Pre- and post-surgery brain tumor multimodal magnetic resonance imaging data optimized for large scale computational modelling.

We present a dataset of magnetic resonance imaging (MRI) data (T1, diffusion, BOLD) acquired in 25 brain tumor patients before the tumor resection surgery, and six months after the surgery, together with the tumor masks, and in 11 controls (recruited among the patients' caregivers). The dataset also contains behavioral and emotional scores obtained with standardized questionnaires. To simulate personalized computational models of the brain, we also provide structural connectivity matrices, necessary to perform whole-brain modelling with tools such as The Virtual Brain. In addition, we provide blood-oxygen-level-dependent imaging time series averaged across regions of interest for comparison with simulation results. An average resting state hemodynamic response function for each region of interest, as well as shape maps for each voxel, are also contributed.

MRI Clustering Reveals Three ALS Subtypes With Unique Neurodegeneration Patterns.

OBJECTIVE: The purpose of this study was to identify subtypes of amyotrophic lateral sclerosis (ALS) by comparing patterns of neurodegeneration using brain magnetic resonance imaging (MRI) and explore their phenotypes. METHODS: We performed T1-weighted and diffusion tensor imaging in 488 clinically well-characterized patients with ALS and 338 control subjects. Measurements of whole-brain cortical thickness and white matter connectome fractional anisotropy were adjusted for disease-unrelated variation. A probabilistic network-based clustering algorithm was used to divide patients into subgroups of similar neurodegeneration patterns. Clinical characteristics and cognitive profiles were assessed for each subgroup. In total, 512 follow-up scans were used to validate clustering results longitudinally. RESULTS: The clustering algorithm divided patients with ALS into 3 subgroups of 187, 163, and 138 patients. All subgroups displayed involvement of the precentral gyrus and are characterized, respectively, by (1) pure motor involvement (pure motor cluster [PM]), (2) orbitofrontal and temporal involvement (frontotemporal cluster [FT]), and (3) involvement of the posterior cingulate cortex, parietal white matter, temporal operculum, and cerebellum (cingulate-parietal-temporal cluster [CPT]). These subgroups had significantly distinct clinical profiles regarding male-to-female ratio, age at symptom onset, and frequency of bulbar symptom onset. FT and CPT revealed higher rates of cognitive impairment on the Edinburgh cognitive and behavioral ALS screen (ECAS). Longitudinally, clustering remained stable: at 90.4% of their follow-up visits, patients clustered in the same subgroup as their baseline visit. INTERPRETATION: ALS can manifest itself in 3 main patterns of cerebral neurodegeneration, each associated with distinct clinical characteristics and cognitive profiles. Besides the pure motor and frontotemporal dementia (FTD)-like variants of ALS, a new neuroimaging phenotype has emerged, characterized by posterior cingulate, parietal, temporal, and cerebellar involvement. ANN NEUROL 2022;92:1030-1045.

Predicting time-resolved electrophysiological brain networks from structural eigenmodes.

How temporal modulations in functional interactions are shaped by the underlying anatomical connections remains an open question. Here, we analyse the role of structural eigenmodes, in the formation and dissolution of temporally evolving functional brain networks using resting-state magnetoencephalography and diffusion magnetic resonance imaging data at the individual subject level. Our results show that even at short timescales, phase and amplitude connectivity can partly be expressed by structural eigenmodes, but hardly by direct structural connections. Albeit a stronger relationship was found between structural eigenmodes and time-resolved amplitude connectivity. Time-resolved connectivity for both phase and amplitude was mostly characterised by a stationary process, superimposed with very brief periods that showed deviations from this stationary process. For these brief periods, dynamic network states were extracted that showed different expressions of eigenmodes. Furthermore, the eigenmode expression was related to overall cognitive performance and co-occurred with fluctuations in community structure of functional networks. These results implicate that ongoing time-resolved resting-state networks, even at short timescales, can to some extent be understood in terms of activation and deactivation of structural eigenmodes and that these eigenmodes play a role in the dynamic integration and segregation of information across the cortex, subserving cognitive functions.

Virtual deep brain stimulation: Multiscale co-simulation of a spiking basal ganglia model and a whole-brain mean-field model with The Virtual Brain.

Deep brain stimulation (DBS) has been successfully applied in various neurodegenerative diseases as an effective symptomatic treatment. However, its mechanisms of action within the brain network are still poorly understood. Many virtual DBS models analyze a subnetwork around the basal ganglia and its dynamics as a spiking network with their details validated by experimental data. However, connectomic evidence shows widespread effects of DBS affecting many different cortical and subcortical areas. From a clinical perspective, various effects of DBS besides the motoric impact have been demonstrated. The neuroinformatics platform The Virtual Brain (TVB) offers a modeling framework allowing us to virtually perform stimulation, including DBS, and forecast the outcome from a dynamic systems perspective prior to invasive surgery with DBS lead placement. For an accurate prediction of the effects of DBS, we implement a detailed spiking model of the basal ganglia, which we combine with TVB via our previously developed co-simulation environment. This multiscale co-simulation approach builds on the extensive previous literature of spiking models of the basal ganglia while simultaneously offering a whole-brain perspective on widespread effects of the stimulation going beyond the motor circuit. In the first demonstration of our model, we show that virtual DBS can move the firing rates of a Parkinson's disease patient's thalamus - basal ganglia network towards the healthy regime while, at the same time, altering the activity in distributed cortical regions with a pronounced effect in frontal regions. Thus, we provide proof of concept for virtual DBS in a co-simulation environment with TVB. The developed modeling approach has the potential to optimize DBS lead placement and configuration and forecast the success of DBS treatment for individual patients.

Bridging Scales in Alzheimer's Disease: Biological Framework for Brain Simulation With The Virtual Brain.

Despite the acceleration of knowledge and data accumulation in neuroscience over the last years, the highly prevalent neurodegenerative disease of AD remains a growing problem. Alzheimer's Disease (AD) is the most common cause of dementia and represents the most prevalent neurodegenerative disease. For AD, disease-modifying treatments are presently lacking, and the understanding of disease mechanisms continues to be incomplete. In the present review, we discuss candidate contributing factors leading to AD, and evaluate novel computational brain simulation methods to further disentangle their potential roles. We first present an overview of existing computational models for AD that aim to provide a mechanistic understanding of the disease. Next, we outline the potential to link molecular aspects of neurodegeneration in AD with large-scale brain network modeling using The Virtual Brain (www.thevirtualbrain.org), an open-source, multiscale, whole-brain simulation neuroinformatics platform. Finally, we discuss how this methodological approach may contribute to the understanding, improved diagnostics, and treatment optimization of AD.

Multimodal longitudinal study of structural brain involvement in amyotrophic lateral sclerosis.

OBJECTIVE: To understand the progressive nature of amyotrophic lateral sclerosis (ALS) by investigating differential brain patterns of gray and white matter involvement in clinically or genetically defined subgroups of patients using cross-sectional, longitudinal, and multimodal MRI. METHODS: We assessed cortical thickness, subcortical volumes, and white matter connectivity from T1-weighted and diffusion-weighted MRI in 292 patients with ALS (follow-up: n = 150) and 156 controls (follow-up: n = 72). Linear mixed-effects models were used to assess changes in structural brain measurements over time in patients compared to controls. RESULTS: Patients with a C9orf72 mutation (n = 24) showed widespread gray and white matter involvement at baseline, and extensive loss of white matter integrity in the connectome over time. In C9orf72-negative patients, we detected cortical thinning of motor and frontotemporal regions, and loss of white matter integrity of connections linked to the motor cortex. Patients with spinal onset displayed widespread white matter involvement at baseline and gray matter atrophy over time, whereas patients with bulbar onset started out with prominent gray matter involvement. Patients with unaffected cognition or behavior displayed predominantly motor system involvement, while widespread cerebral changes, including frontotemporal regions with progressive white matter involvement over time, were associated with impaired behavior or cognition. Progressive loss of gray and white matter integrity typically occurred in patients with shorter disease durations (<13 months), independent of progression rate. CONCLUSIONS: Heterogeneity of phenotype and C9orf72 genotype relates to distinct patterns of cerebral degeneration. We demonstrate that imaging studies have the potential to monitor disease progression and early intervention may be required to limit cerebral degeneration.

Mapping functional brain networks from the structural connectome: Relating the series expansion and eigenmode approaches.

Functional brain networks are shaped and constrained by the underlying structural network. However, functional networks are not merely a one-to-one reflection of the structural network. Several theories have been put forward to understand the relationship between structural and functional networks. However, it remains unclear how these theories can be unified. Two existing recent theories state that 1) functional networks can be explained by all possible walks in the structural network, which we will refer to as the series expansion approach, and 2) functional networks can be explained by a weighted combination of the eigenmodes of the structural network, the so-called eigenmode approach. To elucidate the unique or common explanatory power of these approaches to estimate functional networks from the structural network, we analysed the relationship between these two existing views. Using linear algebra, we first show that the eigenmode approach can be written in terms of the series expansion approach, i.e., walks on the structural network associated with different hop counts correspond to different weightings of the eigenvectors of this network. Second, we provide explicit expressions for the coefficients for both the eigenmode and series expansion approach. These theoretical results were verified by empirical data from Diffusion Tensor Imaging (DTI) and functional Magnetic Resonance Imaging (fMRI), demonstrating a strong correlation between the mappings based on both approaches. Third, we analytically and empirically demonstrate that the fit of the eigenmode approach to measured functional data is always at least as good as the fit of the series expansion approach, and that errors in the structural data lead to large errors of the estimated coefficients for the series expansion approach. Therefore, we argue that the eigenmode approach should be preferred over the series expansion approach. Results hold for eigenmodes of the weighted adjacency matrices as well as eigenmodes of the graph Laplacian. â€‹Taken together, these results provide an important step towards unification of existing theories regarding the structure-function relationships in brain networks.

Connectome-Based Propagation Model in Amyotrophic Lateral Sclerosis.

OBJECTIVE: Clinical trials in amyotrophic lateral sclerosis (ALS) continue to rely on survival or functional scales as endpoints, despite the emergence of quantitative biomarkers. Neuroimaging-based biomarkers in ALS have been shown to detect ALS-associated pathology in vivo, although anatomical patterns of disease spread are poorly characterized. The objective of this study is to simulate disease propagation using network analyses of cerebral magnetic resonance imaging (MRI) data to predict disease progression. METHODS: Using brain networks of ALS patients (n = 208) and matched controls across longitudinal time points, network-based statistics unraveled progressive network degeneration originating from the motor cortex and expanding in a spatiotemporal manner. We applied a computational model to the MRI scan of patients to simulate this progressive network degeneration. Simulated aggregation levels at the group and individual level were validated with empirical impairment observed at later time points of white matter and clinical decline using both internal and external datasets. RESULTS: We observe that computer-simulated aggregation levels mimic true disease patterns in ALS patients. Simulated patterns of involvement across cortical areas show significant overlap with the patterns of empirically impaired brain regions on later scans, at both group and individual levels. These findings are validated using an external longitudinal dataset of 30 patients. INTERPRETATION: Our results are in accordance with established pathological staging systems and may have implications for patient stratification in future clinical trials. Our results demonstrate the utility of computational models in ALS to predict disease progression and underscore their potential as a prognostic biomarker. ANN NEUROL 2020;87:725-738.

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.

Cross-sectional and longitudinal assessment of the upper cervical spinal cord in motor neuron disease.

BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a progressive neuromuscular disease characterized by both upper and lower motor neuron degeneration. While neuroimaging studies of the brain can detect upper motor neuron degeneration, these brain MRI scans also include the upper part of the cervical spinal cord, which offers the possibility to expand the focus also towards lower motor neuron degeneration. Here, we set out to investigate cross-sectional and longitudinal disease effects in the upper cervical spinal cord in patients with ALS, progressive muscular atrophy (PMA: primarily lower motor neuron involvement) and primary lateral sclerosis (PLS: primarily upper motor neuron involvement), and their relation to disease severity and grey and white matter brain measurements. METHODS: We enrolled 108 ALS patients without C9orf72 repeat expansion (ALS C9-), 26 ALS patients with C9orf72 repeat expansion (ALS C9+), 28 PLS patients, 56 PMA patients and 114 controls. During up to five visits, longitudinal T1-weighted brain MRI data were acquired and used to segment the upper cervical spinal cord (UCSC, up to C3) and individual cervical segments (C1 to C4) to calculate cross-sectional areas (CSA). Using linear (mixed-effects) models, the CSA differences were assessed between groups and correlated with disease severity. Furthermore, a relationship between CSA and brain measurements was examined in terms of cortical thickness of the precentral gyrus and white matter integrity of the corticospinal tract. RESULTS: Compared to controls, CSAs at baseline showed significantly thinner UCSC in all groups in the MND spectrum. Over time, ALS C9- patients demonstrated significant thinning of the UCSC and, more specifically, of segment C3 compared to controls. Progressive thinning over time was also observed in C1 of PMA patients, while ALS C9+ and PLS patients did not show any longitudinal changes. Longitudinal spinal cord measurements showed a significant relationship with disease severity and we found a significant correlation between spinal cord and motor cortex thickness or corticospinal tract integrity for PLS and PMA, but not for ALS patients. DISCUSSION: Our findings demonstrate atrophy of the upper cervical spinal cord in the motor neuron disease spectrum, which was progressive over time for all but PLS patients. Cervical spinal cord imaging in ALS seems to capture different disease effects than brain neuroimaging. Atrophy of the cervical spinal cord is therefore a promising additional biomarker for both diagnosis and disease progression and could help in the monitoring of treatment effects in future clinical trials.

Comparing multilayer brain networks between groups: Introducing graph metrics and recommendations.

There is an increasing awareness of the advantages of multi-modal neuroimaging. Networks obtained from different modalities are usually treated in isolation, which is however contradictory to accumulating evidence that these networks show non-trivial interdependencies. Even networks obtained from a single modality, such as frequency-band specific functional networks measured from magnetoencephalography (MEG) are often treated independently. Here, we discuss how a multilayer network framework allows for integration of multiple networks into a single network description and how graph metrics can be applied to quantify multilayer network organisation for group comparison. We analyse how well-known biases for single layer networks, such as effects of group differences in link density and/or average connectivity, influence multilayer networks, and we compare four schemes that aim to correct for such biases: the minimum spanning tree (MST), effective graph resistance cost minimisation, efficiency cost optimisation (ECO) and a normalisation scheme based on singular value decomposition (SVD). These schemes can be applied to the layers independently or to the multilayer network as a whole. For correction applied to whole multilayer networks, only the SVD showed sufficient bias correction. For correction applied to individual layers, three schemes (ECO, MST, SVD) could correct for biases. By using generative models as well as empirical MEG and functional magnetic resonance imaging (fMRI) data, we further demonstrated that all schemes were sensitive to identify network topology when the original networks were perturbed. In conclusion, uncorrected multilayer network analysis leads to biases. These biases may differ between centres and studies and could consequently lead to unreproducible results in a similar manner as for single layer networks. We therefore recommend using correction schemes prior to multilayer network analysis for group comparisons.

Brain network clustering with information flow motifs.

Recent work has revealed frequency-dependent global patterns of information flow by a network analysis of magnetoencephalography data of the human brain. However, it is unknown which properties on a small subgraph-scale of those functional brain networks are dominant at different frequencies bands. Motifs are the building blocks of networks on this level and have previously been identified as important features for healthy and abnormal brain function. In this study, we present a network construction that enables us to search and analyze motifs in different frequency bands. We give evidence that the bi-directional two-hop path is the most important motif for the information flow in functional brain networks. A clustering based on this motif exposes a spatially coherent yet frequency-dependent sub-division between the posterior, occipital and frontal brain regions.

Integrating cross-frequency and within band functional networks in resting-state MEG: A multi-layer network approach.

Neuronal oscillations exist across a broad frequency spectrum, and are thought to provide a mechanism of interaction between spatially separated brain regions. Since ongoing mental activity necessitates the simultaneous formation of multiple networks, it seems likely that the brain employs interactions within multiple frequency bands, as well as cross-frequency coupling, to support such networks. Here, we propose a multi-layer network framework that elucidates this pan-spectral picture of network interactions. Our network consists of multiple layers (frequency-band specific networks) that influence each other via inter-layer (cross-frequency) coupling. Applying this model to MEG resting-state data and using envelope correlations as connectivity metric, we demonstrate strong dependency between within layer structure and inter-layer coupling, indicating that networks obtained in different frequency bands do not act as independent entities. More specifically, our results suggest that frequency band specific networks are characterised by a common structure seen across all layers, superimposed by layer specific connectivity, and inter-layer coupling is most strongly associated with this common mode. Finally, using a biophysical model, we demonstrate that there are two regimes of multi-layer network behaviour; one in which different layers are independent and a second in which they operate highly dependent. Results suggest that the healthy human brain operates at the transition point between these regimes, allowing for integration and segregation between layers. Overall, our observations show that a complete picture of global brain network connectivity requires integration of connectivity patterns across the full frequency spectrum.

A Mapping Between Structural and Functional Brain Networks.

The relationship between structural and functional brain networks is still highly debated. Most previous studies have used a single functional imaging modality to analyze this relationship. In this work, we use multimodal data, from functional MRI, magnetoencephalography, and diffusion tensor imaging, and assume that there exists a mapping between the connectivity matrices of the resting-state functional and structural networks. We investigate this mapping employing group averaged as well as individual data. We indeed find a significantly high goodness of fit level for this structure-function mapping. Our analysis suggests that a functional connection is shaped by all walks up to the diameter in the structural network in both modality cases. When analyzing the inverse mapping, from function to structure, longer walks in the functional network also seem to possess minor influence on the structural connection strengths. Even though similar overall properties for the structure-function mapping are found for different functional modalities, our results indicate that the structure-function relationship is modality dependent.

The Union of Shortest Path Trees of Functional Brain Networks.

Communication between brain regions is still insufficiently understood. Applying concepts from network science has shown to be successful in gaining insight in the functioning of the brain. Recent work has implicated that especially shortest paths in the structural brain network seem to play a major role in the communication within the brain. So far, for the functional brain network, only the average length of the shortest paths has been analyzed. In this article, we propose to construct the union of shortest path trees (USPT) as a new topology for the functional brain network. The minimum spanning tree, which has been successful in a lot of recent studies to comprise important features of the functional brain network, is always included in the USPT. After interpreting the link weights of the functional brain network as communication probabilities, the USPT of this network can be uniquely defined. Using data from magnetoencephalography, we applied the USPT as a method to find differences in the network topology of multiple sclerosis patients and healthy controls. The new concept of the USPT of the functional brain network also allows interesting interpretations and may represent the highways of the brain.

Hierarchical clustering in minimum spanning trees.

The identification of clusters or communities in complex networks is a reappearing problem. The minimum spanning tree (MST), the tree connecting all nodes with minimum total weight, is regarded as an important transport backbone of the original weighted graph. We hypothesize that the clustering of the MST reveals insight in the hierarchical structure of weighted graphs. However, existing theories and algorithms have difficulties to define and identify clusters in trees. Here, we first define clustering in trees and then propose a tree agglomerative hierarchical clustering (TAHC) method for the detection of clusters in MSTs. We then demonstrate that the TAHC method can detect clusters in artificial trees, and also in MSTs of weighted social networks, for which the clusters are in agreement with the previously reported clusters of the original weighted networks. Our results therefore not only indicate that clusters can be found in MSTs, but also that the MSTs contain information about the underlying clusters of the original weighted network.