frequency bands. Overall, these findings incorporate fMRI spatial localization and EEG frequency information which could not be obtained by examining only one modality. This work provides a new approach to examine EEG-fMRI associations within a graph theoretic framework with potential application to many topics.

Reduced specialized processing in psychotic disorder: a graph theoretical analysis of cerebral functional connectivity

BACKGROUND

Previous research has shown that the human brain can be represented as a complex functional network that is characterized by specific topological properties, such as clustering coefficient, characteristic path length, and global/local efficiency. Patients with psychotic disorder may have alterations in these properties with respect to controls, indicating altered efficiency of network organization. This study examined graph theoretical changes in relation to differential genetic risk for the disorder and aimed to identify clinical correlates.

METHODS

Anatomical and resting-state MRI brain scans were obtained from 73 patients with psychotic disorder, 83 unaffected siblings, and 72 controls. Topological measures (i.e., clustering coefficient, characteristic path length, and small-worldness) were used as dependent variables in a multilevel random regression analysis to investigate group differences. In addition, associations with (subclinical) psychotic/cognitive symptoms were examined.

RESULTS

Patients had a significantly lower clustering coefficient compared to siblings and controls, with no difference between the latter groups. No group differences were observed for characteristic path length and small-worldness. None of the topological properties were associated with (sub)clinical psychotic and cognitive symptoms.

CONCLUSIONS

The reduced ability for specialized processing (reflected by a lower clustering coefficient) within highly interconnected brain regions observed in the patient group may indicate state-related network alterations. There was no evidence for an intermediate phenotype and no evidence for psychopathology-related alterations.

Brain imaging and networks in restless legs syndrome

Several studies provide information useful to our understanding of restless legs syndrome (RLS), using various imaging techniques to investigate different aspects putatively involved in the pathophysiology of RLS, although there are discrepancies between these findings. The majority of magnetic resonance imaging (MRI) studies using iron-sensitive sequences supports the presence of a diffuse, but regionally variable low brain-iron content, mainly at the level of the substantia nigra, but there is increasing evidence of reduced iron levels in the thalamus. Positron emission tomography (PET) and single positron emission computed tomography (SPECT) findings mainly support dysfunction of dopaminergic pathways involving not only the nigrostriatal but also mesolimbic pathways. None or variable brain structural or microstructural abnormalities have been reported in RLS patients; reports are slightly more consistent concerning levels of white matter. Most of the reported changes were in regions belonging to sensorimotor and limbic/nociceptive networks. Functional MRI studies have demonstrated activation or connectivity changes in the same networks. The thalamus, which includes different sensorimotor and limbic/nociceptive networks, appears to have lower iron content, metabolic abnormalities, dopaminergic dysfunction, and changes in activation and functional connectivity. Summarizing these findings, the primary change could be the reduction of brain iron content, which leads to dysfunction of mesolimbic and nigrostriatal dopaminergic pathways, and in turn to a dysregulation of limbic and sensorimotor networks. Future studies in RLS should evaluate the actual causal relationship among these findings, better investigate the role of neurotransmitters other than dopamine, focus on brain networks by connectivity analysis, and test the reversibility of the different imaging findings following therapy.

Lateralized Resting-State Functional Brain Network Organization Changes in Heart Failure

Heart failure (HF) patients show brain injury in autonomic, affective, and cognitive sites, which can change resting-state functional connectivity (FC), potentially altering overall functional brain network organization. However, the status of such connectivity or functional organization is unknown in HF. Determination of that status was the aim here, and we examined region-to-region FC and brain network topological properties across the whole-brain in 27 HF patients compared to 53 controls with resting-state functional MRI procedures. Decreased FC in HF appeared between the caudate and cerebellar regions, olfactory and cerebellar sites, vermis and medial frontal regions, and precentral gyri and cerebellar areas. However, increased FC emerged between the middle frontal gyrus and sensorimotor areas, superior parietal gyrus and orbito/medial frontal regions, inferior temporal gyrus and lingual gyrus/cerebellar lobe/pallidum, fusiform gyrus and superior orbitofrontal gyrus and cerebellar sites, and within vermis and cerebellar areas; these connections were largely in the right hemisphere (p<0.005; 10,000 permutations). The topology of functional integration and specialized characteristics in HF are significantly changed in regions showing altered FC, an outcome which would interfere with brain network organization (p<0.05; 10,000 permutations). Brain dysfunction in HF extends to resting conditions, and autonomic, cognitive, and affective deficits may stem from altered FC and brain network organization that may contribute to higher morbidity and mortality in the condition. Our findings likely result from the prominent axonal and nuclear structural changes reported earlier in HF; protecting neural tissue may improve FC integrity, and thus, increase quality of life and reduce morbidity and mortality.

Prediction of Conversion from Mild Cognitive Impairment to Alzheimer's Disease Using MRI and Structural Network Features

Optimized magnetic resonance imaging (MRI) features and abnormalities of brain network architectures may allow earlier detection and accurate prediction of the progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD). In this study, we proposed a classification framework to distinguish MCI converters (MCIc) from MCI non-converters (MCInc) by using a combination of FreeSurfer-derived MRI features and nodal features derived from the thickness network. At the feature selection step, we first employed sparse linear regression with stability selection, for the selection of discriminative features in the iterative combinations of MRI and network measures. Subsequently the top K features of available combinations were selected as optimal features for classification. To obtain unbiased results, support vector machine (SVM) classifiers with nested cross validation were used for classification. The combination of 10 features including those from MRI and network measures attained accuracies of 66.04, 76.39, 74.66, and 73.91% for mixed conversion time, 6, 12, and 18 months before diagnosis of probable AD, respectively. Analysis of the diagnostic power of different time periods before diagnosis of probable AD showed that short-term prediction (6 and 12 months) achieved more stable and higher AUC scores compared with long-term prediction (18 months), with K-values from 1 to 30. The present results suggest that meaningful predictors composed of MRI and network measures may offer the possibility for early detection of progression from MCI to AD.

Distinct disruptions of resting-state functional brain networks in familial and sporadic schizophrenia

Clinical and brain structural differences have been reported between patients with familial and sporadic schizophrenia; however, little is known about the brain functional differences between the two subtypes of schizophrenia. Twenty-six patients with familial schizophrenia (PFS), 26 patients with sporadic schizophrenia (PSS) and 26 healthy controls (HC) underwent a resting-state functional magnetic resonance imaging. The whole-brain functional network was constructed and analyzed using graph theoretical approaches. Topological properties (including global, nodal and edge measures) were compared among the three groups. We found that PFS, PSS and HC exhibited common small-world architecture of the functional brain networks. However, at a global level, only PFS showed significantly lower normalized clustering coefficient, small-worldness, and local efficiency, indicating a randomization shift of their brain networks. At a regional level, PFS and PSS disrupted different neural circuits, consisting of abnormal nodes (increased or decreased nodal centrality) and edges (decreased functional connectivity strength), which were widely distributed throughout the entire brain. Furthermore, some of these altered network measures were significantly correlated with severity of psychotic symptoms. These results suggest that familial and sporadic schizophrenia had segregated disruptions in the topological organization of the intrinsic functional brain network, which may be due to different etiological contributions.

Single-subject morphological brain networks: connectivity mapping, topological characterization and test-retest reliability

INTRODUCTION

Structural MRI has long been used to characterize local morphological features of the human brain. Coordination patterns of the local morphological features among regions, however, are not well understood. Here, we constructed individual-level morphological brain networks and systematically examined their topological organization and long-term test-retest reliability under different analytical schemes of spatial smoothing, brain parcellation, and network type.

METHODS

This study included 57 healthy participants and all participants completed two MRI scan sessions. Individual morphological brain networks were constructed by estimating interregional similarity in the distribution of regional gray matter volume in terms of the Kullback-Leibler divergence measure. Graph-based global and nodal network measures were then calculated, followed by the statistical comparison and intra-class correlation analysis.

RESULTS

The morphological brain networks were highly reproducible between sessions with significantly larger similarities for interhemispheric connections linking bilaterally homotopic regions. Further graph-based analyses revealed that the morphological brain networks exhibited nonrandom topological organization of small-worldness, high parallel efficiency and modular architecture regardless of the analytical choices of spatial smoothing, brain parcellation and network type. Moreover, several paralimbic and association regions were consistently revealed to be potential hubs. Nonetheless, the three studied factors particularly spatial smoothing significantly affected quantitative characterization of morphological brain networks. Further examination of long-term reliability revealed that all the examined network topological properties showed fair to excellent reliability irrespective of the analytical strategies, but performing spatial smoothing significantly improved reliability. Interestingly, nodal centralities were positively correlated with their reliabilities, and nodal degree and efficiency outperformed nodal betweenness with respect to reliability.

CONCLUSIONS

Our findings support single-subject morphological network analysis as a meaningful and reliable method to characterize structural organization of the human brain; this method thus opens a new avenue toward understanding the substrate of intersubject variability in behavior and function and establishing morphological network biomarkers in brain disorders.

An Efficient and Reliable Statistical Method for Estimating Functional Connectivity in Large Scale Brain Networks Using Partial Correlation

Currently, network-oriented analysis of fMRI data has become an important tool for understanding brain organization and brain networks. Among the range of network modeling methods, partial correlation has shown great promises in accurately detecting true brain network connections. However, the application of partial correlation in investigating brain connectivity, especially in large-scale brain networks, has been limited so far due to the technical challenges in its estimation. In this paper, we propose an efficient and reliable statistical method for estimating partial correlation in large-scale brain network modeling. Our method derives partial correlation based on the precision matrix estimated via Constrained L1-minimization Approach (CLIME), which is a recently developed statistical method that is more efficient and demonstrates better performance than the existing methods. To help select an appropriate tuning parameter for sparsity control in the network estimation, we propose a new Dens-based selection method that provides a more informative and flexible tool to allow the users to select the tuning parameter based on the desired sparsity level. Another appealing feature of the Dens-based method is that it is much faster than the existing methods, which provides an important advantage in neuroimaging applications. Simulation studies show that the Dens-based method demonstrates comparable or better performance with respect to the existing methods in network estimation. We applied the proposed partial correlation method to investigate resting state functional connectivity using rs-fMRI data from the Philadelphia Neurodevelopmental Cohort (PNC) study. Our results show that partial correlation analysis removed considerable between-module marginal connections identified by full correlation analysis, suggesting these connections were likely caused by global effects or common connection to other nodes. Based on partial correlation, we find that the most significant direct connections are between homologous brain locations in the left and right hemisphere. When comparing partial correlation derived under different sparse tuning parameters, an important finding is that the sparse regularization has more shrinkage effects on negative functional connections than on positive connections, which supports previous findings that many of the negative brain connections are due to non-neurophysiological effects. An R package “DensParcorr” can be downloaded from CRAN for implementing the proposed statistical methods.

Hyper-connectivity of functional networks for brain disease diagnosis

Exploring structural and functional interactions among various brain regions enables better understanding of pathological underpinnings of neurological disorders. Brain connectivity network, as a simplified representation of those structural and functional interactions, has been widely used for diagnosis and classification of neurodegenerative diseases, especially for Alzheimer's disease (AD) and its early stage - mild cognitive impairment (MCI). However, the conventional functional connectivity network is usually constructed based on the pairwise correlation among different brain regions and thus ignores their higher-order relationships. Such loss of high-order information could be important for disease diagnosis, since neurologically a brain region predominantly interacts with more than one other brain regions. Accordingly, in this paper, we propose a novel framework for estimating the hyper-connectivity network of brain functions and then use this hyper-network for brain disease diagnosis. Here, the functional connectivity hyper-network denotes a network where each of its edges representing the interactions among multiple brain regions (i.e., an edge can connect with more than two brain regions), which can be naturally represented by a hyper-graph. Specifically, we first construct connectivity hyper-networks from the resting-state fMRI (R-fMRI) time series by using sparse representation. Then, we extract three sets of brain-region specific features from the connectivity hyper-networks, and further exploit a manifold regularized multi-task feature selection method to jointly select the most discriminative features. Finally, we use multi-kernel support vector machine (SVM) for classification. The experimental results on both MCI dataset and attention deficit hyperactivity disorder (ADHD) dataset demonstrate that, compared with the conventional connectivity network-based methods, the proposed method can not only improve the classification performance, but also help discover disease-related biomarkers important for disease diagnosis.

Functional Connectome before and following Temporal Lobectomy in Mesial Temporal Lobe Epilepsy

As mesial temporal lobe epilepsy (mTLE) has been recognized as a network disorder, a longitudinal connectome investigation may shed new light on the understanding of the underlying pathophysiology related to distinct surgical outcomes. Resting-state functional MRI data was acquired from mTLE patients before (n = 37) and after (n = 24) anterior temporal lobectomy. According to surgical outcome, patients were classified as seizure-free (SF, n = 14) or non-seizure-free (NSF, n = 10). First, we found higher network resilience to targeted attack on topologically central nodes in the SF group compared to the NSF group, preoperatively. Next, a two-way mixed analysis of variance with between-subject factor ‘outcome’ (SF vs. NSF) and within-subject factor ‘treatment’ (pre-operation vs. post-operation) revealed divergent dynamic reorganization in nodal topological characteristics between groups, in the temporoparietal junction and its connection with the ventral prefrontal cortex. We also correlated the network damage score (caused by surgical resection) with postsurgical brain function, and found that the damage score negatively correlated with postoperative global and local parallel information processing. Taken together, dynamic connectomic architecture provides vital information for selecting surgical candidates and for understanding brain recovery mechanisms following epilepsy surgery.

Graph-theoretical analysis of resting-state fMRI in pediatric obsessive-compulsive disorder

BACKGROUND

fMRI graph theory reveals resting-state brain networks, but has never been used in pediatric OCD.

METHODS

Whole-brain resting-state fMRI was acquired at 3T from 21 children with OCD and 20 age-matched healthy controls. BOLD connectivity was analyzed yielding global and local graph-theory metrics across 100 child-based functional nodes. We also compared local metrics between groups in frontopolar, supplementary motor, and sensorimotor cortices, regions implicated in recent neuroimaging and/or brain stimulation treatment studies in OCD.

RESULTS

As in adults, the global metric small-worldness was significantly (P<0.05) lower in patients than controls, by 13.5% (%mean difference=100%X(OCD mean - control mean)/control mean). This suggests less efficient information transfer in patients. In addition, modularity was lower in OCD (15.1%, P<0.01), suggesting less granular - or differently organized - functional brain parcellation. Higher clustering coefficients (23.9-32.4%, P<0.05) were observed in patients in frontopolar, supplementary motor, sensorimotor, and cortices with lower betweenness centrality (-63.6%, P<0.01) at one frontopolar site. These findings are consistent with more locally intensive connectivity or less interaction with other brain regions at these sites.

LIMITATIONS

Relatively large node size; relatively small sample size, comorbidities in some patients.

CONCLUSIONS

Pediatric OCD patients demonstrate aberrant global and local resting-state network connectivity topologies compared to healthy children. Local results accord with recent views of OCD as a disorder with sensorimotor component.

Alterations of Functional and Structural Networks in Schizophrenia Patients with Auditory Verbal Hallucinations

Background: There have been many attempts at explaining the underlying neuropathological mechanisms of auditory verbal hallucinations (AVH) in schizophrenia on the basis of regional brain changes, with the most consistent findings being that AVH are associated with functional and structural impairments in auditory and speech-related regions. However, the human brain is a complex network and the global topological alterations specific to AVH in schizophrenia remain unclear.

Methods: Thirty-five schizophrenia patients with AVH, 41 patients without AVH, and 50 healthy controls underwent resting-state functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI). The whole-brain functional and structural networks were constructed and analyzed using graph theoretical approaches. Inter-group differences in global network metrics (including small-world properties and network efficiency) were investigated.

Results: We found that three groups had a typical small-world topology in both functional and structural networks. More importantly, schizophrenia patients with and without AVH exhibited common disruptions of functional networks, characterized by decreased clustering coefficient, global efficiency and local efficiency, and increased characteristic path length; structural networks of only schizophrenia patients with AVH showed increased characteristic path length compared with those of healthy controls.

Conclusion: Our findings suggest that less “small-worldization” and lower network efficiency of functional networks may be an independent trait characteristic of schizophrenia, and regularization of structural networks may be the underlying pathological process engaged in schizophrenic AVH symptom expression.

Disrupted functional brain network organization in patients with obstructive sleep apnea

INTRODUCTION

Obstructive sleep apnea (OSA) subjects show impaired autonomic, affective, executive, sensorimotor, and cognitive functions. Brain injury in OSA subjects appears in multiple sites regulating these functions, but the integrity of functional networks within the regulatory sites remains unclear. Our aim was to examine the functional interactions and the complex network organization of these interactions across the whole brain in OSA, using regional functional connectivity (FC) and brain network topological properties.

METHODS

We collected resting-state functional magnetic resonance imaging (MRI) data, using a 3.0-Tesla MRI scanner, from 69 newly diagnosed, treatment-naïve, moderate-to-severe OSA (age, 48.3 ± 9.2 years; body mass index, 31 ± 6.2 kg/m(2); apnea-hypopnea index (AHI), 35.6 ± 23.3 events/h) and 82 control subjects (47.6 ± 9.1 years; body mass index, 25.1 ± 3.5 kg/m(2)). Data were analyzed to examine FC in OSA over controls as interregional correlations and brain network topological properties.

RESULTS

Obstructive sleep apnea subjects showed significantly altered FC in the cerebellar, frontal, parietal, temporal, occipital, limbic, and basal ganglia regions (FDR, P < 0.05). Entire functional brain networks in OSA subjects showed significantly less efficient integration, and their regional topological properties of functional integration and specialization characteristics also showed declined trends in areas showing altered FC, an outcome which would interfere with brain network organization (P < 0.05; 10,000 permutations). Brain sites with abnormal topological properties in OSA showed significant relationships with AHI scores.

CONCLUSIONS

Our findings suggest that the dysfunction extends to resting conditions, and the altered FC and impaired network organization may underlie the impaired responses in autonomic, cognitive, and sensorimotor functions. The outcomes likely result from the prominent structural changes in both axons and nuclear structures, which occur in the condition.

Preprocessing strategy influences graph-based exploration of altered functional networks in major depression

Resting-state fMRI studies have gained widespread use in exploratory studies of neuropsychiatric disorders. Graph metrics derived from whole brain functional connectivity studies have been used to reveal disease-related variations in many neuropsychiatric disorders including major depression (MDD). These techniques show promise in developing diagnostics for these often difficult to identify disorders. However, the analysis of resting-state datasets is increasingly beset by a myriad of approaches and methods, each with underlying assumptions. Choosing the most appropriate preprocessing parameters a priori is difficult. Nevertheless, the specific methodological choice influences graph-theoretical network topologies as well as regional metrics. The aim of this study was to systematically compare different preprocessing strategies by evaluating their influence on group differences between healthy participants (HC) and depressive patients. We thus investigated the effects of common preprocessing variants, including global mean-signal regression (GMR), temporal filtering, detrending, and network sparsity on group differences between brain networks of HC and MDD patients measured by global and nodal graph theoretical metrics. Occurrence of group differences in global metrics was absent in the majority of tested preprocessing variants, but in local graph metrics it is sparse, variable, and highly dependent on the combination of preprocessing variant and sparsity threshold. Sparsity thresholds between 16 and 22% were shown to have the greatest potential to reveal differences between HC and MDD patients in global and local network metrics. Our study offers an overview of consequences of methodological decisions and which neurobiological characteristics of MDD they implicate, adding further caution to this rapidly growing field.

A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain

BACKGROUND

Networks or graphs play an important role in the biological sciences. Protein interaction networks and metabolic networks support the understanding of basic cellular mechanisms. In the human brain, networks of functional or structural connectivity model the information-flow between cortex regions. In this context, measures of network properties are needed. We propose a new measure, Ndim, estimating the complexity of arbitrary networks. This measure is based on a fractal dimension, which is similar to recently introduced box-covering dimensions. However, box-covering dimensions are only applicable to fractal networks. The construction of these network-dimensions relies on concepts proposed to measure fractality or complexity of irregular sets in [Formula: see text].

RESULTS

The network measure Ndim grows with the proliferation of increasing network connectivity and is essentially determined by the cardinality of a maximum k-clique, where k is the characteristic path length of the network. Numerical applications to lattice-graphs and to fractal and non-fractal graph models, together with formal proofs show, that Ndim estimates a dimension of complexity for arbitrary graphs. Box-covering dimensions for fractal graphs rely on a linear log-log plot of minimum numbers of covering subgraph boxes versus the box sizes. We demonstrate the affinity between Ndim and the fractal box-covering dimensions but also that Ndim extends the concept of a fractal dimension to networks with non-linear log-log plots. Comparisons of Ndim with topological measures of complexity (cost and efficiency) show that Ndim has larger informative power. Three different methods to apply Ndim to weighted networks are finally presented and exemplified by comparisons of functional brain connectivity of healthy and depressed subjects.

CONCLUSION

We introduce a new measure of complexity for networks. We show that Ndim has the properties of a dimension and overcomes several limitations of presently used topological and fractal complexity-measures. It allows the comparison of the complexity of networks of different type, e.g., between fractal graphs characterized by hub repulsion and small world graphs with strong hub attraction. The large informative power and a convenient computational CPU-time for moderately sized networks may make Ndim a valuable tool for the analysis of biological networks.

Topological Alterations of the Intrinsic Brain Network in Patients with Functional Dyspepsia

BACKGROUND/AIMS

Previous studies reported that integrated information in the brain ultimately determines the subjective experience of patients with chronic pain, but how the information is integrated in the brain connectome of functional dyspepsia (FD) patients remains largely unclear. The study aimed to quantify the topological changes of the brain network in FD patients.

METHODS

Small-world properties, network efficiency and nodal centrality were utilized to measure the changes in topological architecture in 25 FD patients and 25 healthy controls based on functional magnetic resonance imaging. Pearson's correlation assessed the relationship of each topological property with clinical symptoms.

RESULTS

FD patients showed an increase of clustering coefficients and local efficiency relative to controls from the perspective of a whole network as well as elevated nodal centrality in the right orbital part of the inferior frontal gyrus, left anterior cingulate gyrus and left hippocampus, and decreased nodal centrality in the right posterior cingulate gyrus, left cuneus, right putamen, left middle occipital gyrus and right inferior occipital gyrus. Moreover, the centrality in the anterior cingulate gyrus was significantly associated with symptom severity and duration in FD patients. Nevertheless, the inclusion of anxiety and depression scores as covariates erased the group differences in nodal centralities in the orbital part of the inferior frontal gyrus and hippocampus.

CONCLUSIONS

The results suggest topological disruption of the functional brain networks in FD patients, presumably in response to disturbances of sensory information integrated with emotion, memory, pain modulation, and selective attention in patients.

Resting-state low-frequency fluctuations reflect individual differences in spoken language learning

A major challenge in language learning studies is to identify objective, pre-training predictors of success. Variation in the low-frequency fluctuations (LFFs) of spontaneous brain activity measured by resting-state functional magnetic resonance imaging (RS-fMRI) has been found to reflect individual differences in cognitive measures. In the present study, we aimed to investigate the extent to which initial spontaneous brain activity is related to individual differences in spoken language learning. We acquired RS-fMRI data and subsequently trained participants on a sound-to-word learning paradigm in which they learned to use foreign pitch patterns (from Mandarin Chinese) to signal word meaning. We performed amplitude of spontaneous low-frequency fluctuation (ALFF) analysis, graph theory-based analysis, and independent component analysis (ICA) to identify functional components of the LFFs in the resting-state. First, we examined the ALFF as a regional measure and showed that regional ALFFs in the left superior temporal gyrus were positively correlated with learning performance, whereas ALFFs in the default mode network (DMN) regions were negatively correlated with learning performance. Furthermore, the graph theory-based analysis indicated that the degree and local efficiency of the left superior temporal gyrus were positively correlated with learning performance. Finally, the default mode network and several task-positive resting-state networks (RSNs) were identified via the ICA. The "competition" (i.e., negative correlation) between the DMN and the dorsal attention network was negatively correlated with learning performance. Our results demonstrate that a) spontaneous brain activity can predict future language learning outcome without prior hypotheses (e.g., selection of regions of interest--ROIs) and b) both regional dynamics and network-level interactions in the resting brain can account for individual differences in future spoken language learning success.

Multivariate classification of smokers and nonsmokers using SVM-RFE on structural MRI images

Voxel-based morphometry (VBM) studies have revealed gray matter alterations in smokers, but this type of analysis has poor predictive value for individual cases, which limits its applicability in clinical diagnoses and treatment. A predictive model would essentially embody a complex biomarker that could be used to evaluate treatment efficacy. In this study, we applied VBM along with a multivariate classification method consisting of a support vector machine with recursive feature elimination to discriminate smokers from nonsmokers using their structural MRI data. Mean gray matter volumes in 1,024 cerebral cortical regions of interest created using a subparcellated version of the Automated Anatomical Labeling template were calculated from 60 smokers and 60 nonsmokers, and served as input features to the classification procedure. The classifier achieved the highest accuracy of 69.6% when taking the 139 highest ranked features via 10-fold cross-validation. Critically, these features were later validated on an independent testing set that consisted of 28 smokers and 28 nonsmokers, yielding a 64.04% accuracy level (binomial P = 0.01). Following classification, exploratory post hoc regression analyses were performed, which revealed that gray matter volumes in the putamen, hippocampus, prefrontal cortex, cingulate cortex, caudate, thalamus, pre-/postcentral gyrus, precuneus, and the parahippocampal gyrus, were inversely related to smoking behavioral characteristics. These results not only indicate that smoking related gray matter alterations can provide predictive power for group membership, but also suggest that machine learning techniques can reveal underlying smoking-related neurobiology.

Identification of infants at high-risk for autism spectrum disorder using multiparameter multiscale white matter connectivity networks

Autism spectrum disorder (ASD) is a wide range of disabilities that cause life-long cognitive impairment and social, communication, and behavioral challenges. Early diagnosis and medical intervention are important for improving the life quality of autistic patients. However, in the current practice, diagnosis often has to be delayed until the behavioral symptoms become evident during childhood. In this study, we demonstrate the feasibility of using machine learning techniques for identifying high-risk ASD infants at as early as six months after birth. This is based on the observation that ASD-induced abnormalities in white matter (WM) tracts and whole-brain connectivity have already started to appear within 24 months after birth. In particular, we propose a novel multikernel support vector machine classification framework by using the connectivity features gathered from WM connectivity networks, which are generated via multiscale regions of interest (ROIs) and multiple diffusion statistics such as fractional anisotropy, mean diffusivity, and average fiber length. Our proposed framework achieves an accuracy of 76% and an area of 0.80 under the receiver operating characteristic curve (AUC), in comparison to the accuracy of 70% and the AUC of 70% provided by the best single-parameter single-scale network. The improvement in accuracy is mainly due to the complementary information provided by multiparameter multiscale networks. In addition, our framework also provides the potential imaging connectomic markers and an objective means for early ASD diagnosis.

Spontaneous functional network dynamics and associated structural substrates in the human brain

Recent imaging connectomics studies have demonstrated that the spontaneous human brain functional networks derived from resting-state functional MRI (R-fMRI) include many non-trivial topological properties, such as highly efficient small-world architecture and densely connected hub regions. However, very little is known about dynamic functional connectivity (D-FC) patterns of spontaneous human brain networks during rest and about how these spontaneous brain dynamics are constrained by the underlying structural connectivity. Here, we combined sub-second multiband R-fMRI data with graph-theoretical approaches to comprehensively investigate the dynamic characteristics of the topological organization of human whole-brain functional networks, and then employed diffusion imaging data in the same participants to further explore the associated structural substrates. At the connection level, we found that human whole-brain D-FC patterns spontaneously fluctuated over time, while homotopic D-FC exhibited high connectivity strength and low temporal variability. At the network level, dynamic functional networks exhibited time-varying but evident small-world and assortativity architecture, with several regions (e.g., insula, sensorimotor cortex and medial prefrontal cortex) emerging as functionally persistent hubs (i.e., highly connected regions) while possessing large temporal variability in their degree centrality. Finally, the temporal characteristics (i.e., strength and variability) of the connectional and nodal properties of the dynamic brain networks were significantly associated with their structural counterparts. Collectively, we demonstrate the economical, efficient, and flexible characteristics of dynamic functional coordination in large-scale human brain networks during rest, and highlight their relationship with underlying structural connectivity, which deepens our understandings of spontaneous brain network dynamics in humans.

Persistent Homology in Sparse Regression and Its Application to Brain Morphometry

Sparse systems are usually parameterized by a tuning parameter that determines the sparsity of the system. How to choose the right tuning parameter is a fundamental and difficult problem in learning the sparse system. In this paper, by treating the the tuning parameter as an additional dimension, persistent homological structures over the parameter space is introduced and explored. The structures are then further exploited in drastically speeding up the computation using the proposed soft-thresholding technique. The topological structures are further used as multivariate features in the tensor-based morphometry (TBM) in characterizing white matter alterations in children who have experienced severe early life stress and maltreatment. These analyses reveal that stress-exposed children exhibit more diffuse anatomical organization across the whole white matter region.

Developmental Changes in Brain Network Hub Connectivity in Late Adolescence

The human brain undergoes substantial development throughout adolescence and into early adulthood. This maturational process is thought to include the refinement of connectivity between putative connectivity hub regions of the brain, which collectively form a dense core that enhances the functional integration of anatomically distributed, and functionally specialized, neural systems. Here, we used longitudinal diffusion magnetic resonance imaging to characterize changes in connectivity between 80 cortical and subcortical anatomical regions over a 2 year period in 31 adolescents between the ages of 15 and 19 years. Connectome-wide analysis indicated that only a small subset of connections showed evidence of statistically significant developmental change over the study period, with 8% and 6% of connections demonstrating decreased and increased structural connectivity, respectively. Nonetheless, these connections linked 93% and 90% of the 80 regions, respectively, pointing to a selective, yet anatomically distributed pattern of developmental changes that involves most of the brain. Hub regions showed a distinct tendency to be highly connected to each other, indicating robust "rich-club" organization. Moreover, connectivity between hubs was disproportionately influenced by development, such that connectivity between subcortical hubs decreased over time, whereas frontal-subcortical and frontal-parietal hub-hub connectivity increased over time. These findings suggest that late adolescence is characterized by selective, yet significant remodeling of hub-hub connectivity, with the topological organization of hubs shifting emphasis from subcortical hubs in favor of an increasingly prominent role for frontal hub regions.

Persistency and flexibility of complex brain networks underlie dual-task interference

Previous studies on multitasking suggest that performance decline during concurrent task processing arises from interfering brain modules. Here, we used graph-theoretical network analysis to define functional brain modules and relate the modular organization of complex brain networks to behavioral dual-task costs. Based on resting-state and task fMRI we explored two organizational aspects potentially associated with behavioral interference when human subjects performed a visuospatial and speech task simultaneously: the topological overlap between persistent single-task modules, and the flexibility of single-task modules in adaptation to the dual-task condition. Participants showed a significant decline in visuospatial accuracy in the dual-task compared with single visuospatial task. Global analysis of topological similarity between modules revealed that the overlap between single-task modules significantly correlated with the decline in visuospatial accuracy. Subjects with larger overlap between single-task modules showed higher behavioral interference. Furthermore, lower flexible reconfiguration of single-task modules in adaptation to the dual-task condition significantly correlated with larger decline in visuospatial accuracy. Subjects with lower modular flexibility showed higher behavioral interference. At the regional level, higher overlap between single-task modules and less modular flexibility in the somatomotor cortex positively correlated with the decline in visuospatial accuracy. Additionally, higher modular flexibility in cingulate and frontal control areas and lower flexibility in right-lateralized nodes comprising the middle occipital and superior temporal gyri supported dual-tasking. Our results suggest that persistency and flexibility of brain modules are important determinants of dual-task costs. We conclude that efficient dual-tasking benefits from a specific balance between flexibility and rigidity of functional brain modules.