Non-negative data-driven mapping of structural connections with application to the neonatal brain

Multiplex dynamic networks in the newborn brain disclose latent links with neurobehavioral phenotypes

The higher brain functions arise from coordinated neural activity between distinct brain regions, but the spatial, temporal, and spectral complexity of these functional connectivity networks (FCNs) has challenged the identification of correlates with neurobehavioral phenotypes. Characterizing behavioral correlates of early life FCNs is important to understand the activity dependent emergence of neurodevelopmental performance and for improving health outcomes. Here, we develop an analysis pipeline for identifying multiplex dynamic FCNs that combine spectral and spatiotemporal characteristics of the newborn cortical activity. This data-driven approach automatically uncovers latent networks that show robust neurobehavioral correlations and consistent effects by in utero drug exposure. Altogether, the proposed pipeline provides a robust end-to-end solution for an objective assessment and quantitation of neurobehaviorally meaningful network constellations in the highly dynamic cortical functions.

Source-based morphometry reveals structural brain pattern abnormalities in 22q11.2 deletion syndrome

22q11.2 deletion syndrome (22q11DS) is the most frequently occurring microdeletion in humans. It is associated with a significant impact on brain structure, including prominent reductions in gray matter volume (GMV), and neuropsychiatric manifestations, including cognitive impairment and psychosis. It is unclear whether GMV alterations in 22q11DS occur according to distinct structural patterns. Then, 783 participants (470 with 22q11DS: 51% females, mean age [SD] 18.2 [9.2]; and 313 typically developing [TD] controls: 46% females, mean age 18.0 [8.6]) from 13 datasets were included in the present study. We segmented structural T1-weighted brain MRI scans and extracted GMV images, which were then utilized in a novel source-based morphometry (SBM) pipeline (SS-Detect) to generate structural brain patterns (SBPs) that capture co-varying GMV. We investigated the impact of the 22q11.2 deletion, deletion size, intelligence quotient, and psychosis on the SBPs. Seventeen GMV-SBPs were derived, which provided spatial patterns of GMV covariance associated with a quantitative metric (i.e., loading score) for analysis. Patterns of topographically widespread differences in GMV covariance, including the cerebellum, discriminated individuals with 22q11DS from healthy controls. The spatial extents of the SBPs that revealed disparities between individuals with 22q11DS and controls were consistent with the findings of the univariate voxel-based morphometry analysis. Larger deletion size was associated with significantly lower GMV in frontal and occipital SBPs; however, history of psychosis did not show a strong relationship with these covariance patterns. 22q11DS is associated with distinct structural abnormalities captured by topographical GMV covariance patterns that include the cerebellum. Findings indicate that structural anomalies in 22q11DS manifest in a nonrandom manner and in distinct covarying anatomical patterns, rather than a diffuse global process. These SBP abnormalities converge with previously reported cortical surface area abnormalities, suggesting disturbances of early neurodevelopment as the most likely underlying mechanism.

Scalable Orthonormal Projective NMF via Diversified Stochastic Optimization

The increasing availability of large-scale neuroimaging initiatives opens exciting opportunities for discovery science of human brain structure and function. Data-driven techniques, such as Orthonormal Projective Non-negative Matrix Factorization (opNMF), are well positioned to explore multivariate relationships in big data towards uncovering brain organization. opNMF enjoys advantageous interpretability and reproducibility compared to commonly used matrix factorization methods like Principal Component Analysis (PCA) and Independent Component Analysis (ICA), which led to its wide adoption in clinical computational neuroscience. However, applying opNMF in large-scale cohort studies is hindered by its limited scalability caused by its accompanying computational complexity. In this work, we address the computational challenges of opNMF using a stochastic optimization approach that learns over mini-batches of the data. Additionally, we diversify the stochastic batches via repulsive point processes, which reduce redundancy in the mini-batches and in turn lead to lower variance in the updates. We validated our framework on gray matter tissue density maps estimated from 1000 subjects part of the Open Access Series of Imaging (OASIS) dataset. We demonstrated that operations over mini-batches of data yield significant reduction in computational cost. Importantly, we showed that our novel optimization does not compromise the accuracy or interpretability of factors when compared to standard opNMF. The proposed model enables new investigations of brain structure using big neuroimaging data that could improve our understanding of brain structure in health and disease.

Scalable NMF via linearly optimized data compression

Orthonormal projective non-negative matrix factorization (opNMF) has been widely used in neuroimaging and clinical neuroscience applications to derive representations of the brain in health and disease. The non-negativity and orthonormality constraints of opNMF result in intuitive and well-localized factors. However, the advantages of opNMF come at a steep computational cost that prohibits its use in large-scale data. In this work, we propose novel and scalable optimization schemes for orthonormal projective non-negative matrix factorization that enable the use of the method in large-scale neuroimaging settings. We replace the high-dimensional data matrix with its corresponding singular value decomposition (SVD) and QR decompositions and combine the decompositions with opNMF multiplicative update algorithm. Empirical validation of the proposed methods demonstrated significant speed-up in computation time while keeping memory consumption low without compromising the accuracy of the solution.

Concurrent mapping of brain ontogeny and phylogeny within a common space: Standardized tractography and applications

Developmental and evolutionary effects on brain organization are complex, yet linked, as evidenced by the correspondence in cortical area expansion across these vastly different time scales. However, it is still not possible to study concurrently the ontogeny and phylogeny of cortical areal connections, which is arguably more relevant to brain function than allometric measurements. Here, we propose a novel framework that allows the integration of structural connectivity maps from humans (adults and neonates) and nonhuman primates (macaques) onto a common space. We use white matter bundles to anchor the common space and use the uniqueness of cortical connection patterns to these bundles to probe area specialization. This enabled us to quantitatively study divergences and similarities in connectivity over evolutionary and developmental scales, to reveal brain maturation trajectories, including the effect of premature birth, and to translate cortical atlases between diverse brains. Our findings open new avenues for an integrative approach to imaging neuroanatomy.

Empirical transmit field bias correction of T1w/T2w myelin maps

T1-weighted divided by T2-weighted (T1w/T2w) myelin maps were initially developed for neuroanatomical analyses such as identifying cortical areas, but they are increasingly used in statistical comparisons across individuals and groups with other variables of interest. Existing T1w/T2w myelin maps contain radiofrequency transmit field (B1+) biases, which may be correlated with these variables of interest, leading to potentially spurious results. Here we propose two empirical methods for correcting these transmit field biases using either explicit measures of the transmit field or alternatively a 'pseudo-transmit' approach that is highly correlated with the transmit field at 3T. We find that the resulting corrected T1w/T2w myelin maps are both better neuroanatomical measures (e.g., for use in cross-species comparisons), and more appropriate for statistical comparisons of relative T1w/T2w differences across individuals and groups (e.g., sex, age, or body-mass-index) within a consistently acquired study at 3T. We recommend that investigators who use the T1w/T2w approach for mapping cortical myelin use these B1+ transmit field corrected myelin maps going forward.

The Human Connectome Project: A retrospective

The Human Connectome Project (HCP) was launched in 2010 as an ambitious effort to accelerate advances in human neuroimaging, particularly for measures of brain connectivity; apply these advances to study a large number of healthy young adults; and freely share the data and tools with the scientific community. NIH awarded grants to two consortia; this retrospective focuses on the "WU-Minn-Ox" HCP consortium centered at Washington University, the University of Minnesota, and University of Oxford. In just over 6 years, the WU-Minn-Ox consortium succeeded in its core objectives by: 1) improving MR scanner hardware, pulse sequence design, and image reconstruction methods, 2) acquiring and analyzing multimodal MRI and MEG data of unprecedented quality together with behavioral measures from more than 1100 HCP participants, and 3) freely sharing the data (via the ConnectomeDB database) and associated analysis and visualization tools. To date, more than 27 Petabytes of data have been shared, and 1538 papers acknowledging HCP data use have been published. The "HCP-style" neuroimaging paradigm has emerged as a set of best-practice strategies for optimizing data acquisition and analysis. This article reviews the history of the HCP, including comments on key events and decisions associated with major project components. We discuss several scientific advances using HCP data, including improved cortical parcellations, analyses of connectivity based on functional and diffusion MRI, and analyses of brain-behavior relationships. We also touch upon our efforts to develop and share a variety of associated data processing and analysis tools along with detailed documentation, tutorials, and an educational course to train the next generation of neuroimagers. We conclude with a look forward at opportunities and challenges facing the human neuroimaging field from the perspective of the HCP consortium.

Integrated structural and functional atlases of Asian children from infancy to childhood

The developing brain grows exponentially in the first few years of life. There is a need to have age-appropriate brain atlases that coherently characterize the geometry of the cerebral cortex, white matter tracts, and functional organization. This study employed multi-modal brain images of an Asian cohort and constructed brain structural and functional atlases for 6-month-old infants, 4.5-, 6-, and 7.5-year-old children. We exploited large deformation diffeomorphic metric mapping and probabilistic atlas generation approaches to integrate structural MRI and diffusion weighted images (DWIs) and to create the atlas where white matter tracts well fit into the cortical folding pattern. Based on this structural atlas, we then employed spectral clustering to parcellate the brain into functional networks from resting-state fMRI (rs-fMRI). Our results provided the atlas that characterizes the cortical folding geometry, subcortical regions, deep white matter tracts, as well as functional networks in a stereotaxic coordinate space for the four different age groups. The functional networks consisting of the primary cortex were well established in infancy and remained stable to childhood, while specific higher-order functional networks showed specific patterns of hemispherical, subcortical-cerebellar, and cortical-cortical integration and segregation from infancy to childhood. Our multi-modal fusion analysis demonstrated the use of the integrated structural and functional atlas for understanding coherent patterns of brain anatomical and functional development during childhood. Hence, our atlases can be potentially used to study coherent patterns of brain anatomical and functional development.

Highly Reproducible Whole Brain Parcellation in Individuals via Voxel Annotation with Fiber Clusters

A central goal in systems neuroscience is to parcellate the brain into discrete units that are neurobiologically coherent. Here, we propose a strategy for consistent whole-brain parcellation of white matter (WM) and gray matter (GM) in individuals. We parcellate the brain into coherent parcels using non-negative matrix factorization based on voxel annotation using fiber clusters. Tractography is performed using an algorithm that mitigates gyral bias, allowing full gyral and sulcal coverage for reliable parcellation of the cortical ribbon. Experimental results indicate that parcellation using our approach is highly reproducible with 100% test-retest parcel identification rate and is highly consistent with significantly lower inter-subject variability than FreeSurfer parcellation. This implies that reproducible parcellation can be obtained for subject-specific investigation of brain structure and function.

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.

Concurrent brain parcellation and connectivity estimation via co-clustering of resting state fMRI data: A novel approach

Connectional topography mapping has been gaining widespread attention in human brain imaging studies. However, existing methods might not effectively utilize the information from neuroimaging data, thus hindering the understanding of the underlying connectional organization in the brain and uncovering the optimal clustering number from the data. In this study, we propose a novel method for the automated construction of inherent functional connectivity topography in a data‐driven manner by leveraging the power of co‐clustering‐based on resting state fMRI (rs‐fMRI) data. We propose the co‐clustering‐based method not only for concurrently parcellating two interconnected brain regions of interest (ROIs) under consideration into functionally homogenous subregions, but also for estimating the connectivity between these subregions from the two brain ROIs. In particular, we first model the connectional topography mapping as a co‐clustering‐based bipartite graph partitioning problem for constructing the inherent functional connectivity topography between the two interconnected brain ROIs. We also adopt an objective criterion, that is, silhouette width index measuring clustering quality, for determining the optimal number of clusters. The proposed method has been validated for mapping thalamocortical connectional topography based on rs‐fMRI data of 57 subjects. Validation results have demonstrated that our method identified the optimal solution with five pairs of mutually connected subregions of the thalamocortical system from the rs‐fMRI data, and could yield more meaningful, interpretable, and homogenous connectional topography than existing methods. The proposed method was further validated by the high symmetry of the mapped connectional topography between two hemispheres.