Mapping connectomes with diffusion MRI: deterministic or probabilistic tractography?

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

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

The pontine-driven somatic gaze tract contributes to affective processing in humans

The relevance of subcortical structures for affective processing is not fully understood. Inspired by the gerbil retino-raphe pathway that has been shown to regulate affective behavior and previous human work showing that the pontine region is important for processing emotion, we asked whether well-established tracts in humans traveling between the eye and the brain stem contribute to functions beyond their conventionally understood roles. Here we report neuroimaging findings showing that optic chiasm-brain stem diffusivity predict responses reflecting perceived arousal and valence. Analyses of subsequent task-evoked connectivity further revealed that visual affective processing implicates the brain stem, particularly the pontine region at an early stage of the cascade, projecting to cortico-limbic regions in a feedforward manner. The optimal model implies that all intrinsic connections between the regions of interest are unidirectional and outwards from the pontine region. These findings suggest that affective processing implicates regions outside the cortico-limbic network. The involvement of a phylogenetically older locus in the pons that has consequences in oculomotor control may imply adaptive consequences of affect detection.

Neural network correlates of high-altitude adaptive genetic variants in Tibetans: A pilot, exploratory study

Although substantial progress has been made in the identification of genetic substrates underlying physiology, neuropsychology, and brain organization, the genotype–phenotype associations remain largely unknown in the context of high‐altitude (HA) adaptation. Here, we related HA adaptive genetic variants in three gene loci (EGLN1, EPAS1, and PPARA) to interindividual variance in a set of physiological characteristics, neuropsychological tests, and topological attributes of large‐scale structural and functional brain networks in 135 indigenous Tibetan highlanders. Analyses of individual HA adaptive single‐nucleotide polymorphisms (SNPs) revealed that specific SNPs selectively modulated physiological characteristics (erythrocyte level, ratio between forced expiratory volume in the first second to forced vital capacity, arterial oxygen saturation, and heart rate) and structural network centrality (the left anterior orbital gyrus) with no effects on neuropsychology or functional brain networks. Further analyses of genetic adaptive scores, which summarized the overall degree of genetic adaptation to HA, revealed significant correlations only with structural brain networks with respect to local interconnectivity of the whole networks, intermodule communication between the right frontal and parietal module and the left occipital module, nodal centrality in several frontal regions, and connectivity strength of a subnetwork predominantly involving in intramodule edges in the right temporal and occipital module. Moreover, the associations were dependent on gene loci, weight types, or topological scales. Together, these findings shed new light on genotype–phenotype interactions under HA hypoxia and have important implications for developing new strategies to optimize organism and tissue responses to chronic hypoxia induced by extreme environments or diseases.

The effect of network thresholding and weighting on structural brain networks in the UK Biobank

Whole-brain structural networks can be constructed using diffusion MRI and probabilistic tractography. However, measurement noise and the probabilistic nature of the tracking procedure result in an unknown proportion of spurious white matter connections. Faithful disentanglement of spurious and genuine connections is hindered by a lack of comprehensive anatomical information at the network-level. Therefore, network thresholding methods are widely used to remove ostensibly false connections, but it is not yet clear how different thresholding strategies affect basic network properties and their associations with meaningful demographic variables, such as age. In a sample of 3153 generally healthy volunteers from the UK Biobank Imaging Study (aged 44-77 years), we constructed whole-brain structural networks and applied two principled network thresholding approaches (consistency and proportional thresholding). These were applied over a broad range of threshold levels across six alternative network weightings (streamline count, fractional anisotropy, mean diffusivity and three novel weightings from neurite orientation dispersion and density imaging) and for four common network measures (mean edge weight, characteristic path length, network efficiency and network clustering coefficient). We compared network measures against age associations and found that: 1) measures derived from unthresholded matrices yielded the weakest age-associations (0.033 ​≤ ​|β| ​≤ ​0.409); and 2) the most commonly-used level of proportional-thresholding from the literature (retaining 68.7% of all possible connections) yielded significantly weaker age-associations (0.070 ​≤ ​|β| ​≤ ​0.406) than the consistency-based approach which retained only 30% of connections (0.140 ​≤ ​|β| ​≤ ​0.409). However, we determined that the stringency of the threshold was a stronger determinant of the network-age association than the choice of threshold method and the two thresholding approaches identified a highly overlapping set of connections (ICC ​= ​0.84), when matched at 70% network sparsity. Generally, more stringent thresholding resulted in more age-sensitive network measures in five of the six network weightings, except at the highest levels of sparsity (>90%), where crucial connections were then removed. At two commonly-used threshold levels, the age-associations of the connections that were discarded (mean β ​≤ ​|0.068|) were significantly smaller in magnitude than the corresponding age-associations of the connections that were retained (mean β ​≤ ​|0.219|, p ​< ​0.001, uncorrected). Given histological evidence of widespread degeneration of structural brain connectivity with increasing age, these results indicate that stringent thresholding methods may be most accurate in identifying true white matter connections.

Neuroanatomical Dysconnectivity Underlying Cognitive Deficits in Bipolar Disorder

BACKGROUND

Graph theory applied to brain networks is an emerging approach to understanding the brain's topological associations with human cognitive ability. Despite well-documented cognitive impairments in bipolar disorder (BD) and recent reports of altered anatomical network organization, the association between connectivity and cognitive impairments in BD remains unclear.

METHODS

We examined the role of anatomical network connectivity derived from T1- and diffusion-weighted magnetic resonance imaging in impaired cognitive performance in individuals with BD (n = 32) compared with healthy control individuals (n = 38). Fractional anisotropy- and number of streamlines-weighted anatomical brain networks were generated by mapping constrained spherical deconvolution-reconstructed white matter among 86 cortical/subcortical bilateral brain regions delineated in the individual's own coordinate space. Intelligence and executive function were investigated as distributed functions using measures of global, rich-club, and interhemispheric connectivity, while memory and social cognition were examined in relation to subnetwork connectivity.

RESULTS

Lower executive functioning related to higher global clustering coefficient in participants with BD, and lower IQ performance may present with a differential relationship between global and interhemispheric efficiency in individuals with BD relative to control individuals. Spatial recognition memory accuracy and response times were similar between diagnostic groups and associated with basal ganglia and thalamus interconnectivity and connectivity within extended anatomical subnetworks in all participants. No anatomical subnetworks related to episodic memory, short-term memory, or social cognition generally or differently in BD.

CONCLUSIONS

Results demonstrate selective influence of subnetwork patterns of connectivity in underlying cognitive performance generally and abnormal global topology underlying discrete cognitive impairments in BD.

Bipolar Disorder and Gender Are Associated with Frontolimbic and Basal Ganglia Dysconnectivity: A Study of Topological Variance Using Network Analysis

Well-established structural abnormalities, mostly involving the limbic system, have been associated with disorders of emotion regulation. Understanding the arrangement and connections of these regions with other functionally specialized cortico-subcortical subnetworks is key to understanding how the human brain's architecture underpins abnormalities of mood and emotion. We investigated topological patterns in bipolar disorder (BD) with the anatomically improved precision conferred by combining subject-specific parcellation/segmentation with nontensor-based tractograms derived using a high-angular resolution diffusion-weighted approach. Connectivity matrices were constructed using 34 cortical and 9 subcortical bilateral nodes (Desikan-Killiany), and edges that were weighted by fractional anisotropy and streamline count derived from deterministic tractography using constrained spherical deconvolution. Whole-brain and rich-club connectivity alongside a permutation-based statistical approach was used to investigate topological variance in predominantly euthymic BD relative to healthy volunteers. BP patients (n = 40) demonstrated impairments across whole-brain topological arrangements (density, degree, and efficiency), and a dysconnected subnetwork involving limbic and basal ganglia relative to controls (n = 45). Increased rich-club connectivity was most evident in females with BD, with frontolimbic and parieto-occipital nodes not members of BD rich-club. Increased centrality in females relative to males was driven by basal ganglia and fronto-temporo-limbic nodes. Our subject-specific cortico-subcortical nontensor-based connectome map presents a neuroanatomical model of BD dysconnectivity that differentially involves communication within and between emotion-regulatory and reward-related subsystems. Moreover, the female brain positions more dependence on nodes belonging to these two differently specialized subsystems for communication relative to males, which may confer increased susceptibility to processes dependent on integration of emotion and reward-related information.

Connectome-Based Patterns of First-Episode Medication-Naïve Patients With Schizophrenia

Emerging evidence indicates that a disruption in brain network organization may play an important role in the pathophysiology of schizophrenia. The neuroimaging fingerprint reflecting the pathophysiology of first-episode schizophrenia remains to be identified. Here, we aimed at characterizing the connectome organization of first-episode medication-naïve patients with schizophrenia. A cross-sectional structural and functional neuroimaging study using two independent samples (principal dataset including 42 medication-naïve, previously untreated patients and 48 healthy controls; replication dataset including 39 first-episode patients [10 untreated patients] and 66 healthy controls) was performed. Brain network architecture was assessed by means of white matter fiber integrity measures derived from diffusion-weighted imaging (DWI) and by means of structural-functional (SC-FC) coupling measured by combining DWI and resting-state functional magnetic resonance imaging. Connectome rich club organization was found to be significantly disrupted in medication-naïve patients as compared with healthy controls (P = .012, uncorrected), with rich club connection strength (P = .032, uncorrected) and SC-FC coupling (P < .001, corrected for false discovery rate) decreased in patients. Similar results were found in the replication dataset. Our findings suggest that a disruption of rich club organization and functional dynamics may reflect an early feature of schizophrenia pathophysiology. These findings add to our understanding of the neuropathological mechanisms of schizophrenia and provide new insights into the early stages of the disorder.

Inferring neural signalling directionality from undirected structural connectomes

Neural information flow is inherently directional. To date, investigation of directional communication in the human structural connectome has been precluded by the inability of non-invasive neuroimaging methods to resolve axonal directionality. Here, we demonstrate that decentralized measures of network communication, applied to the undirected topology and geometry of brain networks, can infer putative directions of large-scale neural signalling. We propose the concept of send-receive communication asymmetry to characterize cortical regions as senders, receivers or neutral, based on differences between their incoming and outgoing communication efficiencies. Our results reveal a send-receive cortical hierarchy that recapitulates established organizational gradients differentiating sensory-motor and multimodal areas. We find that send-receive asymmetries are significantly associated with the directionality of effective connectivity derived from spectral dynamic causal modeling. Finally, using fruit fly, mouse and macaque connectomes, we provide further evidence suggesting that directionality of neural signalling is significantly encoded in the undirected architecture of nervous systems.

MR g-ratio-weighted connectome analysis in patients with multiple sclerosis

Multiple sclerosis (MS) is a brain network disconnection syndrome. Although the brain network topology in MS has been evaluated using diffusion MRI tractography, the mechanism underlying disconnection in the disorder remains unclear. In this study, we evaluated the brain network topology in MS using connectomes with connectivity strengths based on the ratio of the inner to outer myelinated axon diameter (i.e., g-ratio), thereby providing enhanced sensitivity to demyelination compared with the conventional measures of connectivity. We mapped g-ratio-based connectomes in 14 patients with MS and compared them with those of 14 age- and sex-matched healthy controls. For comparison, probabilistic tractography was also used to map connectomes based on the number of streamlines (NOS). We found that g-ratio- and NOS-based connectomes comprised significant connectivity reductions in patients with MS, predominantly in the motor, somatosensory, visual, and limbic regions. However, only the g-ratio-based connectome enabled detection of significant increases in nodal strength in patients with MS. Finally, we found that the g-ratio-weighted nodal strength in motor, visual, and limbic regions significantly correlated with inter-individual variation in measures of disease severity. The g-ratio-based connectome can serve as a sensitive biomarker for diagnosing and monitoring disease progression.

The Seven Deadly Sins of Measuring Brain Structural Connectivity Using Diffusion MRI Streamlines Fibre-Tracking

There is great interest in the study of brain structural connectivity, as white matter abnormalities have been implicated in many disease states. Diffusion magnetic resonance imaging (MRI) provides a powerful means to characterise structural connectivity non-invasively, by using a fibre-tracking algorithm. The most widely used fibre-tracking strategy is based on the step-wise generation of streamlines. Despite their popularity and widespread use, there are a number of practical considerations that must be taken into account in order to increase the robustness of streamlines tracking results, particularly when these methods are used to study brain structural connectivity, and the connectome. This review article describes what we consider the ‘seven deadly sins’ of mapping structural connections using diffusion MRI streamlines fibre-tracking, with particular emphasis on ‘sins’ that can be practically avoided and they can have an important impact in the results. It is shown that there are important ‘deadly sins’ to be avoided at every step of the pipeline, such as during data acquisition, during data modelling to estimate local fibre architecture, during the fibre-tracking process itself, and during quantification of the tracking results. The recommendations here are intended to inform users on potential important shortcomings of their current tracking protocols, as well as to guide future users on some of the key issues and decisions that must be faced when designing their processing pipelines.

Synchronization lag in post stroke: relation to motor function and structural connectivity

Stroke is characterized by delays in the resting-state hemodynamic response, resulting in synchronization lag in neural activity between brain regions. However, the structural basis of this lag remains unclear. In this study, we used resting-state functional MRI (rs-fMRI) to characterize synchronization lag profiles between homotopic regions in 15 individuals (14 males, 1 female) with brain lesions consequent to stroke as well as a group of healthy comparison individuals. We tested whether the network communication efficiency of each individual's structural brain network (connectome) could explain interindividual and interregional variation in synchronization lag profiles. To this end, connectomes were mapped using diffusion MRI data, and communication measures were evaluated under two schemes: shortest paths and navigation. We found that interindividual variation in synchronization lags was inversely associated with communication efficiency under both schemes. Interregional variation in lag was related to navigation efficiency and navigation distance, reflecting its dependence on both distance and structural constraints. Moreover, severity of motor deficits significantly correlated with average synchronization lag in stroke. Our results provide a structural basis for the delay of information transfer between homotopic regions inferred from rs-fMRI and provide insight into the clinical significance of structural-functional relationships in stroke individuals.

Comparison between diffusion MRI tractography and histological tract-tracing of cortico-cortical structural connectivity in the ferret brain

The anatomical wiring of the brain is a central focus in network neuroscience. Diffusion MRI tractography offers the unique opportunity to investigate the brain fiber architecture in vivo and noninvasively. However, its reliability is still highly debated. Here, we explored the ability of diffusion MRI tractography to match invasive anatomical tract-tracing connectivity data of the ferret brain. We also investigated the influence of several state-of-the-art tractography algorithms on this match to ground truth connectivity data. Tract-tracing connectivity data were obtained from retrograde tracer injections into the occipital, parietal, and temporal cortices of adult ferrets. We found that the relative densities of projections identified from the anatomical experiments were highly correlated with the estimates from all the studied diffusion tractography algorithms (Spearman's rho ranging from 0.67 to 0.91), while only small, nonsignificant variations appeared across the tractography algorithms. These results are comparable to findings reported in mouse and monkey, increasing the confidence in diffusion MRI tractography results. Moreover, our results provide insights into the variations of sensitivity and specificity of the tractography algorithms, and hence into the influence of choosing one algorithm over another.

A macaque connectome for large-scale network simulations in TheVirtualBrain

Models of large-scale brain networks that are informed by the underlying anatomical connectivity contribute to our understanding of the mapping between the structure of the brain and its dynamical function. Connectome-based modelling is a promising approach to a more comprehensive understanding of brain function across spatial and temporal scales, but it must be constrained by multi-scale empirical data from animal models. Here we describe the construction of a macaque (Macaca mulatta and Macaca fascicularis) connectome for whole-cortex simulations in TheVirtualBrain, an open-source simulation platform. We take advantage of available axonal tract-tracing datasets and enhance the existing connectome data using diffusion-based tractography in macaques. We illustrate the utility of the connectome as an extension of TheVirtualBrain by simulating resting-state BOLD-fMRI data and fitting it to empirical resting-state data.

The human connectome from an evolutionary perspective

The connectome describes the comprehensive set of neuronal connections of a species' central nervous system. Identifying the network characteristics of the human macroscale connectome and comparing these features with connectomes of other species provides insight into the evolution of human brain connectivity and its role in brain function. Several network properties of the human connectome are conserved across species, with emerging evidence also indicating potential human-specific adaptations of connectome topology. This review describes the human macroscale structural and functional connectome, focusing on common themes of brain wiring in the animal kingdom and network adaptations that may underlie human brain function. Evidence is drawn from comparative studies across a wide range of animal species, and from research comparing human brain wiring with that of non-human primates. Approaching the human connectome from a comparative perspective paves the way for network-level insights into the evolution of human brain structure and function.

A combined diffusion-weighted and electroencephalography study on age-related differences in connectivity in the motor network during bimanual performance

We studied the relationship between age-related differences in inter- and intra-hemispheric structural and functional connectivity in the bilateral motor network. Our focus was on the correlation between connectivity and declined motor performance in older adults. Structural and functional connectivity were estimated using diffusion weighted imaging and resting-state electro-encephalography, respectively. A total of 48 young and older healthy participants were measured. In addition, motor performances were assessed using bimanual coordination tasks. To pre-select regions-of-interest (ROIs), a neural model was adopted that accounts for intra-hemispheric functional connectivity between dorsal premotor area (PMd) and primary motor cortex (M1) and inter-hemispheric connections between left and right M1 (M1_L and M1_R ). Functional connectivity was determined via the weighted phase-lag index (wPLI) in the source-reconstructed beta activity during rest. We quantified structural connectivity using kurtosis anisotropy (KA) values of tracts derived from diffusion tensor-based fiber tractography between the aforementioned areas. In the group of older adults, wPLI values between M1_L -M1_R were negatively associated with the quality of bimanual motor performance. The additional association between wPLI values of PMd_L --M1_L and PMd_R -M1_L supports that functional connectivity with the left hemisphere mediated (bimanual) motor control in older adults. The correlational analysis between the selected structural and functional connections revealed a strong association between wPLI values in the left intra-hemispheric PMd_L -M1_L pathway and KA values in M1_L -M1_R and PMd_R -M1_L pathways in the group of older adults. This suggests that weaker structural connections in older adults correlate with stronger functional connectivity and, hence, poorer motor performance.