The generation and validation of white matter connectivity importance maps

MRI factors associated with cognitive functioning after acute onset brain injury: Systematic review and meta-analysis

Impairments of memory, attention, and executive functioning are frequently reported after acute onset brain injury. MRI markers hold potential to contribute to identification of patients at risk for cognitive impairments and clarification of mechanisms. The aim of this systematic review was to summarize and value the evidence on MRI markers of memory, attention, and executive functioning after acute onset brain injury. We included ninety-eight studies, on six classes of MRI factors (location and severity of damage (n = 15), volume/atrophy (n = 36), signs of small vessel disease (n = 15), diffusion-weighted imaging measures (n = 36), resting-state functional MRI measures (n = 13), and arterial spin labeling measures (n = 1)). Three measures showed consistent results regarding their association with cognition. Smaller hippocampal volume was associated with worse memory in fourteen studies (pooled correlation 0.58 [95% CI: 0.46-0.68] for whole, 0.11 [95% CI: 0.04-0.19] for left, and 0.34 [95% CI: 0.17-0.49] for right hippocampus). Lower fractional anisotropy in cingulum and fornix was associated with worse memory in six and five studies (pooled correlation 0.20 [95% CI: 0.08-0.32] and 0.29 [95% CI: 0.20-0.37], respectively). Lower functional connectivity within the default-mode network was associated with worse cognition in four studies. In conclusion, hippocampal volume, fractional anisotropy in cingulum and fornix, and functional connectivity within the default-mode network showed consistent associations with cognitive performance in all types of acute onset brain injury. External validation and cut off values for predicting cognitive impairments are needed for clinical implementation.

Network-constrained technique to characterize pathology progression rate in Alzheimer's disease

Current methods for measuring the chronic rates of cognitive decline and degeneration in Alzheimer’s disease rely on the sensitivity of longitudinal neuropsychological batteries and clinical neuroimaging, particularly structural magnetic resonance imaging of brain atrophy, either at a global or regional scale. There is particular interest in approaches predictive of future disease progression and clinical outcomes using a single time point. If successful, such approaches could have great impact on differential diagnosis, therapeutic treatment and clinical trial inclusion. Unfortunately, it has proven quite challenging to accurately predict clinical and degeneration progression rates from baseline data. Specifically, a key limitation of the previously proposed approaches for disease progression based on the brain atrophy measures has been the limited incorporation of the knowledge from disease pathology progression models, which suggest a prion-like spread of disease pathology and hence the neurodegeneration. Here, we present a new metric for disease progression rate in Alzheimer that uses only MRI-derived atrophy data yet is able to infer the underlying rate of pathology transmission. This is enabled by imposing a spread process driven by the brain networks using a Network Diffusion Model. We first fit this model to each patient’s longitudinal brain atrophy data defined on a brain network structure to estimate a patient-specific rate of pathology diffusion, called the pathology progression rate. Using machine learning algorithms, we then build a baseline data model and tested this rate metric on data from longitudinal Alzheimer’s Disease Neuroimaging Initiative study including 810 subjects. Our measure of disease progression differed significantly across diagnostic groups as well as between groups with different genetic risk factors. Remarkably, hierarchical clustering revealed 3 distinct clusters based on CSF profiles with >90% accuracy. These pathological clusters exhibit progressive atrophy and clinical impairments that correspond to the proposed rate measure. We demonstrate that a subject’s degeneration speed can be best predicted from baseline neuroimaging volumetrics and fluid biomarkers for subjects in the middle of their degenerative course, which may be a practical, inexpensive screening tool for future prognostic applications.

Estimated connectivity networks outperform observed connectivity networks when classifying people with multiple sclerosis into disability groups

BACKGROUND

Multiple Sclerosis (MS), a neurodegenerative and neuroinflammatory disease, causing lesions that disrupt the brain's anatomical and physiological connectivity networks, resulting in cognitive, visual and/or motor disabilities. Advanced imaging techniques like diffusion and functional MRI allow measurement of the brain's structural connectivity (SC) and functional connectivity (FC) networks, and can enable a better understanding of how their disruptions cause disability in people with MS (pwMS). However, advanced MRI techniques are used mainly for research purposes as they are expensive, time-consuming and require high-level expertise to acquire and process. As an alternative, the Network Modification (NeMo) Tool can be used to estimate SC and FC using lesion masks derived from pwMS and a reference set of controls' connectivity networks.

OBJECTIVE

Here, we test the hypothesis that estimated SC and FC (eSC and eFC) from the NeMo Tool, based only on an individual's lesion masks, can be used to classify pwMS into disability categories just as well as SC and FC extracted from advanced MRI directly in pwMS. We also aim to find the connections most important for differentiating between no disability vs evidence of disability groups.

MATERIALS AND METHODS

One hundred pwMS (age:45.5 ± 11.4 years, 66% female, disease duration: 12.97 ± 8.07 years) were included in this study. Expanded Disability Status Scale (EDSS) was used to assess disability, 67 pwMS had no disability (EDSS < 2). Observed SC and FC were extracted from diffusion and functional MRI directly in pwMS, respectively. The NeMo Tool was used to estimate the remaining structural connectome (eSC), by removing streamlines in a reference set of tractograms that intersected the lesion mask. The NeMo Tool's eSC was used then as input to a deep neural network to estimate the corresponding FC (eFC). Logistic regression with ridge regularization was used to classify pwMS into disability categories (no disability vs evidence of disability), based on demographics/clinical information (sex, age, race, disease duration, clinical phenotype, and spinal lesion burden) and either pairwise entries or regional summaries from one of the following matrices: SC, FC, eSC, and eFC. The area under the ROC curve (AUC) was used to assess the classification performance. Both univariate statistics and parameter coefficients from the classification models were used to identify features important to differentiating between the groups.

RESULTS

The regional eSC and eFC models outperformed their observed FC and SC counterparts (p-value < 0.05), while the pairwise eSC and SC performed similarly (p = 0.10). Regional eSC and eFC models had higher AUC (0.66-0.68) than the pairwise models (0.60-0.65), with regional eFC having highest classification accuracy across all models. Ridge regression coefficients for the regional eFC and regional observed FC models were significantly correlated (Pearson's r = 0.52, p-value < 10e-7). Decreased estimated SC node strength in default mode and ventral attention networks and increased eFC node strength in visual networks was associated with evidence of disability.

DISCUSSION

Here, for the first time, we use clinically acquired lesion masks to estimate both structural and functional connectomes in patient populations to better understand brain lesion-dysfunction mapping in pwMS. Models based on the NeMo Tool's estimates of SC and FC better classified pwMS by disability level than SC and FC observed directly in the individual using advanced MRI. This work provides a viable alternative to performing high-cost, advanced MRI in patient populations, bringing the connectome one step closer to the clinic.

Predicted disconnectome associated with progressive periventricular white matter ischemia

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

Quantitative multimodal imaging in traumatic brain injuries producing impaired cognition

PURPOSE OF REVIEW

Cognitive impairments are a devastating long-term consequence following traumatic brain injury (TBI). This review provides an update on the quantitative mutimodal neuroimaging studies that attempt to elucidate the mechanism(s) underlying cognitive impairments and their recovery following TBI.

RECENT FINDINGS

Recent studies have linked individual specific behavioural impairments and their changes over time to physiological activity and structural changes using EEG, PET and MRI. Multimodal studies that combine measures of physiological activity with knowledge of neuroanatomical and connectivity damage have also illuminated the multifactorial function-structure relationships that underlie impairment and recovery following TBI.

SUMMARY

The combined use of multiple neuroimaging modalities, with focus on individual longitudinal studies, has the potential to accurately classify impairments, enhance sensitivity of prognoses, inform targets for interventions and precisely track spontaneous and intervention-driven recovery.

Cognitive impairment after focal brain lesions is better predicted by damage to structural than functional network hubs

Hubs are highly connected brain regions important for coordinating processing in brain networks. It is unclear, however, which measures of network "hubness" are most useful in identifying brain regions critical to human cognition. We tested how closely two measures of hubness-edge density and participation coefficient, derived from white and gray matter, respectively-were associated with general cognitive impairment after brain damage in two large cohorts of patients with focal brain lesions (N = 402 and 102, respectively) using cognitive tests spanning multiple cognitive domains. Lesions disrupting white matter regions with high edge density were associated with cognitive impairment, whereas lesions damaging gray matter regions with high participation coefficient had a weaker, less consistent association with cognitive outcomes. Similar results were observed with six other gray matter hubness measures. This suggests that damage to densely connected white matter regions is more cognitively impairing than similar damage to gray matter hubs, helping to explain interindividual differences in cognitive outcomes after brain damage.

Network model of pathology spread recapitulates neurodegeneration and selective vulnerability in Huntington's Disease

Huntington's Disease (HD), an autosomal dominant genetic disorder caused by a mutation in the Huntingtin gene (HTT), displays a stereotyped topography in the human brain and a stereotyped progression, initially appearing in the striatum. Like other degenerative diseases, spatial topography of HD is divorced from where implicated genes are expressed, a dissociation whose mechanistic underpinning is not currently understood. Cell autonomous molecular factors characterized by gene expression signatures, including proteolytic and post translational modifications, play a role in vulnerability to disease. Non-autonomous mechanisms, likely involving the brain's anatomic or functional connectivity patterns, might also be responsible for selective vulnerability in HD. Leveraging a large dataset of 635 subjects from a multinational study, this paper tests various cell-autonomous and non-autonomous models that can explain HD topography. We test whether the expression patterns of implicated genes is sufficient to explain regional HD atrophy, or whether the network transmission of protein products is required to explain them. We find that network models are capable of predicting, to a high degree, observed atrophy in human subjects. Lastly, we propose a model of anterograde network transmission, and show that it is the most parsimonious yet most likely to explain observed atrophy patterns in HD. Collectively, these data indicate that pathology spread in HD may be mediated by the brain's intrinsic structural network organization. This is the first study to systematically and quantitatively test multiple hypotheses of pathology spread in living human subjects with HD.

Investigating Brain Network Changes and Their Association With Cognitive Recovery After Traumatic Brain Injury: A Longitudinal Analysis

Traumatic brain injury (TBI) can result in acute cognitive deficits and diffuse axonal injury reflected in white matter brain network alterations, which may, or may not, later recover. Our objective is to first characterize the ways in which brain networks change after TBI and, second, investigate if those changes are associated with recovery of cognitive deficits. We aim to make initial progress in discerning the relationships between brain network changes, and their (dys)functional correlates. We analyze longitudinally acquired MRI from 23 TBI patients (two time points: 6 days, 12 months post-injury) and cross-sectional data from 28 controls to construct white matter brain networks. Cognitive assessment was also performed. Graph theory and regression analysis were applied to identify changed brain network metrics after injury that are associated with subsequent improvements in cognitive function. Sixteen brain network metrics were found to be discriminative of different post-injury phases. Eleven of those explain 90% (adjusted R 2) of the variability observed in cognitive recovery following TBI. Brain network metrics that had a high contribution to the explained variance were found in frontal and temporal cortex, additional to the anterior cingulate cortex. Our preliminary study suggests that network reorganization may be related to recovery of impaired cognitive function in the first year after a TBI.

Longitudinal increases in structural connectome segregation and functional connectome integration are associated with better recovery after mild TBI

Traumatic brain injury damages white matter pathways that connect brain regions, disrupting transmission of electrochemical signals and causing cognitive and emotional dysfunction. Connectome-level mechanisms for how the brain compensates for injury have not been fully characterized. Here, we collected serial MRI-based structural and functional connectome metrics and neuropsychological scores in 26 mild traumatic brain injury subjects (29.4 ± 8.0 years, 20 males) at 1 and 6 months postinjury. We quantified the relationship between functional and structural connectomes using network diffusion (ND) model propagation time, a measure that can be interpreted as how much of the structural connectome is being utilized for the spread of functional activation, as captured via the functional connectome. Overall cognition showed significant improvement from 1 to 6 months (t25 = -2.15, p = .04). None of the structural or functional global connectome metrics was significantly different between 1 and 6 months, or when compared to 34 age- and gender-matched controls (28.6 ± 8.8 years, 25 males). We predicted longitudinal changes in overall cognition from changes in global connectome measures using a partial least squares regression model (cross-validated R2 = .27). We observe that increased ND model propagation time, increased structural connectome segregation, and increased functional connectome integration were related to better cognitive recovery. We interpret these findings as suggesting two connectome-based postinjury recovery mechanisms: one of neuroplasticity that increases functional connectome integration and one of remote white matter degeneration that increases structural connectome segregation. We hypothesize that our inherently multimodal measure of ND model propagation time captures the interplay between these two mechanisms.

Baseline biomarkers of connectome disruption and atrophy predict future processing speed in early multiple sclerosis

The development of accurate prognoses in multiple sclerosis is difficult, as the disease is characterized by heterogeneous patterns of brain abnormalities that relate in an unclear way to future impairments. Here, we use a statistical modeling approach to determine if the baseline pattern of connectome disruption due to T2-FLAIR lesions could predict a patient's future processing speed, as measured using the Symbol Digits Modality Test scores. Imaging data, demographics and Symbol Digits Modality Test scores were collected from 61 early relapsing remitting multiple sclerosis patients. The Network Modification Tool was used to estimate damage to the connectome by quantifying white matter abnormalities' effects on 1) global network properties, 2) regional connectivity and 3) connectivity between pairs of regions. MS subjects showed significant improvement of processing speed between baseline and follow-up (t = −2.6, p = 0.0096); however, both baseline (t = −4.01, p = 0.00012) and follow-up (t = −2.10, p = 0.038) processing speed were significantly lower than age-matched healthy controls. Partial Least Squares Regression was used to create models that predict future processing speed from between baseline imaging metrics and demographics. The model based on region-pair disconnection and gray matter atrophy had the lowest AIC and highest prediction accuracy (R² = 0.79) compared to models based on global (R² = 0.41) or regional (R² = 0.66) disconnection and gray matter atrophy, overlap with an ROI-based atlas and gray matter atrophy (R² = 0.73) or gray matter atrophy alone (R² = 0.71). We found that baseline measures of connectivity disruption in various parietal, temporal, occipital and subcortical regions and atrophy in the putamen were important predictors of future processing speed. We conclude that information about disruptions to pairwise brain connections is more informative of future processing speed than regional or global metrics or gray matter atrophy alone. The combination of quantitative disconnectome metrics, gray matter atrophy and statistical modeling approaches could enable clinicians in developing more accurate, individualized prognoses of future cognitive status in multiple sclerosis patients.

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Atrophy and structural disconnection estimates via NeMo Tool were collected in MS.

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Future cognitive functioning in MS patients was predicted by baseline MRI measures.

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Measures of atrophy and disconnection between region-pairs had best goodness-of-fit.

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More caudate atrophy was significantly predictive of worse future cognition.

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Disconnections in parietal/temporal/occipital areas predicted worse future cognition.

Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease

Recent research has demonstrated the use of the structural connectome as a powerful tool to characterize the network architecture of the brain and potentially generate biomarkers for neurologic and psychiatric disorders. In particular, the anatomic embedding of the edges of the cerebral graph have been postulated to elucidate the relative importance of white matter tracts to the overall network connectivity, explaining the varying effects of localized white matter pathology on cognition and behavior. Here, we demonstrate the use of a linear diffusion model to quantify the impact of these perturbations on brain connectivity. We show that the eigenmodes governing the dynamics of this model are strongly conserved between healthy subjects regardless of cortical and sub-cortical parcellations, but show significant, interpretable deviations in improperly developed brains. More specifically, we investigated the effect of agenesis of the corpus callosum (AgCC), one of the most common brain malformations to identify differences in the effect of virtual corpus callosotomies and the neurodevelopmental disorder itself. These findings, including the strong correspondence between regions of highest importance from graph eigenmodes of network diffusion and nexus regions of white matter from edge density imaging, show converging evidence toward understanding the relationship between white matter anatomy and the structural connectome.

While the structural connectome of the brain has emerged as a powerful tool towards understanding the progression of neurologic and psychiatric disorders, links between the anatomy of connections within the brain and the effects of localized white matter pathology on cognition are still an active area of investigation. Here, we propose the use of the diffusion process towards understanding perturbations of brain connectivity. We find that while the dynamics of this process are strongly conserved in healthy subjects, they display significant, interpretable deviations in agenesis of the corpus callosum, one of the most common brain malformations. These findings, including the strong similarity between regions identified to be crucial towards diffusion and nexus regions of white matter from edge density imaging, show converging evidence towards understanding the relationship between white matter anatomy and the structural connectome.

Assessing connectivity related injury burden in diffuse traumatic brain injury

Many of the clinical and behavioral manifestations of traumatic brain injury (TBI) are thought to arise from disruption to the structural network of the brain due to diffuse axonal injury (DAI). However, a principled way of summarizing diffuse connectivity alterations to quantify injury burden is lacking. In this study, we developed a connectome injury score, Disruption Index of the Structural Connectome (DISC), which summarizes the cumulative effects of TBI-induced connectivity abnormalities across the entire brain. Forty patients with moderate-to-severe TBI examined at 3 months postinjury and 35 uninjured healthy controls underwent magnetic resonance imaging with diffusion tensor imaging, and completed behavioral assessment including global clinical outcome measures and neuropsychological tests. TBI patients were selected to maximize the likelihood of DAI in the absence of large focal brain lesions. We found that hub-like regions, with high betweenness centrality, were most likely to be impaired as a result of diffuse TBI. Clustering of participants revealed a subgroup of TBI patients with similar connectivity abnormality profiles who exhibited relatively poor cognitive performance. Among TBI patients, DISC was significantly correlated with post-traumatic amnesia, verbal learning, executive function, and processing speed. Our experiments jointly demonstrated that assessing structural connectivity alterations may be useful in development of patient-oriented diagnostic and prognostic tools. Hum Brain Mapp 38:2913-2922, 2017. © 2017 Wiley Periodicals, Inc.

The application of a mathematical model linking structural and functional connectomes in severe brain injury

Following severe injuries that result in disorders of consciousness, recovery can occur over many months or years post-injury. While post-injury synaptogenesis, axonal sprouting and functional reorganization are known to occur, the network-level processes underlying recovery are poorly understood. Here, we test a network-level functional rerouting hypothesis in recovery of patients with disorders of consciousness following severe brain injury. This hypothesis states that the brain recovers from injury by restoring normal functional connections via alternate structural pathways that circumvent impaired white matter connections. The so-called network diffusion model, which relates an individual's structural and functional connectomes by assuming that functional activation diffuses along structural pathways, is used here to capture this functional rerouting. We jointly examined functional and structural connectomes extracted from MRIs of 12 healthy and 16 brain-injured subjects. Connectome properties were quantified via graph theoretic measures and network diffusion model parameters. While a few graph metrics showed groupwise differences, they did not correlate with patients' level of consciousness as measured by the Coma Recovery Scale — Revised. There was, however, a strong and significant partial Pearson's correlation (accounting for age and years post-injury) between level of consciousness and network diffusion model propagation time (r = 0.76, p < 0.05, corrected), i.e. the time functional activation spends traversing the structural network. We concluded that functional rerouting via alternate (and less efficient) pathways leads to increases in network diffusion model propagation time. Simulations of injury and recovery in healthy connectomes confirmed these results. This work establishes the feasibility for using the network diffusion model to capture network-level mechanisms in recovery of consciousness after severe brain injury.

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A “functional rerouting” hypothesis in recovery from brain injury is tested.

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The connectome-based network diffusion model measures functional rerouting.

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Recovery in severe brain injury correlates with a network diffusion model parameter.

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Simulation in healthy connectomes independently validates the results in patients.

Segregation of anterior temporal regions critical for retrieving names of unique and non-unique entities reflects underlying long-range connectivity

Lesion-deficit studies support the hypothesis that the left anterior temporal lobe (ATL) plays a critical role in retrieving names of concrete entities. They further suggest that different regions of the left ATL process different conceptual categories. Here we test the specificity of these relationships and whether the anatomical segregation is related to the underlying organization of white matter connections. We reanalyzed data from a previous lesion study of naming and recognition across five categories of concrete entities. In voxelwise logistic regressions of lesion-deficit associations, we formally incorporated measures of disconnection of long-range association fiber tracts (FTs) and covaried for recognition and non-category-specific naming deficits. We also performed fiber tractwise analyses to assess whether damage to specific FTs was preferentially associated with category-selective naming deficits. Damage to the basolateral ATL was associated with naming deficits for both unique (famous faces) and non-unique entities, whereas the damage to the temporal pole was associated with naming deficits for unique entities only. This segregation pattern remained after accounting for comorbid recognition deficits or naming deficits in other categories. The tractwise analyses showed that damage to the uncinate fasciculus (UNC) was associated with naming impairments for unique entities, while damage to the inferior longitudinal fasciculus (ILF) was associated with naming impairments for non-unique entities. Covarying for FT transection in voxelwise analyses rendered the cortical association for unique entities more focal. These results are consistent with the partial segregation of brain system support for name retrieval of unique and non-unique entities at both the level of cortical components and underlying white matter fiber bundles. Our study reconciles theoretic accounts of the functional organization of the left ATL by revealing both category-related processing and semantic hub sectors.

Exploring the brain's structural connectome: A quantitative stroke lesion-dysfunction mapping study

The aim of this work was to quantitatively model cross-sectional relationships between structural connectome disruptions caused by cerebral infarction and measures of clinical performance. Imaging biomarkers of 41 ischemic stroke patients (72.0 ± 12.0 years, 20 female) were related to their baseline performance in 18 cognitive, physical and daily life activity assessments. Individual estimates of structural connectivity disruption in gray matter regions were computed using the Change in Connectivity (ChaCo) score. ChaCo scores were utilized because they can be calculated using routinely collected clinical magnetic resonance imagings. Partial Least Squares Regression (PLSR) was used to predict various acute impairment and activity measures from ChaCo scores and patient demographics. Statistical methods of cross-validation, bootstrapping and multiple comparisons correction were implemented to minimize over-fitting and Type I errors. Multiple linear regression models based on lesion volume and lateralization information were constructed for comparison. All models based on connectivity disruption had lower Akaike Information Criterion and almost all had better goodness-of-fit values (R(2) : 0.26-0.92) than models based on lesion characteristics (R(2) : 0.06-0.50). Confidence intervals of PLSR coefficients identified brain regions important in predicting each clinical assessment. Appropriate mapping of eloquent functions, that is, language and motor, and replication of results across pathologies provided validation of this method. Models of complex functions provided new insights into brain-behavior relationships. In addition to the potential applications in prognostication and rehabilitation development, this quantitative approach provides insight into the structural networks underlying complex functions like activities of daily living and cognition. Quantitative analysis of big data will be invaluable in understanding complex brain-behavior relationships.

Edge density imaging: mapping the anatomic embedding of the structural connectome within the white matter of the human brain

The structural connectome has emerged as a powerful tool to characterize the network architecture of the human brain and shows great potential for generating important new biomarkers for neurologic and psychiatric disorders. The edges of the cerebral graph traverse white matter to interconnect cortical and subcortical nodes, although the anatomic embedding of these edges is generally overlooked in the literature. Mapping the paths of the connectome edges could elucidate the relative importance of individual white matter tracts to the overall network topology of the brain and also lead to a better understanding of the effect of regionally-specific white matter pathology on cognition and behavior. In this work, we introduce edge density imaging (EDI), which maps the number of network edges that pass through every white matter voxel. Test-retest analysis shows good to excellent reliability for edge density (ED) measurements, with consistent results using different cortical and subcortical parcellation schemes and different diffusion MR imaging acquisition parameters. We also demonstrate that ED yields complementary information to both traditional and emerging voxel-wise metrics of white matter microstructure and connectivity, including fractional anisotropy, track density, fiber orientation dispersion and neurite density. Our results demonstrate spatially ordered variations of ED throughout the white matter, notably including greater ED in posterior than anterior cerebral white matter. The EDI framework is employed to map the white matter regions that are enriched with pathways connecting rich club nodes and also those with high densities of intra-modular and inter-modular edges. We show that periventricular white matter has particularly high ED and high densities of rich club edges, which is significant for diseases in which these areas are selectively affected, ranging from white matter injury of prematurity in infants to leukoaraiosis in the elderly. Using edge betweenness centrality, we identify specific white matter regions involved in a large number of shortest paths, some containing highly connected rich club edges while others are relatively isolated within individual modules. Overall, these findings reveal an intricate relationship between white matter anatomy and the structural connectome, motivating further exploration of EDI for biomarkers of cognition and behavior.

Validation of network communicability metrics for the analysis of brain structural networks

Computational network analysis provides new methods to analyze the brain's structural organization based on diffusion imaging tractography data. Networks are characterized by global and local metrics that have recently given promising insights into diagnosis and the further understanding of psychiatric and neurologic disorders. Most of these metrics are based on the idea that information in a network flows along the shortest paths. In contrast to this notion, communicability is a broader measure of connectivity which assumes that information could flow along all possible paths between two nodes. In our work, the features of network metrics related to communicability were explored for the first time in the healthy structural brain network. In addition, the sensitivity of such metrics was analysed using simulated lesions to specific nodes and network connections. Results showed advantages of communicability over conventional metrics in detecting densely connected nodes as well as subsets of nodes vulnerable to lesions. In addition, communicability centrality was shown to be widely affected by the lesions and the changes were negatively correlated with the distance from lesion site. In summary, our analysis suggests that communicability metrics that may provide an insight into the integrative properties of the structural brain network and that these metrics may be useful for the analysis of brain networks in the presence of lesions. Nevertheless, the interpretation of communicability is not straightforward; hence these metrics should be used as a supplement to the more standard connectivity network metrics.

The Network Modification (NeMo) Tool: elucidating the effect of white matter integrity changes on cortical and subcortical structural connectivity

Accurate prediction of brain dysfunction caused by disease or injury requires the quantification of resultant neural connectivity changes compared with the normal state. There are many methods with which to assess anatomical changes in structural or diffusion magnetic resonance imaging, but most overlook the topology of white matter (WM) connections that make up the healthy brain network. Here, a new neuroimaging software pipeline called the Network Modification (NeMo) Tool is presented that associates alterations in WM integrity with expected changes in neural connectivity between gray matter regions. The NeMo Tool uses a large reference set of healthy tractograms to assess implied network changes arising from a particular pattern of WM alteration on a region- and network-wise level. In this way, WM integrity changes can be extrapolated to the cortices and deep brain nuclei, enabling assessment of functional and cognitive alterations. Unlike current techniques that assess network dysfunction, the NeMo tool does not require tractography in pathological brains for which the algorithms may be unreliable or diffusion data are unavailable. The versatility of the NeMo Tool is demonstrated by applying it to data from patients with Alzheimer's disease, fronto-temporal dementia, normal pressure hydrocephalus, and mild traumatic brain injury. This tool fills a gap in the quantitative neuroimaging field by enabling an investigation of morphological and functional implications of changes in structural WM integrity.

Neuroinformatics challenges to the structural, connectomic, functional and electrophysiological multimodal imaging of human traumatic brain injury

Throughout the past few decades, the ability to treat and rehabilitate traumatic brain injury (TBI) patients has become critically reliant upon the use of neuroimaging to acquire adequate knowledge of injury-related effects upon brain function and recovery. As a result, the need for TBI neuroimaging analysis methods has increased in recent years due to the recognition that spatiotemporal computational analyses of TBI evolution are useful for capturing the effects of TBI dynamics. At the same time, however, the advent of such methods has brought about the need to analyze, manage, and integrate TBI neuroimaging data using informatically inspired approaches which can take full advantage of their large dimensionality and informational complexity. Given this perspective, we here discuss the neuroinformatics challenges for TBI neuroimaging analysis in the context of structural, connectivity, and functional paradigms. Within each of these, the availability of a wide range of neuroimaging modalities can be leveraged to fully understand the heterogeneity of TBI pathology; consequently, large-scale computer hardware resources and next-generation processing software are often required for efficient data storage, management, and analysis of TBI neuroimaging data. However, each of these paradigms poses challenges in the context of informatics such that the ability to address them is critical for augmenting current capabilities to perform neuroimaging analysis of TBI and to improve therapeutic efficacy.

Spatial patterns of genome-wide expression profiles reflect anatomic and fiber connectivity architecture of healthy human brain

Unraveling the relationship between molecular signatures in the brain and their functional, architectonic, and anatomic correlates is an important neuroscientific goal. It is still not well understood whether the diversity demonstrated by histological studies in the human brain is reflected in the spatial patterning of whole brain transcriptional profiles. Using genome-wide maps of transcriptional distribution of the human brain by the Allen Brain Institute, we test the hypothesis that gene expression profiles are specific to anatomically described brain regions. In this work, we demonstrate that this is indeed the case by showing that gene similarity clusters appear to respect conventional basal-cortical and caudal-rostral gradients. To fully investigate the causes of this observed spatial clustering, we test a connectionist hypothesis that states that the spatial patterning of gene expression in the brain is simply reflective of the fiber tract connectivity between brain regions. We find that although gene expression and structural connectivity are not determined by each other, they do influence each other with a high statistical significance. This implies that spatial diversity of gene expressions is a result of mainly location-specific features but is influenced by neuronal connectivity, such that like cellular species preferentially connects with like cells.

Test-retest reliability of computational network measurements derived from the structural connectome of the human brain

Structural magnetic resonance (MR) connectomics holds promise for the diagnosis, outcome prediction, and treatment monitoring of many common neurodevelopmental, psychiatric, and neurodegenerative disorders for which there is currently no clinical utility for MR imaging (MRI). Before computational network metrics from the human connectome can be applied in a clinical setting, their precision and their normative intersubject variation must be understood to guide the study design and the interpretation of longitudinal data. In this work, the reproducibility of commonly used graph theoretic measures is investigated, as applied to the structural connectome of healthy adult volunteers. Two datasets are examined, one consisting of 10 subjects scanned twice at one MRI facility and one consisting of five subjects scanned once each at two different facilities using the same imaging platform. Global graph metrics are calculated for unweighed and weighed connectomes, and two levels of granularity of the connectome are evaluated: one based on the 82-node cortical and subcortical parcellation from FreeSurfer and one based on an atlas-free parcellation of the gray-white matter boundary consisting of 1000 cortical nodes. The consistency of the unweighed and weighed edges and the module assignments are also computed for the 82-node connectomes. Overall, the results demonstrate good-to-excellent test-retest reliability for the entire connectome-processing pipeline, including the graph analytics, in both the intrasite and intersite datasets. These findings indicate that measurements of computational network metrics derived from the structural connectome have sufficient precision to be tested as potential biomarkers for diagnosis, prognosis, and monitoring of interventions in neurological and psychiatric diseases.

White matter structural connectivity is associated with sensorimotor function in stroke survivors

Purpose

Diffusion tensor imaging (DTI) provides functionally relevant information about white matter structure. Local anatomical connectivity information combined with fractional anisotropy (FA) and mean diffusivity (MD) may predict functional outcomes in stroke survivors. Imaging methods for predicting functional outcomes in stroke survivors are not well established. This work uses DTI to objectively assess the effects of a stroke lesion on white matter structure and sensorimotor function.

Methods

A voxel-based approach is introduced to assess a stroke lesion's global impact on motor function. Anatomical T1-weighted and diffusion tensor images of the brain were acquired for nineteen subjects (10 post-stroke and 9 age-matched controls). A manually selected volume of interest was used to alleviate the effects of stroke lesions on image registration. Images from all subjects were registered to the images of the control subject that was anatomically closest to Talairach space. Each subject's transformed image was uniformly seeded for DTI tractography. Each seed was inversely transformed into the individual subject space, where DTI tractography was conducted and then the results were transformed back to the reference space. A voxel-wise connectivity matrix was constructed from the fibers, which was then used to calculate the number of directly and indirectly connected neighbors of each voxel. A novel voxel-wise indirect structural connectivity (VISC) index was computed as the average number of direct connections to a voxel's indirect neighbors. Voxel-based analyses (VBA) were performed to compare VISC, FA, and MD for the detection of lesion-induced changes in sensorimotor function. For each voxel, a t-value was computed from the differences between each stroke brain and the 9 controls. A series of linear regressions was performed between Fugl-Meyer (FM) assessment scores of sensorimotor impairment and each DTI metric's log number of voxels that differed from the control group.

Results

Correlation between the logarithm of the number of significant voxels in the ipsilesional hemisphere and total Fugl-Meyer score was moderate for MD (R2 = 0.512), and greater for VISC (R2 = 0.796) and FA (R2 = 0.674). The slopes of FA (p = 0.0036), VISC (p = 0.0005), and MD (p = 0.0199) versus the total FM score were significant. However, these correlations were driven by the upper extremity motor component of the FM score (VISC: R2 = 0.879) with little influence of the lower extremity motor component (FA: R2 = 0.177).

Conclusion

The results suggest that a voxel-wise metric based on DTI tractography can predict upper extremity sensorimotor function of stroke survivors, and that supraspinal intraconnectivity may have a less dominant role in lower extremity function.

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An intrinsic voxel-based structural connectivity metric is proposed.

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The metric enhances the impact of stroke lesions on the distant voxels.

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Whole-brain extralesional anatomical connectivity predicts functional outcome.

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Functional impact of a lesion is determined by residual anatomical connectivity.

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Connectivity to the posterior parietal cortex is a key to sensorimotor function.

The structural connectome of the human brain in agenesis of the corpus callosum

Adopting a network perspective, the structural connectome reveals the large-scale white matter connectivity of the human brain, yielding insights into cerebral organization otherwise inaccessible to researchers and clinicians. Connectomics has great potential for elucidating abnormal connectivity in congenital brain malformations, especially axonal pathfinding disorders. Agenesis of the corpus callosum (AgCC) is one of the most common brain malformations and can also be considered a prototypical genetic disorder of axonal guidance in humans. In this exploratory study, the structural connectome of AgCC is mapped and compared to that of the normal human brain. Multiple levels of granularity of the AgCC connectome are investigated, including summary network metrics, modularity analysis, and network consistency measures, with comparison to the normal structural connectome after simulated removal of all callosal connections ("virtual callostomy"). These investigations reveal four major findings. First, global connectivity is abnormally reduced in AgCC, but local connectivity is increased. Second, the network topology of AgCC is more variable than that of the normal human connectome, contradicting the predictions of the virtual callostomy model. Third, modularity analysis reveals that many of the tracts that comprise the structural core of the cerebral cortex have relatively weak connectivity in AgCC, especially the cingulate bundles bilaterally. Finally, virtual lesions of the Probst bundles in the AgCC connectome demonstrate that there is consistency across subjects in many of the connections generated by these ectopic white matter tracts, and that they are a mixture of cortical and subcortical fibers. These results go beyond prior diffusion tractography studies to provide a systems-level perspective on anomalous connectivity in AgCC. Furthermore, this work offers a proof of principle for the utility of the connectome framework in neurodevelopmental disorders.

Neuropathology of mild traumatic brain injury: relationship to neuroimaging findings

Neuroimaging identified abnormalities associated with traumatic brain injury (TBI) are but gross indicators that reflect underlying trauma-induced neuropathology at the cellular level. This review examines how cellular pathology relates to neuroimaging findings with the objective of more closely relating how neuroimaging findings reveal underlying neuropathology. Throughout this review an attempt will be made to relate what is directly known from post-mortem microscopic and gross anatomical studies of TBI of all severity levels to the types of lesions and abnormalities observed in contemporary neuroimaging of TBI, with an emphasis on mild traumatic brain injury (mTBI). However, it is impossible to discuss the neuropathology of mTBI without discussing what occurs with more severe injury and viewing pathological changes on some continuum from the mildest to the most severe. Historical milestones in understanding the neuropathology of mTBI are reviewed along with implications for future directions in the examination of neuroimaging and neuropathological correlates of TBI.

Neuroimaging of structural pathology and connectomics in traumatic brain injury: Toward personalized outcome prediction

Recent contributions to the body of knowledge on traumatic brain injury (TBI) favor the view that multimodal neuroimaging using structural and functional magnetic resonance imaging (MRI and fMRI, respectively) as well as diffusion tensor imaging (DTI) has excellent potential to identify novel biomarkers and predictors of TBI outcome. This is particularly the case when such methods are appropriately combined with volumetric/morphometric analysis of brain structures and with the exploration of TBI-related changes in brain network properties at the level of the connectome. In this context, our present review summarizes recent developments on the roles of these two techniques in the search for novel structural neuroimaging biomarkers that have TBI outcome prognostication value. The themes being explored cover notable trends in this area of research, including (1) the role of advanced MRI processing methods in the analysis of structural pathology, (2) the use of brain connectomics and network analysis to identify outcome biomarkers, and (3) the application of multivariate statistics to predict outcome using neuroimaging metrics. The goal of the review is to draw the community's attention to these recent advances on TBI outcome prediction methods and to encourage the development of new methodologies whereby structural neuroimaging can be used to identify biomarkers of TBI outcome.

Combining the finite element method with structural connectome-based analysis for modeling neurotrauma: connectome neurotrauma mechanics

This article presents the integration of brain injury biomechanics and graph theoretical analysis of neuronal connections, or connectomics, to form a neurocomputational model that captures spatiotemporal characteristics of trauma. We relate localized mechanical brain damage predicted from biofidelic finite element simulations of the human head subjected to impact with degradation in the structural connectome for a single individual. The finite element model incorporates various length scales into the full head simulations by including anisotropic constitutive laws informed by diffusion tensor imaging. Coupling between the finite element analysis and network-based tools is established through experimentally-based cellular injury thresholds for white matter regions. Once edges are degraded, graph theoretical measures are computed on the “damaged” network. For a frontal impact, the simulations predict that the temporal and occipital regions undergo the most axonal strain and strain rate at short times (less than 24 hrs), which leads to cellular death initiation, which results in damage that shows dependence on angle of impact and underlying microstructure of brain tissue. The monotonic cellular death relationships predict a spatiotemporal change of structural damage. Interestingly, at 96 hrs post-impact, computations predict no network nodes were completely disconnected from the network, despite significant damage to network edges. At early times () network measures of global and local efficiency were degraded little; however, as time increased to 96 hrs the network properties were significantly reduced. In the future, this computational framework could help inform functional networks from physics-based structural brain biomechanics to obtain not only a biomechanics-based understanding of injury, but also neurophysiological insight.

According to the Centers for Disease Control and Prevention in the United States, approximately 1.7 million people, on average, sustain a traumatic brain injury annually. During the last few decades, brain neurotrauma biomechanics has been an active area of research involving medical clinicians and a broad range of scientists and engineers. In addition, advances and fast growth of human connectomics continues to reveal new insights into the damaged brain. With recent advances in computational methods and high performance computing, we see the need and the exciting possibility to merge brain neurotrauma biomechanics and human connectomics science to form a new area of investigation - connectome neurotrauma mechanics. For neurotrauma, the idea is simple - inform human structural connectome analysis using physics-based predictions of biomechanical brain injury. If successful, this technique may be further used to inform human functional connectome analysis, thus providing a new tool to help understand the pathophysiology of mild traumatic brain injury.

Loss in connectivity among regions of the brain reward system in alcohol dependence

A recently developed measure of structural brain connectivity disruption, the loss in connectivity (LoCo), is adapted for studies in alcohol dependence. LoCo uses independent tractography information from young healthy controls to project the location of white matter (WM) microstructure abnormalities in alcohol-dependent versus nondependent individuals onto connected gray matter (GM) regions. LoCo scores are computed from WM abnormality masks derived at two levels: (1) groupwise differences of alcohol-dependent individuals (ALC) versus light-drinking (LD) controls and (2) differences of each ALC individual versus the LD control group. LoCo scores based on groupwise WM differences show that GM regions belonging to the extended brain reward system (BRS) network have significantly higher LoCo (i.e., disconnectivity) than those not in this network (t = 2.18, P = 0.016). LoCo scores based on individuals' WM differences are also higher in BRS versus non-BRS (t = 5.26, P = 3.92 × 10(-6) ) of ALC. These results suggest that WM alterations in alcohol dependence, although subtle and spatially heterogeneous across the population, are nonetheless preferentially localized to the BRS. LoCo is shown to provide a more sensitive estimate of GM involvement than conventional volumetric GM measures by better differentiating between brains of ALC and LD controls (rates of 89.3% vs. 69.6%). However, just as volumetric measures, LoCo is not significantly correlated with standard metrics of drinking severity. LoCo is a sensitive WM measure of regional cortical disconnectivity that uniquely characterizes anatomical network disruptions in alcohol dependence.

Linking white matter integrity loss to associated cortical regions using structural connectivity information in Alzheimer's disease and fronto-temporal dementia: the Loss in Connectivity (LoCo) score

It is well known that gray matter changes occur in neurodegenerative diseases like Alzheimer's (AD) and fronto-temporal dementia (FTD), and several studies have investigated their respective patterns of atrophy progression. Recent work, however, has revealed that diffusion MRI that is able to detect white matter integrity changes may be an earlier or more sensitive biomarker in both diseases. However, studies that examine white matter changes only are limited in that they do not provide the functional specificity of GM region-based analysis. In this study, we develop a new metric called the Loss in Connectivity (LoCo) score that gives the amount of structural network disruption incurred by a gray matter region for a particular pattern of white matter integrity loss. Leveraging the relative strengths of WM and GM markers, this metric links areas of WM integrity loss to their connected GM regions as a first step in understanding their functional implications. The LoCo score is calculated for three groups: 18AD, 18 FTD, and 19 age-matched normal controls. We show significant correlations of the LoCo with the respective atrophy patterns in AD (R=0.51, p=2.2 × 10(-9)) and FTD (R=0.49, p=2.5 × 10(-8)) for a standard 116 region gray matter atlas. In addition, we demonstrate that the LoCo outperforms a measure of gray matter atrophy when classifying individuals into AD, FTD, and normal groups.