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

Premature birth changes wiring constraints in neonatal structural brain networks

Structural brain organization in infancy is associated with later cognitive, behavioral, and educational outcomes. Due to practical limitations, such as technological advancements and data availability of fetal MRI, there is still much we do not know about the early emergence of topological organization. We combine the developing Human Connectome Project's large infant dataset with generative network modeling to simulate the emergence of network organization over early development. Preterm infants had reduced connectivity, shorter connection lengths, and lower network efficiency compared to term-born infants. The models were able to recapitulate the organizational differences between term and preterm networks and revealed that preterm infant networks are better simulated under tighter wiring constraints than term infants. Tighter constraints for preterm models resulted in shorter connection lengths while preserving vital, long-range rich club connections. These simulations suggest that preterm birth is associated with a renegotiation of the cost-value wiring trade-off that may drive the emergence of different network organization.

Decoding cortical chronotopy-Comparing the influence of different cortical organizational schemes

The brain's diverse intrinsic timescales enable us to perceive stimuli with varying temporal persistency. This study aimed to uncover the cortical organizational schemes underlying these variations, revealing the neural architecture for processing a wide range of sensory experiences. We collected resting-state fMRI, task-fMRI, and diffusion-weighted imaging data from 47 individuals. Based on this data, we extracted six organizational schemes: (1) the structural Rich Club (RC) architecture, shown to synchronize the connectome; (2) the structural Diverse Club architecture, as an alternative to the RC based on the network's module structure; (3) the functional uni-to-multimodal gradient, reflected in a wide range of structural and functional features; and (4) the spatial posterior/lateral-to-anterior/medial gradient, established for hierarchical levels of cognitive control. Also, we explored the effects of (5) structural graph theoretical measures of centrality and (6) cytoarchitectural differences. Using Bayesian model comparison, we contrasted the impact of these organizational schemes on (1) intrinsic resting-state timescales and (2) inter-subject correlation (ISC) from a task involving hierarchically nested digit sequences. As expected, resting-state timescales were slower in structural network hubs, hierarchically higher areas defined by the functional and spatial gradients, and thicker cortical regions. ISC analysis demonstrated hints for the engagement of higher cortical areas with more temporally persistent stimuli. Finally, the model comparison identified the uni-to-multimodal gradient as the best organizational scheme for explaining the chronotopy in both task and rest. Future research should explore the microarchitectural features that shape this gradient, elucidating how our brain adapts and evolves across different modes of processing.

Disrupted topologic efficiency of white matter structural connectome in migraine: a graph-based connectomics study

OBJECTIVE

To delineate the structural connectome alterations in patients with chronic migraine (CM), episodic migraine (EM), and healthy controls (HCs).

BACKGROUND

The pathogenesis of migraine chronification remains elusive, with structural brain network changes potentially playing a key role. However, there is a paucity of research employing graph theory analysis to explore changes in the whole brain structural networks in patients with CM and EM.

METHODS

The individual structural brain connectome of 60 patients with CM, 34 patients with EM, and 39 healthy control participants were constructed by using deterministic diffusion-tensor tractography. Graph metrics including global efficiency, characteristic path length, local efficiency, clustering coefficient, and small-world parameters were evaluated to describe the topologic organization of the white matter structural networks. Additionally, nodal clustering coefficient and efficiency were considered to assess the regional characteristics of the brain connectome. A graph-based statistic was used to assess brain network properties across the groups.

RESULTS

Graph theory analysis revealed significant disruptions in the structural brain networks of CM patients, characterized by reduced global efficiency, local efficiency, and increased characteristic path length compared to HCs. Additionally, CM patients exhibited significantly lower local efficiency than EM patients. Notably, the CM group demonstrated marked reductions in local clustering coefficient and nodal local efficiency in the frontal and temporal regions compared with the healthy control group and EM group. Nodal local efficiency can effectively distinguish CM from EM and HCs. Moreover, the disrupted topologic efficiency was significantly associated with attack frequency and MIDAS score in patients with migraine after Bonferroni correction.

CONCLUSION

Decreased structural connectivity in the frontal and temporal regions may serve as a neuroimaging marker for migraine chronification and disease progression, providing valuable insights into the pathophysiology of chronic migraine.

Competitive interactions shape brain dynamics and computation across species

Adaptive cognition relies on cooperation across anatomically distributed brain circuits. However, specialised neural systems are also in constant competition for limited processing resources. How does the brain's network architecture enable it to balance these cooperative and competitive tendencies? Here we use computational whole-brain modelling to examine the dynamical and computational relevance of cooperative and competitive interactions in the mammalian connectome. Across human, macaque, and mouse we show that the architecture of the models that most faithfully reproduce brain activity, consistently combines modular cooperative interactions with diffuse, long-range competitive interactions. The model with competitive interactions consistently outperforms the cooperative-only model, with excellent fit to both spatial and dynamical properties of the living brain, which were not explicitly optimised but rather emerge spontaneously. Competitive interactions in the effective connectivity produce greater levels of synergistic information and local-global hierarchy, and lead to superior computational capacity when used for neuromorphic computing. Altogether, this work provides a mechanistic link between network architecture, dynamical properties, and computation in the mammalian brain.

Involvement of the cerebellum in structural connectivity enhancement in episodic migraine

BACKGROUND

The pathophysiology of migraine remains poorly understood, yet a growing number of studies have shown structural connectivity disruptions across large-scale brain networks. Although both structural and functional changes have been found in the cerebellum of migraine patients, the cerebellum has barely been assessed in previous structural connectivity studies of migraine. Our objective is to investigate the structural connectivity of the entire brain, including the cerebellum, in individuals diagnosed with episodic migraine without aura during the interictal phase, compared with healthy controls.

METHODS

To that end, 14 migraine patients and 15 healthy controls were recruited (all female), and diffusion-weighted and T1-weighted MRI data were acquired. The structural connectome was estimated for each participant based on two different whole-brain parcellations, including cortical and subcortical regions as well as the cerebellum. The structural connectivity patterns, as well as global and local graph theory metrics, were compared between patients and controls, for each of the two parcellations, using network-based statistics and a generalized linear model (GLM), respectively. We also compared the number of connectome streamlines within specific white matter tracts using a GLM.

RESULTS

We found increased structural connectivity in migraine patients relative to healthy controls with a distinct involvement of cerebellar regions, using both parcellations. Specifically, the node degree of the posterior lobe of the cerebellum was greater in patients than in controls and patients presented a higher number of streamlines within the anterior limb of the internal capsule. Moreover, the connectomes of patients exhibited greater global efficiency and shorter characteristic path length, which correlated with the age onset of migraine.

CONCLUSIONS

A distinctive pattern of heightened structural connectivity and enhanced global efficiency in migraine patients compared to controls was identified, which distinctively involves the cerebellum. These findings provide evidence for increased integration within structural brain networks in migraine and underscore the significance of the cerebellum in migraine pathophysiology.

Increased prevalence of vertebrobasilar dolichoectasia in Parkinson's disease and its effect on white matter microstructure and network

This study aimed to investigate the prevalence of vertebrobasilar dolichoectasia (VBD) in Parkinson's disease (PD) patients and analyze its role in gray matter changes, white matter (WM) microstructure and network alterations in PD. This is a cross-sectional study including 341 PD patients. Prevalence of VBD in these PD patients was compared with general population. Diffusion tensor imaging and T1-weighted imaging analysis were performed among 174 PD patients with or without VBD. Voxel-based morphometry analysis was used to estimate gray matter volume changes. Tract-based spatial statistics and region of interest-based analysis were used to evaluate WM microstructure changes. WM network analysis was also performed. Significantly higher prevalence of VBD in PD patients was identified compared with general population. Lower fractional anisotropy and higher diffusivity, without significant gray matter involvement, were found in PD patients with VBD in widespread areas. Decreased global and local efficiency, increased hierarchy, decreased degree centrality at left Rolandic operculum, increased betweenness centrality at left postcentral gyrus and decreased average connectivity strength between and within several modules were identified in PD patients with VBD. VBD is more prevalent in PD patients than general population. Widespread impairments in WM microstructure and WM network involving various motor and nonmotor PD symptom-related areas are more prominent in PD patients with VBD compared with PD patients without VBD.

Weighting the structural connectome: Exploring its impact on network properties and predicting cognitive performance in the human brain

Brain function does not emerge from isolated activity, but rather from the interactions and exchanges between neural elements that form a network known as the connectome. The human connectome consists of structural and functional aspects. The structural connectome (SC) represents the anatomical connections, and the functional connectome represents the resulting dynamics that emerge from this arrangement of structures. As there are different ways of weighting these connections, it is important to consider how such different approaches impact study conclusions. Here, we propose that different weighted connectomes result in varied network properties, and while neither superior the other, selection might affect interpretation and conclusions in different study cases. We present three different weighting models, namely, number of streamlines (NOS), fractional anisotropy (FA), and axon diameter distribution (ADD), to demonstrate these differences. The later, is extracted using recently published AxSI method and is first compared to commonly used weighting methods. Moreover, we explore the functional relevance of each weighted SC, using the Human Connectome Project (HCP) database. By analyzing intelligence-related data, we develop a predictive model for cognitive performance based on graph properties and the National Institutes of Health (NIH) toolbox. Results demonstrate that the ADD SC, combined with a functional subnetwork model, outperforms other models in estimating cognitive performance.

Uncinate fasciculus microstructural organisation and emotion recognition in schizophrenia: controlling for hit rate bias

Introduction

Schizophrenia (SCZ) is a complex neurodevelopmental disorder characterised by functional and structural brain dysconnectivity and disturbances in perception, cognition, emotion, and social functioning. In the present study, we investigated whether the microstructural organisation of the uncinate fasciculus (UF) was associated with emotion recognition (ER) performance. Additionally, we investigated the usefulness of an unbiased hit rate (UHR) score to control for response biases (i.e., participant guessing) during an emotion recognition task (ERT).

Methods

Fifty-eight individuals diagnosed with SCZ were included. The CANTAB ERT was used to measure social cognition. Specific ROI manual tract segmentation was completed using ExploreDTI and followed the protocol previously outlined by Coad et al. (2020).

Results

We found that the microstructural organisation of the UF was significantly correlated with physical neglect and ER outcomes. Furthermore, we found that the UHR score was more sensitive to ERT subscale emotion items than the standard HR score. Finally, given the association between childhood trauma (in particular childhood neglect) and social cognition in SCZ, a mediation analysis found evidence that microstructural alterations of the UF mediated an association between childhood trauma and social cognitive performance.

Discussion

The mediating role of microstructural alterations in the UF on the association between childhood trauma and social cognitive performance suggests that early life adversity impacts both brain development and social cognitive outcomes for people with SCZ. Limitations of the present study include the restricted ability of the tensor model to correctly assess multi-directionality at regions where fibre populations intersect.

Modeling brain network flexibility in networks of coupled oscillators: a feasibility study

Modeling the functionality of the human brain is a major goal in neuroscience for which many powerful methodologies have been developed over the last decade. The impact of working memory and the associated brain regions on the brain dynamics is of particular interest due to their connection with many functions and malfunctions in the brain. In this context, the concept of brain flexibility has been developed for the characterization of brain functionality. We discuss emergence of brain flexibility that is commonly measured by the identification of changes in the cluster structure of co-active brain regions. We provide evidence that brain flexibility can be modeled by a system of coupled FitzHugh-Nagumo oscillators where the network structure is obtained from human brain Diffusion Tensor Imaging (DTI). Additionally, we propose a straightforward and computationally efficient alternative macroscopic measure, which is derived from the Pearson distance of functional brain matrices. This metric exhibits similarities to the established patterns of brain template flexibility that have been observed in prior investigations. Furthermore, we explore the significance of the brain's network structure and the strength of connections between network nodes or brain regions associated with working memory in the observation of patterns in networks flexibility. This work enriches our understanding of the interplay between the structure and function of dynamic brain networks and proposes a modeling strategy to study brain flexibility.

A novel method for PET connectomics guided by fibre-tracking MRI: Application to Alzheimer's disease

This study introduces a novel brain connectome matrix, track-weighted PET connectivity (twPC) matrix, which combines positron emission tomography (PET) and diffusion magnetic resonance imaging data to compute a PET-weighted connectome at the individual subject level. The new method is applied to characterise connectivity changes in the Alzheimer's disease (AD) continuum. The proposed twPC samples PET tracer uptake guided by the underlying white matter fibre-tracking streamline point-to-point connectivity calculated from diffusion MRI (dMRI). Using tau-PET, dMRI and T1-weighted MRI from the Alzheimer's Disease Neuroimaging Initiative database, structural connectivity (SC) and twPC matrices were computed and analysed using the network-based statistic (NBS) technique to examine topological alterations in early mild cognitive impairment (MCI), late MCI and AD participants. Correlation analysis was also performed to explore the coupling between SC and twPC. The NBS analysis revealed progressive topological alterations in both SC and twPC as cognitive decline progressed along the continuum. Compared to healthy controls, networks with decreased SC were identified in late MCI and AD, and networks with increased twPC were identified in early MCI, late MCI and AD. The altered network topologies were mostly different between twPC and SC, although with several common edges largely involving the bilateral hippocampus, fusiform gyrus and entorhinal cortex. Negative correlations were observed between twPC and SC across all subject groups, although displaying an overall reduction in the strength of anti-correlation with disease progression. twPC provides a new means for analysing subject-specific PET and MRI-derived information within a hybrid connectome using established network analysis methods, providing valuable insights into the relationship between structural connections and molecular distributions. PRACTITIONER POINTS: New method is proposed to compute patient-specific PET connectome guided by MRI fibre-tracking. Track-weighted PET connectivity (twPC) matrix allows to leverage PET and structural connectivity information. twPC was applied to dementia, to characterise the PET nework abnormalities in Alzheimer's disease and mild cognitive impairment.

The significance of structural rich club hubs for the processing of hierarchical stimuli

The brain's structural network follows a hierarchy that is described as rich club (RC) organization, with RC hubs forming the well-interconnected top of this hierarchy. In this study, we tested whether RC hubs are involved in the processing of hierarchically higher structures in stimulus sequences. Moreover, we explored the role of previously suggested cortical gradients along anterior-posterior and medial-lateral axes throughout the frontal cortex. To this end, we conducted a functional magnetic resonance imaging (fMRI) experiment and presented participants with blocks of digit sequences that were structured on different hierarchically nested levels. We additionally collected diffusion weighted imaging data of the same subjects to identify RC hubs. This classification then served as the basis for a region of interest analysis of the fMRI data. Moreover, we determined structural network centrality measures in areas that were found as activation clusters in the whole-brain fMRI analysis. Our findings support the previously found anterior and medial shift for processing hierarchically higher structures of stimuli. Additionally, we found that the processing of hierarchically higher structures of the stimulus structure engages RC hubs more than for lower levels. Areas involved in the functional processing of hierarchically higher structures were also more likely to be part of the structural RC and were furthermore more central to the structural network. In summary, our results highlight the potential role of the structural RC organization in shaping the cortical processing hierarchy.

Tractography with T1-weighted MRI and associated anatomical constraints on clinical quality diffusion MRI

Diffusion MRI (dMRI) streamline tractography, the gold-standard for in vivo estimation of white matter (WM) pathways in the brain, has long been considered as a product of WM microstructure. However, recent advances in tractography demonstrated that convolutional recurrent neural networks (CoRNN) trained with a teacher-student framework have the ability to learn to propagate streamlines directly from T1 and anatomical context. Training for this network has previously relied on high resolution dMRI. In this paper, we generalize the training mechanism to traditional clinical resolution data, which allows generalizability across sensitive and susceptible study populations. We train CoRNN on a small subset of the Baltimore Longitudinal Study of Aging (BLSA), which better resembles clinical scans. We define a metric, termed the epsilon ball seeding method, to compare T1 tractography and traditional diffusion tractography at the streamline level. We show that under this metric T1 tractography generated by CoRNN reproduces diffusion tractography with approximately three millimeters of error.

Similarity between structural and proxy estimates of brain connectivity

Functional magnetic resonance and diffusion weighted imaging have so far made a major contribution to delineation of the brain connectome at the macroscale. While functional connectivity (FC) was shown to be related to structural connectivity (SC) to a certain degree, their spatial overlap is unknown. Even less clear are relations of SC with estimates of connectivity from inter-subject covariance of regional F18-fluorodeoxyglucose uptake (FDGcov) and grey matter volume (GMVcov). Here, we asked to what extent SC underlies three proxy estimates of brain connectivity: FC, FDGcov and GMVcov. Simultaneous PET/MR acquisitions were performed in 56 healthy middle-aged individuals. Similarity between four networks was assessed using Spearman correlation and convergence ratio (CR), a measure of spatial overlap. Spearman correlation coefficient was 0.27 for SC-FC, 0.40 for SC-FDGcov, and 0.15 for SC-GMVcov. Mean CRs were 51% for SC-FC, 48% for SC-FDGcov, and 37% for SC-GMVcov. These results proved to be reproducible and robust against image processing steps. In sum, we found a relevant similarity of SC with FC and FDGcov, while GMVcov consistently showed the weakest similarity. These findings indicate that white matter tracts underlie FDGcov to a similar degree as FC, supporting FDGcov as estimate of functional brain connectivity.

Evaluation of tractogram filtering methods using human-like connectome phantoms

Tractography algorithms are prone to reconstructing spurious connections. The set of streamlines generated with tractography can be post-processed to retain the streamlines that are most biologically plausible. Several microstructure-informed filtering algorithms are available for this purpose, however, the comparative performance of these methods has not been extensively evaluated. In this study, we aim to evaluate streamline filtering and post-processing algorithms using simulated connectome phantoms. We first establish a framework for generating connectome phantoms featuring brain-like white matter fiber architectures. We then use our phantoms to systematically evaluate the performance of a range of streamline filtering algorithms, including SIFT, COMMIT, and LiFE. We find that all filtering methods successfully improve connectome accuracy, although filter performance depends on the complexity of the underlying white matter fiber architecture. Filtering algorithms can markedly improve tractography accuracy for simple tubular fiber bundles (F-measure deterministic- unfiltered: 0.49 and best filter: 0.72; F-measure probabilistic- unfiltered: 0.37 and best filter: 0.81), but for more complex brain-like fiber architectures, the improvement is modest (F-measure deterministic- unfiltered: 0.53 and best filter: 0.54; F-measure probabilistic- unfiltered: 0.46 and best filter: 0.50). Overall, filtering algorithms have the potential to improve the accuracy of connectome mapping pipelines, particularly for weighted connectomes and pipelines using probabilistic tractography methods. Our results highlight the need for further advances tractography and streamline filtering to improve the accuracy of connectome mapping.

versaFlow: a versatile pipeline for resolution adapted diffusion MRI processing and its application to studying the variability of the PRIME-DE database

The lack of "gold standards" in Diffusion Weighted Imaging (DWI) makes validation cumbersome. To tackle this task, studies use translational analysis where results in humans are benchmarked against findings in other species. Non-Human Primates (NHP) are particularly interesting for this, as their cytoarchitecture is closely related to humans. However, tools used for processing and analysis must be adapted and finely tuned to work well on NHP images. Here, we propose versaFlow, a modular pipeline implemented in Nextflow, designed for robustness and scalability. The pipeline is tailored to in vivo NHP DWI at any spatial resolution; it allows for maintainability and customization. Processes and workflows are implemented using cutting-edge and state-of-the-art Magnetic Resonance Imaging (MRI) processing technologies and diffusion modeling algorithms, namely Diffusion Tensor Imaging (DTI), Constrained Spherical Deconvolution (CSD), and DIstribution of Anisotropic MicrOstructural eNvironments in Diffusion-compartment imaging (DIAMOND). Using versaFlow, we provide an in-depth study of the variability of diffusion metrics computed on 32 subjects from 3 sites of the Primate Data Exchange (PRIME-DE), which contains anatomical T1-weighted (T1w) and T2-weighted (T2w) images, functional MRI (fMRI), and DWI of NHP brains. This dataset includes images acquired over a range of resolutions, using single and multi-shell gradient samplings, on multiple scanner vendors. We perform a reproducibility study of the processing of versaFlow using the Aix-Marseilles site's data, to ensure that our implementation has minimal impact on the variability observed in subsequent analyses. We report very high reproducibility for the majority of metrics; only gamma distribution parameters of DIAMOND display less reproducible behaviors, due to the absence of a mechanism to enforce a random number seed in the software we used. This should be taken into consideration when future applications are performed. We show that the PRIME-DE diffusion data exhibits a great level of variability, similar or greater than results obtained in human studies. Its usage should be done carefully to prevent instilling uncertainty in statistical analyses. This hints at a need for sufficient harmonization in acquisition protocols and for the development of robust algorithms capable of managing the variability induced in imaging due to differences in scanner models and/or vendors.

Expanding connectomics to the laminar level: A perspective

Despite great progress in uncovering the complex connectivity patterns of the human brain over the last two decades, the field of connectomics still experiences a bias in its viewpoint of the cerebral cortex. Due to a lack of information regarding exact end points of fiber tracts inside cortical gray matter, the cortex is commonly reduced to a single homogenous unit. Concurrently, substantial developments have been made over the past decade in the use of relaxometry and particularly inversion recovery imaging for exploring the laminar microstructure of cortical gray matter. In recent years, these developments have culminated in an automated framework for cortical laminar composition analysis and visualization, followed by studies of cortical dyslamination in epilepsy patients and age-related differences in laminar composition in healthy subjects. This perspective summarizes the developments and remaining challenges of multi-T1 weighted imaging of cortical laminar substructure, the current limitations in structural connectomics, and the recent progress in integrating these fields into a new model-based subfield termed 'laminar connectomics'. In the coming years, we predict an increased use of similar generalizable, data-driven models in connectomics with the purpose of integrating multimodal MRI datasets and providing a more nuanced and detailed characterization of brain connectivity.

Towards reliable reconstruction of the mouse brain corticothalamic connectivity using diffusion MRI

Diffusion magnetic resonance imaging (dMRI) tractography has yielded intriguing insights into brain circuits and their relationship to behavior in response to gene mutations or neurological diseases across a number of species. Still, existing tractography approaches suffer from limited sensitivity and specificity, leading to uncertain interpretation of the reconstructed connections. Hence, in this study, we aimed to optimize the imaging and computational pipeline to achieve the best possible spatial overlaps between the tractography and tracer-based axonal projection maps within the mouse brain corticothalamic network. We developed a dMRI-based atlas of the mouse forebrain with structural labels imported from the Allen Mouse Brain Atlas (AMBA). Using the atlas and dMRI tractography, we first reconstructed detailed node-to-node mouse brain corticothalamic structural connectivity matrices using different imaging and tractography parameters. We then investigated the effects of each condition for accurate reconstruction of the corticothalamic projections by quantifying the similarities between the tractography and the tracer data from the Allen Mouse Brain Connectivity Atlas (AMBCA). Our results suggest that these parameters significantly affect tractography outcomes and our atlas can be used to investigate macroscopic structural connectivity in the mouse brain. Furthermore, tractography in mouse brain gray matter still face challenges and need improved imaging and tractography methods.

A structural magnetic resonance imaging review of clinical motor outcomes from deep brain stimulation in movement disorders

Patients with movement disorders treated by deep brain stimulation do not always achieve successful therapeutic alleviation of motor symptoms, even in cases where surgery is without complications. Magnetic resonance imaging (MRI) offers methods to investigate structural brain-related factors that may be predictive of clinical motor outcomes. This review aimed to identify features which have been associated with variability in clinical post-operative motor outcomes in patients with Parkinson's disease, dystonia, and essential tremor from structural MRI modalities. We performed a literature search for articles published between 1 January 2000 and 1 April 2022 and identified 5197 articles. Following screening through our inclusion criteria, we identified 60 total studies (39 = Parkinson's disease, 11 = dystonia syndromes and 10 = essential tremor). The review captured a range of structural MRI methods and analysis techniques used to identify factors related to clinical post-operative motor outcomes from deep brain stimulation. Morphometric markers, including volume and cortical thickness were commonly identified in studies focused on patients with Parkinson's disease and dystonia syndromes. Reduced metrics in basal ganglia, sensorimotor and frontal regions showed frequent associations with reduced motor outcomes. Increased structural connectivity to subcortical nuclei, sensorimotor and frontal regions was also associated with greater motor outcomes. In patients with tremor, increased structural connectivity to the cerebellum and cortical motor regions showed high prevalence across studies for greater clinical motor outcomes. In addition, we highlight conceptual issues for studies assessing clinical response with structural MRI and discuss future approaches towards optimizing individualized therapeutic benefits. Although quantitative MRI markers are in their infancy for clinical purposes in movement disorder treatments, structural features obtained from MRI offer the powerful potential to identify candidates who are more likely to benefit from deep brain stimulation and provide insight into the complexity of disorder pathophysiology.

Acquisition and Analysis of Excised Neocortex from Pediatric Patients with Focal Cortical Dysplasia Using Mesoscale Diffusion MRI

Non-invasive classification of focal cortical dysplasia (FCD) subtypes remains challenging from a radiology perspective. Quantitative imaging biomarkers (QIBs) have the potential to distinguish subtypes that lack pathognomonic features and might help in defining the extent of abnormal connectivity associated with each FCD subtype. A key motivation of diagnostic imaging is to improve the localization of a "lesion" that can guide the surgical resection of affected tissue, which is thought to cause seizures. Conversely, surgical resections to eliminate or reduce seizures provided unique opportunities to develop magnetic resonance imaging (MRI)-based QIBs by affording long scan times to evaluate multiple contrast mechanisms at the mesoscale (0.5 mm isotropic voxel dimensions). Using ex vivo hybrid diffusion tensor imaging on a 9.4 T MRI scanner, the grey to white matter ratio of scalar indices was lower in the resected middle temporal gyrus (MTG) of two neuropathologically confirmed cases of FCD compared to non-diseased control postmortem fixed temporal lobes. In contrast, fractional anisotropy was increased within FCD and also adjacent white matter tracts. Connectivity (streamlines/mm3) in the MTG was higher in FCD, suggesting that an altered connectivity at the lesion locus can potentially provide a tangible QIB to distinguish and characterize FCD abnormalities. However, as illustrated here, a major challenge for a robust tractographical comparison lies in the considerable differences in the ex vivo processing of bioptic and postmortem samples. Mesoscale diffusion MRI has the potential to better define and characterize epileptic tissues obtained from surgical resection to advance our understanding of disease etiology and treatment.

Spatiotemporal tissue maturation of thalamocortical pathways in the human fetal brain

The development of connectivity between the thalamus and maturing cortex is a fundamental process in the second half of human gestation, establishing the neural circuits that are the basis for several important brain functions. In this study, we acquired high-resolution in utero diffusion magnetic resonance imaging (MRI) from 140 fetuses as part of the Developing Human Connectome Project, to examine the emergence of thalamocortical white matter over the second to third trimester. We delineate developing thalamocortical pathways and parcellate the fetal thalamus according to its cortical connectivity using diffusion tractography. We then quantify microstructural tissue components along the tracts in fetal compartments that are critical substrates for white matter maturation, such as the subplate and intermediate zone. We identify patterns of change in the diffusion metrics that reflect critical neurobiological transitions occurring in the second to third trimester, such as the disassembly of radial glial scaffolding and the lamination of the cortical plate. These maturational trajectories of MR signal in transient fetal compartments provide a normative reference to complement histological knowledge, facilitating future studies to establish how developmental disruptions in these regions contribute to pathophysiology.

Building a tissue-unbiased brain template of fiber orientation distribution and tractography with multimodal registration

PURPOSE

Brain templates provide an essential standard space for statistical analysis of brain structure and function. Despite recent advances, diffusion MRI still lacks a template of fiber orientation distribution (FOD) and tractography that is unbiased for both white and gray matter. Therefore, we aim to build up a set of such templates for better white-matter analysis and joint structural and functional analysis.

METHODS

We have developed a multimodal registration method to leverage the complementary information captured by T1 -weighted, T2 -weighted, and diffusion MRI, so that a coherent transformation is generated to register FODs into a common space and average them into a template. Consequently, the anatomically constrained fiber-tracking method was applied to the FOD template to generate a tractography template. Fiber-centered functional connectivity analysis was then performed as an example of the benefits of such an unbiased template.

RESULTS

Our FOD template preserves fine structural details in white matter and also, importantly, clear folding patterns in the cortex and good contrast in the subcortex. Quantitatively, our templates show better individual-template agreement at the whole-brain scale and segmentation scale. The tractography template aligns well with the gray matter, which led to fiber-centered functional connectivity showing high cross-group consistency.

CONCLUSION

We have proposed a novel methodology for building a tissue-unbiased FOD and anatomically constrained tractography template based on multimodal registration. Our templates provide a standard space and statistical platform for not only white-matter analysis but also joint structural and functional analysis, therefore filling an important gap in multimodal neuroimage analysis.

Structural brain network lateralization across childhood and adolescence

Developmental lateralization of brain function is imperative for behavioral specialization, yet few studies have investigated differences between hemispheres in structural connectivity patterns, especially over the course of development. The present study compares the lateralization of structural connectivity patterns, or topology, across children, adolescents, and young adults. We applied a graph theory approach to quantify key topological metrics in each hemisphere including efficiency of information transfer between regions (global efficiency), clustering of connections between regions (clustering coefficient [CC]), presence of hub-nodes (betweenness centrality [BC]), and connectivity between nodes of high and low complexity (hierarchical complexity [HC]) and investigated changes in these metrics during development. Further, we investigated BC and CC in seven functionally defined networks. Our cross-sectional study consisted of 211 participants between the ages of 6 and 21 years with 93% being right-handed and 51% female. Global efficiency, HC, and CC demonstrated a leftward lateralization, compared to a rightward lateralization of BC. The sensorimotor, default mode, salience, and language networks showed a leftward asymmetry of CC. BC was only lateralized in the salience (right lateralized) and dorsal attention (left lateralized) networks. Only a small number of metrics were associated with age, suggesting that topological organization may stay relatively constant throughout school-age development, despite known underlying changes in white matter properties. Unlike many other imaging biomarkers of brain development, our study suggests topological lateralization is consistent across age, highlighting potential nonlinear mechanisms underlying developmental specialization.

Gradual changes in microarchitectural properties of cortex and juxtacortical white matter: Observed by anatomical and diffusion MRI

PURPOSE

Characterization of cerebral cortex is challenged by the complexity and heterogeneity of its cyto- and myeloarchitecture. This study evaluates quantitative MRI metrics, measured across two cortical depths and in subcortical white matter (WM) adjacent to cortex (juxtacortical WM), indicative of myelin content, neurite density, and diffusion microenvironment, for a comprehensive characterization of cortical microarchitecture.

METHODS

High-quality structural and diffusion MRI data (N = 30) from the Human Connectome Project were processed to compute myelin index, neurite density index, fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity from superficial cortex, deep cortex, and juxtacortical WM. The distributional patterns of these metrics were analyzed individually, correlated to one another, and were compared to established parcellations.

RESULTS

Our results supported that myeloarchitectonic and the coexisting cytoarchitectonic structures influence the diffusion properties of water molecules residing in cortex. Full cortical thickness showed myelination patterns similar to those previously observed in humans. Higher myelin indices with similar distributional patterns were observed in deep cortex whereas lower myelin indices were observed in superficial cortex. Neurite density index and other diffusion MRI derived parameters provided complementary information to myelination. Reliable and reproducible correlations were identified among the cortical microarchitectural properties and fiber distributional patterns in proximal WM structures.

CONCLUSION

We demonstrated gradual changes across the cortical sheath by assessing depth-specific cortical micro-architecture using anatomical and diffusion MRI. Mutually independent but coexisting features of cortical layers and juxtacortical WM provided new insights towards structural organizational units and variabilities across cortical regions and through depth.

Levodopa responsiveness and white matter alterations in Parkinson's disease: A DTI-based study and brain network analysis: A cross-sectional study

BACKGROUND

Patients with Parkinson's disease (PD) present various responsiveness to levodopa, but the cause of such differences in levodopa responsiveness is unclear. Previous studies related the damage of brain white matter (WM) to levodopa responsiveness in PD patients, but no study investigated the relationship between the structural brain network change in PD patients and their levodopa responsiveness.

METHODS

PD patients were recruited and evaluated using the Unified Parkinson's Disease Rating Scale (UPDRS). Each patient received a diffusion tensor imaging (DTI) scan and an acute levodopa challenge test. The improvement rate of UPDRS-III was calculated. PD patients were grouped into irresponsive group (improvement rate < 30%) and responsive group (improvement rate ≥ 30%). Tract-based spatial statistics (TBSS), deterministic tracing (DT), region of interest (ROI) analysis, and automatic fiber identification (AFQ) analyses were performed. The structural brain network was also constructed and the topological parameters were calculated.

RESULTS

Fifty-four PD patients were included. TBSS identified significant differences in fractional anisotropy (FA) values in the corpus callosum and other regions of the brain. DT and ROI analysis of the corpus callosum found a significant difference in FA between the two groups. Graph theory analysis showed statistical differences in global efficiency, local efficiency, and characteristic path length.

CONCLUSION

PD patients with poor responsiveness to levodopa had WM damage in multiple brain areas, especially the corpus callosum, which might cause disruption of information integration of the structural brain network.

New insights into anatomical connectivity along the anterior–posterior axis of the human hippocampus using in vivo quantitative fibre tracking

The hippocampus supports multiple cognitive functions including episodic memory. Recent work has highlighted functional differences along the anterior–posterior axis of the human hippocampus, but the neuroanatomical underpinnings of these differences remain unclear. We leveraged track-density imaging to systematically examine anatomical connectivity between the cortical mantle and the anterior–posterior axis of the in vivo human hippocampus. We first identified the most highly connected cortical areas and detailed the degree to which they preferentially connect along the anterior–posterior axis of the hippocampus. Then, using a tractography pipeline specifically tailored to measure the location and density of streamline endpoints within the hippocampus, we characterised where these cortical areas preferentially connect within the hippocampus. Our results provide new and detailed insights into how specific regions along the anterior–posterior axis of the hippocampus are associated with different cortical inputs/outputs and provide evidence that both gradients and circumscribed areas of dense extrinsic anatomical connectivity exist within the human hippocampus. These findings inform conceptual debates in the field and emphasise the importance of considering the hippocampus as a heterogeneous structure. Overall, our results represent a major advance in our ability to map the anatomical connectivity of the human hippocampus in vivo and inform our understanding of the neural architecture of hippocampal-dependent memory systems in the human brain.

The brain allows us to perceive and interact with our environment and to create and recall memories about our day-to-day lives. A sea-horse shaped structure in the brain, called the hippocampus, is critical for translating our perceptions into memories, and it does so in coordination with other brain regions. For example, different regions of the cerebral cortex (the outer layer of the brain) support different aspects of cognition, and pathways of information flow between the cerebral cortex and hippocampus underpin the healthy functioning of memory.

Decades of research conducted into the brains of non-human primates show that specific regions of the cerebral cortex anatomically connect with different parts of the hippocampus to support this information flow. These insights form the foundation for existing theoretical models of how networks of neurons in the hippocampus and the cerebral cortex are connected. However, the human cerebral cortex has greatly expanded during our evolution, meaning that patterns of connectivity in the human brain may diverge from those in the brains of non-human primates.

Deciphering human brain circuits in greater detail is crucial if we are to gain a better understanding of the structure and operation of the healthy human brain. However, obtaining comprehensive maps of anatomical connections between the hippocampus and cerebral cortex has been hampered by technical limitations. For example, magnetic resonance imaging (MRI), an approach that can be used to study the living human brain, suffers from insufficient image resolution.

To overcome these issues, Dalton et al. used an imaging technique called diffusion weighted imaging which is used to study white matter pathways in the brain. They developed a tailored approach to create high-resolution maps showing how the hippocampus anatomically connects with the cerebral cortex in the healthy human brain. Dalton et al. produced detailed maps illustrating which areas of the cerebral cortex have high anatomical connectivity with the hippocampus and how different parts of the hippocampus preferentially connect to different neural circuits in the cortex. For example, the experiments demonstrate that highly connected areas in a cortical region called the temporal cortex connect to very specific, circumscribed regions within the hippocampus.

These findings suggest that the hippocampus may consist of different neural circuits, each preferentially linked to defined areas of the cortex which are, in turn, associated with specific aspects of cognition. These observations further our knowledge of hippocampal-dependant memory circuits in the human brain and provide a foundation for the study of memory decline in aging and neurodegenerative diseases.

Structural hyperconnectivity of the subthalamic area with limbic cortices underpins anxiety and impulsivity in Tourette syndrome

Tourette syndrome (TS) is a neurodevelopmental disorder characterized by motor and vocal tics, which is often associated with psychiatric comorbidities. Dysfunction of basal ganglia pathways might account for the wide spectrum of symptoms in TS patients. Although psychiatric symptoms may be related to limbic networks, the specific contribution of different limbic structures remains unclear. We used tractography to investigate cortical connectivity with the striatal area (caudate, putamen, core and shell of the nucleus accumbens), the subthalamic nucleus (STN), and the adjacent medial subthalamic region (MSR) in 58 TS patients and 35 healthy volunteers. 82% of TS patients showed psychiatric comorbidities, with significantly higher levels of anxiety and impulsivity compared to controls. Tractography analysis revealed significantly increased limbic cortical connectivity of the left MSR with the entorhinal (BA34), insular (BA48), and temporal (BA38) cortices in TS patients compared to controls. Furthermore, we found that left insular-STN connectivity was positively correlated with impulsivity scores for all subjects and with anxiety scores for all subjects, particularly for TS. Our study highlights a heterogenous modification of limbic structure connectivity in TS, with specific abnormalities found for the subthalamic area. Abnormal connectivity with the insular cortex might underpin the higher level of impulsivity and anxiety observed in TS.

Structural-Functional Connectivity Bandwidth of the Human Brain

BACKGROUND

The human brain is a complex network that seamlessly manifests behaviour and cognition. This network comprises neurons that directly, or indirectly mediate communication between brain regions. Here, we show how multilayer/multiplex network analysis provides a suitable framework to uncover the throughput of structural connectivity (SC) to mediate information transfer-giving rise to functional connectivity (FC).

METHOD

We implemented a novel method to reconcile SC and FC using diffusion and resting-state functional MRI connectivity data from 484 subjects (272 females, 212 males; age = 29.15 ± 3.47) from the Human Connectome Project. First, we counted the number of direct and indirect structural paths that mediate FC. FC nodes with indirect SC paths were then weighted according to their least restrictive SC path. We refer to this as SC-FC Bandwidth. We then mapped paths with the highest SC-FC Bandwidth across 7 canonical resting-state networks.

FINDINGS

We found that most pairs of FC nodes were connected by SC paths of length two and three (SC paths of length >5 were virtually non-existent). Direct SC-FC connections accounted for only 10% of all SC-FC connections. The majority of FC nodes without a direct SC path were mediated by a proportion of two (44%) or three SC path lengths (39%). Only a small proportion of FC nodes were mediated by SC path lengths of four (5%). We found high-bandwidth direct SC-FC connections show dense intra- and sparse inter-network connectivity, with a bilateral, anteroposterior distribution. High bandwidth SC-FC triangles have a right superomedial distribution within the somatomotor network. High-bandwidth SC-FC quads have a superoposterior distribution within the default mode network.

CONCLUSION

Our method allows the measurement of indirect SC-FC using undirected, weighted graphs derived from multimodal MRI data in order to map the location and throughput of SC to mediate FC. An extension of this work may be to explore how SC-FC Bandwidth changes over time, relates to cognition/behavior, and if this measure reflects a marker of neurological injury or psychiatric disorders.

Altered Structural Brain Networks in Refractory and Nonrefractory Idiopathic Generalized Epilepsy

Introduction: Idiopathic generalized epilepsy (IGE) is a collection of generalized nonlesional epileptic network disorders. Around 20-40% of patients with IGE are refractory to antiseizure medication, and mechanisms underlying refractoriness are poorly understood. Here, we characterize structural brain network alterations and determine whether network alterations differ between patients with refractory and nonrefractory IGE. Methods: Thirty-three patients with IGE (10 nonrefractory and 23 refractory) and 39 age- and sex-matched healthy controls were studied. Network nodes were segmented from T1-weighted images, while connections between these nodes (edges) were reconstructed from diffusion magnetic resonance imaging (MRI). Diffusion networks of fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and streamline count (Count) were studied. Differences between all patients, refractory, nonrefractory, and control groups were computed using network-based statistics. Nodal volume differences between groups were computed using Cohen's d effect size calculation. Results: Patients had significantly decreased bihemispheric FA and Count networks and increased MD and RD networks compared with controls. Alterations in network architecture, with respect to controls, differed depending on treatment outcome, including predominant FA network alterations in refractory IGE and increased nodal volume in nonrefractory IGE. Diffusion MRI networks were not influenced by nodal volume. Discussion: Although a nonlesional disorder, patients with IGE have bihemispheric structural network alterations that may differ between patients with refractory and nonrefractory IGE. Given that distinct nodal volume and FA network alterations were observed between treatment outcome groups, a multifaceted network analysis may be useful for identifying imaging biomarkers of refractory IGE.

Structural connections between the noradrenergic and cholinergic system shape the dynamics of functional brain networks

Complex cognitive abilities are thought to arise from the ability of the brain to adaptively reconfigure its internal network structure as a function of task demands. Recent work has suggested that this inherent flexibility may in part be conferred by the widespread projections of the ascending arousal systems. While the different components of the ascending arousal system are often studied in isolation, there are anatomical connections between neuromodulatory hubs that we hypothesise are crucial for mediating key features of adaptive network dynamics, such as the balance between integration and segregation. To test this hypothesis, we estimated the strength of structural connectivity between key hubs of the noradrenergic and cholinergic arousal systems (the locus coeruleus [LC] and nucleus basalis of Meynert [nbM], respectively). We then asked whether the strength of structural LC and nbM inter-connectivity was related to individual differences in the emergent, dynamical signatures of functional integration measured from resting state fMRI data, such as network and attractor topography. We observed a significant positive relationship between the strength of white-matter connections between the LC and nbM and the extent of network-level integration following BOLD signal peaks in LC relative to nbM activity. In addition, individuals with denser white-matter streamlines interconnecting neuromodulatory hubs also demonstrated a heightened ability to shift to novel brain states. These results suggest that individuals with stronger structural connectivity between the noradrenergic and cholinergic systems have a greater capacity to mediate the flexible network dynamics required to support complex, adaptive behaviour. Furthermore, our results highlight the underlying static features of the neuromodulatory hubs can impose some constraints on the dynamic features of the brain.

Prediction of Motor Outcome of Stroke Patients Using a Deep Learning Algorithm with Brain MRI as Input Data

BACKGROUND

Deep learning techniques can outperform traditional machine learning techniques and learn from unstructured and perceptual data, such as images and languages. We evaluated whether a convolutional neural network (CNN) model using whole axial brain T2-weighted magnetic resonance (MR) images as input data can help predict motor outcomes of the upper and lower limbs at the chronic stage in stroke patients.

METHODS

We collected MR images taken at the early stage of stroke in 1,233 consecutive stroke patients. We categorized modified Brunnstrom classification (MBC) scores of ≥5 and functional ambulatory category (FAC) scores of ≥4 at 6 months after stroke as favorable outcomes in the upper and lower limbs, respectively, and MBC scores of <5 and FAC scores of <4 as poor outcomes. We applied a CNN to train the image data. Of the 1,233 patients, 70% (863 patients) were randomly selected for the training set and the remaining 30% (370 patients) were assigned to the validation set.

RESULTS

In the prediction of upper limb motor function on the validation dataset, the area under the curve (AUC) was 0.768, and for lower limb motor function, the AUC was 0.828.

CONCLUSION

We showed that a CNN model trained using whole-brain axial T2-weighted MR images of stroke patients would help predict upper and lower limb motor function at the chronic stage.

CONN-NLM: A Novel CONNectome-Based Non-local Means Filter for PET-MRI Denoising

Background

Advancements in hybrid positron emission tomography-magnetic resonance (PET-MR) systems allow for combining the advantages of each modality. Integrating information from MRI and PET can be valuable for diagnosing and treating neurological disorders. However, combining diffusion MRI (dMRI) and PET data, which provide highly complementary information, has rarely been exploited in image post-processing. dMRI has the ability to investigate the white matter pathways of the brain through fibre tractography, which enables comprehensive mapping of the brain connection networks (the "connectome"). Novel methods are required to combine information present in the connectome and PET to increase the full potential of PET-MRI.

Methods

We developed a CONNectome-based Non-Local Means (CONN-NLM) filter to exploit synergies between dMRI-derived structural connectivity and PET intensity information to denoise PET images. PET-MR data are parcelled into a number of regions based on a brain atlas, and the inter-regional structural connectivity is calculated based on dMRI fibre-tracking. The CONN-NLM filter is then implemented as a post-reconstruction filter by combining the nonlocal means filter and a connectivity-based cortical smoothing. The effect of this approach is to weight voxels with similar PET intensity and highly connected voxels higher when computing the weighted-average to perform more informative denoising. The proposed method was first evaluated using a novel computer phantom framework to simulate realistic hybrid PET-MR images with different lesion scenarios. CONN-NLM was further assessed with clinical dMRI and tau PET examples.

Results

The results showed that CONN-NLM has the capacity to improve the overall PET image quality by reducing noise while preserving lesion contrasts, and it outperformed a range of filters that did not use dMRI information. The simulations demonstrate that CONN-NLM can handle various lesion contrasts consistently, as well as lesions with different levels of inter-connectivity.

Conclusion

CONN-NLM has unique advantages of providing more informative and accurate PET smoothing by adding complementary structural connectivity information from dMRI, representing a new avenue to exploit synergies between MRI and PET.

Finding Cortical Subregions Regarding the Dorsal Language Pathway Based on the Structural Connectivity

Although the language-related fiber pathways in the human brain, such as the superior longitudinal fasciculus (SLF) and arcuate fasciculus (AF), are already well-known, understanding more sophisticated cortical regions connected by the fiber tracts is essential to scrutinize the structural connectivity of language circuits. With the regions of interest that were selected based on the Brainnetome atlas, the fiber orientation distribution estimation method for tractography was used to produce further elaborate connectivity information. The results indicated that both fiber bundles had two distinct connections with the prefrontal cortex (PFC). The SLF-II and dorsal AF are mainly connected to the rostrodorsal part of the inferior parietal cortex (IPC) and lateral part of the fusiform gyrus with the inferior frontal junction (IFJ), respectively. In contrast, the SLF-III and ventral AF were primarily linked to the anterior part of the supramarginal gyrus and superior part of the temporal cortex with the inferior frontal cortex, including the Broca's area. Moreover, the IFJ in the PFC, which has rarely been emphasized as a language-related subregion, also had the strongest connectivity with the previously known language-related subregions among the PFC; consequently, we proposed that these specific regions are interconnected via the SLF and AF within the PFC, IPC, and temporal cortex as language-related circuitry.

FOD-Net: A deep learning method for fiber orientation distribution angular super resolution

Mapping the human connectome using fiber-tracking permits the study of brain connectivity and yields new insights into neuroscience. However, reliable connectome reconstruction using diffusion magnetic resonance imaging (dMRI) data acquired by widely available clinical protocols remains challenging, thus limiting the connectome/tractography clinical applications. Here we develop fiber orientation distribution (FOD) network (FOD-Net), a deep-learning-based framework for FOD angular super-resolution. Our method enhances the angular resolution of FOD images computed from common clinical-quality dMRI data, to obtain FODs with quality comparable to those produced from advanced research scanners. Super-resolved FOD images enable superior tractography and structural connectome reconstruction from clinical protocols. The method was trained and tested with high-quality data from the Human Connectome Project (HCP) and further validated with a local clinical 3.0T scanner as well as with another public available multicenter-multiscanner dataset. Using this method, we improve the angular resolution of FOD images acquired with typical single-shell low-angular-resolution dMRI data (e.g., 32 directions, b=1000s/mm²) to approximate the quality of FODs derived from time-consuming, multi-shell high-angular-resolution dMRI research protocols. We also demonstrate tractography improvement, removing spurious connections and bridging missing connections. We further demonstrate that connectomes reconstructed by super-resolved FODs achieve comparable results to those obtained with more advanced dMRI acquisition protocols, on both HCP and clinical 3.0T data. Advances in deep-learning approaches used in FOD-Net facilitate the generation of high quality tractography/connectome analysis from existing clinical MRI environments. Our code is freely available at https://github.com/ruizengalways/FOD-Net.

Tractography-Based Surgical Targeting for Thalamic Deep Brain Stimulation: A Comparison of Probabilistic vs Deterministic Fiber Tracking of the Dentato-Rubro-Thalamic Tract

BACKGROUND

The ventral intermediate (VIM) thalamic nucleus is the main target for the surgical treatment of refractory tremor. Initial targeting traditionally relies on atlas-based stereotactic targeting formulas, which only minimally account for individual anatomy. Alternative approaches have been proposed, including direct targeting of the dentato-rubro-thalamic tract (DRTT), which, in clinical settings, is generally reconstructed with deterministic tracking. Whether more advanced probabilistic techniques are feasible on clinical-grade magnetic resonance acquisitions and lead to enhanced reconstructions is poorly understood.

OBJECTIVE

To compare DRTT reconstructed with deterministic vs probabilistic tracking.

METHODS

This is a retrospective study of 19 patients with essential tremor who underwent deep brain stimulation (DBS) with intraoperative neurophysiology and stimulation testing. We assessed the proximity of the DRTT to the DBS lead and to the active contact chosen based on clinical response.

RESULTS

In the commissural plane, the deterministic DRTT was anterior (P < 10-4) and lateral (P < 10-4) to the DBS lead. By contrast, although the probabilistic DRTT was also anterior to the lead (P < 10-4), there was no difference in the mediolateral dimension (P = .5). Moreover, the 3-dimensional Euclidean distance from the active contact to the probabilistic DRTT was smaller vs the distance to the deterministic DRTT (3.32 ± 1.70 mm vs 5.01 ± 2.12 mm; P < 10-4).

CONCLUSION

DRTT reconstructed with probabilistic fiber tracking was superior in spatial proximity to the physiology-guided DBS lead and to the empirically chosen active contact. These data inform strategies for surgical targeting of the VIM.

Mapping the human corticoreticular pathway with multimodal delineation of the gigantocellular reticular nucleus and high-resolution diffusion tractography

The corticoreticular pathway (CRP) is a major motor tract that transmits cortical input to the reticular formation motor nuclei and may be an important mediator of motor recovery after central nervous system damage. However, its cortical origins, trajectory and laterality are incompletely understood in humans. This study aimed to map the human CRP and generate an average CRP template in standard MRI space. Following recently established guidelines, we manually delineated the primary reticular formation motor nucleus (gigantocellular reticular nucleus [GRN]) using several group-mean MRI contrasts from the Human Connectome Project (HCP). CRP tractography was then performed with HCP diffusion-weighted MRI data (N = 1065) by selecting diffusion streamlines that reached both the cortex and GRN. Corticospinal tract (CST) tractography was also performed for comparison. Results suggest that the human CRP has widespread origins, which overlap with the CST across most of the motor cortex and include additional exclusive inputs from the medial and anterior prefrontal cortices. The estimated CRP projected through the anterior and posterior limbs of the internal capsule before partially decussating in the midbrain tegmentum and converging bilaterally on the pontomedullary reticular formation. Thus, the CRP trajectory appears to partially overlap the CST, while being more distributed and anteromedial to the CST in the cerebrum before moving posterior to the CST in the brainstem. These findings have important implications for neurophysiologic testing, cortical stimulation and movement recovery after brain lesions. We expect that our GRN and tract maps will also facilitate future CRP research.

A methodological scoping review of the integration of fMRI to guide dMRI tractography. What has been done and what can be improved: A 20-year perspective

Combining MRI modalities is a growing trend in neurosciences. It provides opportunities to investigate the brain architecture supporting cognitive functions. Integrating fMRI activation to guide dMRI tractography offers potential advantages over standard tractography methods. A quick glimpse of the literature on this topic reveals that this technique is challenging, and no consensus or "best practices" currently exist, at least not within a single document. We present the first attempt to systematically analyze and summarize the literature of 80 studies that integrated task-based fMRI results to guide tractography, over the last two decades. We report 19 findings that cover challenges related to sample size, microstructure modelling, seeding methods, multimodal space registration, false negatives/positives, specificity/validity, gray/white matter interface and more. These findings will help the scientific community (1) understand the strengths and limitations of the approaches, (2) design studies using this integrative framework, and (3) motivate researchers to fill the gaps identified. We provide references toward best practices, in order to improve the overall result's replicability, sensitivity, specificity, and validity.

Dynamic primitives of brain network interaction Special Issue "Advances in Mapping the Connectome"

What dynamic processes underly functional brain networks? Functional connectivity (FC) and functional connectivity dynamics (FCD) are used to represent the patterns and dynamics of functional brain networks. FC(D) is related to the synchrony of brain activity: when brain areas oscillate in a coordinated manner this yields a high correlation between their signal time series. To explain the processes underlying FC(D) we review how synchronized oscillations emerge from coupled neural populations in brain network models (BNMs). From detailed spiking networks to more abstract population models, there is strong support for the idea that the brain operates near critical instabilities that give rise to multistable or metastable dynamics that in turn lead to the intermittently synchronized slow oscillations underlying FC(D). We explore further consequences from these fundamental mechanisms and how they fit with reality. We conclude by highlighting the need for integrative brain models that connect separate mechanisms across levels of description and spatiotemporal scales and link them with cognitive function.

A robust framework for characterising diffusion metrics of the median and ulnar nerves: Exploiting state-of-the-art tracking methods

Diffusion-weighted imaging has been used to quantify peripheral nerve properties; however, traditional post-processing techniques have several limitations. Advanced neuroimaging techniques, which overcome many of these limitations, have not been applied to peripheral nerves. Here, we use state-of-the-art diffusion analysis tools to reconstruct the median and ulnar nerves and quantify their diffusion properties. Diffusion-weighted MRI scans were obtained from eight healthy adult subjects. Constrained spherical deconvolution was combined with probabilistic fibre tracking to compute track-weighted fibre orientation distribution (TW-FOD). The tensor was computed and used along with the tracks to estimate TW apparent diffusion coefficient (TW-ADC), TW fractional anisotropy (TW-FA), TW axial diffusivity (TW-AD), and TW radial diffusivity (TW-RD). Variability of TW measurements was used to estimate power size information. The population intersession mean (± SD) measurements for the median nerve were TW-FOD 1.30 (±0.17), TW-ADC 1.16 (±0.13) × 10^-3  mm² /s, TW-FA 0.60 (±0.05), TW-AD 2.05 (±0.16) × 10^-3  mm² /s, and TW-RD 0.72 (±0.12) × 10^-3  mm² /s. The corresponding measurements for the ulnar nerve were TW-FOD 1.25 (±0.14), TW-ADC 1.13 (±0.10) × 10^-3  mm² /s, TW-FA 0.56 (±0.06), TW-AD 1.93 (±0.01) × 10^-3  mm² /s, and TW-RD 0.74 (±0.12) × 10^-3  mm² /s. Based on these measurements, a sample size of 37 would be sufficient to detect a 10% difference in any of the measured TW metrics. A sample size of 20 would be large enough to detect within-subject differences as small as 2.9% (TW-AD, ulnar nerve) and between-subject differences as small as 3.8% (TW-AD, ulnar nerve).

Nonlinear reconfiguration of network edges, topology and information content during an artificial learning task

Here, we combine network neuroscience and machine learning to reveal connections between the brain's network structure and the emerging network structure of an artificial neural network. Specifically, we train a shallow, feedforward neural network to classify hand-written digits and then used a combination of systems neuroscience and information-theoretic tools to perform 'virtual brain analytics' on the resultant edge weights and activity patterns of each node. We identify three distinct phases of network reconfiguration across learning, each of which are characterized by unique topological and information-theoretic signatures. Each phase involves aligning the connections of the neural network with patterns of information contained in the input dataset or preceding layers (as relevant). We also observe a process of low-dimensional category separation in the network as a function of learning. Our results offer a systems-level perspective of how artificial neural networks function-in terms of multi-stage reorganization of edge weights and activity patterns to effectively exploit the information content of input data during edge-weight training-while simultaneously enriching our understanding of the methods used by systems neuroscience.

Mapping the corticoreticular pathway from cortex-wide anterograde axonal tracing in the mouse

The corticoreticular pathway (CRP) has been implicated as an important mediator of motor recovery and rehabilitation after central nervous system damage. However, its origins, trajectory and laterality are not well understood. This study mapped the mouse CRP in comparison with the corticospinal tract (CST). We systematically searched the Allen Mouse Brain Connectivity Atlas (© 2011 Allen Institute for Brain Science) for experiments that used anterograde tracer injections into the right isocortex in mice. For each eligible experiment (N = 607), CRP and CST projection strength were quantified by the tracer volume reaching the reticular formation motor nuclei (RF_motor ) and pyramids, respectively. Tracer density in each brain voxel was also correlated with RF_motor versus pyramids projection strength to explore the relative trajectories of the CRP and CST. We found significant CRP projections originating from the primary and secondary motor cortices, anterior cingulate, primary somatosensory cortex, and medial prefrontal cortex. Compared with the CST, the CRP had stronger projections from each region except the primary somatosensory cortex. Ipsilateral projections were stronger than contralateral for both tracts (above the pyramidal decussation), but the CRP projected more bilaterally than the CST. The estimated CRP trajectory was anteromedial to the CST in the internal capsule and dorsal to the CST in the brainstem. Our findings reveal a widespread distribution of CRP origins and confirm strong bilateral CRP projections, theoretically increasing the potential for partial sparing after brain lesions and contralesional compensation after unilateral injury.

Structural and Functional Connectivity Substrates of Cognitive Impairment in Multiple Sclerosis

Cognitive impairment (CI) occurs in 43 to 70% of multiple sclerosis (MS) patients at both early and later disease stages. Cognitive domains typically involved in MS include attention, information processing speed, memory, and executive control. The growing use of advanced magnetic resonance imaging (MRI) techniques is furthering our understanding on the altered structural connectivity (SC) and functional connectivity (FC) substrates of CI in MS. Regarding SC, different diffusion tensor imaging (DTI) measures (e.g., fractional anisotropy, diffusivities) along tractography-derived white matter (WM) tracts showed relevance toward CI. Novel diffusion MRI techniques, including diffusion kurtosis imaging, diffusion spectrum imaging, high angular resolution diffusion imaging, and neurite orientation dispersion and density imaging, showed more pathological specificity compared to the traditional DTI but require longer scan time and mathematical complexities for their interpretation. As for FC, task-based functional MRI (fMRI) has been traditionally used in MS to brain mapping the neural activity during various cognitive tasks. Analysis methods of resting fMRI (seed-based, independent component analysis, graph analysis) have been applied to uncover the functional substrates of CI in MS by revealing adaptive or maladaptive mechanisms of functional reorganization. The relevance for CI in MS of SC–FC relationships, reflecting common pathogenic mechanisms in WM and gray matter, has been recently explored by novel MRI analysis methods. This review summarizes recent advances on MRI techniques of SC and FC and their potential to provide a deeper understanding of the pathological substrates of CI in MS.

The Use of Dynamic Contrast-Enhanced Magnetic Resonance Imaging for the Evaluation of Blood-Brain Barrier Disruption in Traumatic Brain Injury: What Is the Evidence?

(1) Background: Blood brain barrier (BBB) disruption following traumatic brain injury (TBI) results in a secondary injury by facilitating the entry of neurotoxins to the brain parenchyma without filtration. In the current paper, we aimed to review previous dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) studies to evaluate the occurrence of BBB disruption after TBI. (2) Methods: In electronic databases (PubMed, Scopus, Embase, and the Cochrane Library), we searched for the following keywords: dynamic contrast-enhanced OR DCE AND brain injury. We included studies in which BBB disruption was evaluated in patients with TBI using DCE-MRI. (3) Results: Four articles were included in this review. To assess BBB disruption, linear fit, Tofts, extended Tofts, or Patlak models were used. KTrans and ve were increased, and the values of vp were decreased in the cerebral cortex and predilection sites for diffusion axonal injury. These findings are indicative of BBB disruption following TBI. (4) Conclusions: Our analysis supports the possibility of utilizing DCE-MRI for the detection of BBB disruption following TBI.

Mapping Structural Connectivity Using Diffusion MRI: Challenges and Opportunities

Diffusion MRI-based tractography is the most commonly-used technique when inferring the structural brain connectome, i.e., the comprehensive map of the connections in the brain. The utility of graph theory-a powerful mathematical approach for modeling complex network systems-for analyzing tractography-based connectomes brings important opportunities to interrogate connectome data, providing novel insights into the connectivity patterns and topological characteristics of brain structural networks. When applying this framework, however, there are challenges, particularly regarding methodological and biological plausibility. This article describes the challenges surrounding quantitative tractography and potential solutions. In addition, challenges related to the calculation of global network metrics based on graph theory are discussed.Evidence Level: 5Technical Efficacy: Stage 1.

Effect of Multishell Diffusion MRI Acquisition Strategy and Parcellation Scale on Rich-Club Organization of Human Brain Structural Networks

The majority of network studies of human brain structural connectivity are based on single-shell diffusion-weighted imaging (DWI) data. Recent advances in imaging hardware and software capabilities have made it possible to acquire multishell (b-values) high-quality data required for better characterization of white-matter crossing-fiber microstructures. The purpose of this study was to investigate the extent to which brain structural organization and network topology are affected by the choice of diffusion magnetic resonance imaging (MRI) acquisition strategy and parcellation scale. We performed graph-theoretical network analysis using DWI data from 35 Human Connectome Project subjects. Our study compared four single-shell (b = 1000, 3000, 5000, 10,000 s/mm²) and multishell sampling schemes and six parcellation scales (68, 200, 400, 600, 800, 1000 nodes) using five graph metrics, including small-worldness, clustering coefficient, characteristic path length, modularity and global efficiency. Rich-club analysis was also performed to explore the rich-club organization of brain structural networks. Our results showed that the parcellation scale and imaging protocol have significant effects on the network attributes, with the parcellation scale having a substantially larger effect. Regardless of the parcellation scale, the brain structural networks exhibited a rich-club organization with similar cortical distributions across the parcellation scales involving at least 400 nodes. Compared to single b-value diffusion acquisitions, the deterministic tractography using multishell diffusion imaging data consisting of shells with b-values higher than 5000 s/mm² resulted in significantly improved fiber-tracking results at the locations where fiber bundles cross each other. Brain structural networks constructed using the multishell acquisition scheme including high b-values also exhibited significantly shorter characteristic path lengths, higher global efficiency and lower modularity. Our results showed that both parcellation scale and sampling protocol can significantly impact the rich-club organization of brain structural networks. Therefore, caution should be taken concerning the reproducibility of connectivity results with regard to the parcellation scale and sampling scheme.

Graph Models of Pathology Spread in Alzheimer's Disease: An Alternative to Conventional Graph Theoretic Analysis

Background: Graph theory and connectomics are new techniques for uncovering disease-induced changes in the brain's structural network. Most prior studied have focused on network statistics as biomarkers of disease. However, an emerging body of work involves exploring how the network serves as a conduit for the propagation of disease factors in the brain and has successfully mapped the functional and pathological consequences of disease propagation. In Alzheimer's disease (AD), progressive deposition of misfolded proteins amyloid and tau is well-known to follow fiber projections, under a "prion-like" trans-neuronal transmission mechanism, through which misfolded proteins cascade along neuronal pathways, giving rise to network spread. Methods: In this review, we survey the state of the art in mathematical modeling of connectome-mediated pathology spread in AD. Then we address several open questions that are amenable to mathematically precise parsimonious modeling of pathophysiological processes, extrapolated to the whole brain. We specifically identify current formal models of how misfolded proteins are produced, aggregate, and disseminate in brain circuits, and attempt to understand how this process leads to stereotyped progression in Alzheimer's and other related diseases. Conclusion: This review serves to unify current efforts in modeling of AD progression that together have the potential to explain observed phenomena and serve as a test-bed for future hypothesis generation and testing in silico. Impact statement Graph theory is a powerful new approach that is transforming the study of brain processes. There do not exist many focused reviews of the subfield of graph modeling of how Alzheimer's and other dementias propagate within the brain network, and how these processes can be mapped mathematically. By providing timely and topical review of this subfield, we fill a critical gap in the community and present a unified view that can serve as an in silico test-bed for future hypothesis generation and testing. We also point to several open and unaddressed questions and controversies that future practitioners can tackle.

Cortical Surfaces Integration with Tractography for Structural Connectivity Analysis

Background: Mapping diffusion MRI tractography streamlines to the cortical surface facilitates the integration of white matter features onto gray matter, especially for connectivity analysis. Method: In this work, we present methods that combine cortical surface meshes with tractography reconstruction to improve endpoint precision and coverage. This cortical mapping also enables the study of structural measures from tractography along the cortex and subcortical structures. In addition to structural connectivity analysis, novel adaptive and dynamic surface seeding methods are proposed. These improvements are made by incorporating cortical maps such as endpoint density. Results: The proposed dynamic surface seeding increases the cortical coverage and reduces endpoint location biases. Our results suggest that the use of cortical and subcortical meshes together with a proper seeding strategy can reduce the variability in structural connectivity analysis. Conclusion: The proposed adaptive and dynamic seeding utilize cortical maps to better distribute tractography interconnections, thus increasing cortical coverage and reducing endpoint bias. This also facilitates the analysis of white matter & diffusion MRI features along the cortex, combined with cortical measures or functional activation. Impact statement This research presents an overview of surface mapping methods for tractography to reduce structural connectivity variability. The proposed adaptive and dynamic seeding utilize cortical maps to better distribute tractography interconnections, thus increasing cortical coverage and reducing end-point bias. This also facilitates the analysis of white matter and diffusion magnetic resonance imaging features along the cortex, combined with cortical measures or functional activation.

The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure

Myelin plays a crucial role in how well information travels between brain regions. Complementing the structural connectome, obtained with diffusion MRI tractography, with a myelin-sensitive measure could result in a more complete model of structural brain connectivity and give better insight into white-matter myeloarchitecture. In this work we weight the connectome by the longitudinal relaxation rate (R1), a measure sensitive to myelin, and then we assess its added value by comparing it with connectomes weighted by the number of streamlines (NOS). Our analysis reveals differences between the two connectomes both in the distribution of their weights and the modular organization. Additionally, the rank-based analysis shows that R1 can be used to separate transmodal regions (responsible for higher-order functions) from unimodal regions (responsible for low-order functions). Overall, the R1-weighted connectome provides a different perspective on structural connectivity taking into account white matter myeloarchitecture.

In the present work, we show that by using a myelin-sensitive measure we can complement the diffusion MRI-based connectivity and provide a different picture of the brain organization. We show that the R1-weighted average distribution does not follow the same trend as the number of streamlines strength distribution, and the two connectomes exhibit different modular organization. We also show that unimodal cortical regions tend to be connected by more streamlines, but the connections exhibit a lower R1-weighted average, while the transmodal regions have higher R1-weighted average but fewer streamlines. This could imply that the unimodal regions require more connections with lower myelination, whereas the transmodal regions rely on connections with higher myelination.

Prediction of ambulatory outcome in patients with corona radiata infarction using deep learning

Deep learning (DL) is an advanced machine learning approach used in diverse areas such as bioinformatics, image analysis, and natural language processing. Here, using brain magnetic resonance imaging (MRI) data obtained at early stages of infarcts, we attempted to develop a convolutional neural network (CNN) to predict the ambulatory outcome of corona radiata infarction at six months after onset. We retrospectively recruited 221 patients with corona radiata infarcts. A favorable outcome of ambulatory function was defined as a functional ambulation category (FAC) score of ≥ 4 (able to walk without a guardian's assistance), and a poor outcome of ambulatory function was defined as an FAC score of < 4. We used a CNN algorithm. Of the included subjects, 69.7% (n = 154) were assigned randomly to the training set and the remaining 30.3% (n = 67) were assigned to the validation set to measure the model performance. The area under the curve was 0.751 (95% CI 0.649-0.852) for the prediction of ambulatory function with the validation dataset using the CNN model. We demonstrated that a CNN model trained using brain MRIs captured at an early stage after corona radiata infarction could be helpful in predicting long-term ambulatory outcomes.