A Symmetry-Based Method to Infer Structural Brain Networks from Probabilistic Tractography Data

Mapping the subcortical connectome using in vivo diffusion MRI: Feasibility and reliability

Tractography combined with regions of interest (ROIs) has been used to non-invasively study the structural connectivity of the cortex as well as to assess the reliability of these connections. However, the subcortical connectome (subcortex to subcortex) has not been comprehensively examined, in part due to the difficulty of performing tractography in this complex and compact region. In this study, we performed an in vivo investigation using tractography to assess the feasibility and reliability of mapping known connections between structures of the subcortex using the test-retest dataset from the Human Connectome Project (HCP). We further validated our observations using a separate unrelated subjects dataset from the HCP. Quantitative assessment was performed by computing tract densities and spatial overlap of identified connections between subcortical ROIs. Further, known connections between structures of the basal ganglia and thalamus were identified and visually inspected, comparing tractography reconstructed trajectories with descriptions from tract-tracing studies. Our observations demonstrate both the feasibility and reliability of using a data-driven tractography-based approach to map the subcortical connectome in vivo.

Accounting for Changing Structure in Functional Network Analysis of TBI Patients

Over the last 15 years, network analysis approaches based on MR data have allowed a renewed understanding of the relationship between brain function architecture and consciousness. Application of this approach to Disorders of Consciousness (DOC) highlights the relationship between specific aspects of network topology and levels of consciousness. Nonetheless, such applications do not acknowledge that DOC patients present with a dramatic level of heterogeneity in structural connectivity (SC) across groups (e.g., etiology, diagnostic categories) and within individual patients (e.g., over time), which possibly affects the level and quality of functional connectivity (FC) patterns that can be expressed. In addition, it is rarely acknowledged that the most frequently employed outcome metrics in the study of brain connectivity (e.g., degree distribution, inter- or intra-resting state network connectivity, and clustering coefficient) are interrelated and cannot be assumed to be independent of each other. We present empirical data showing that, when the two points above are not taken into consideration with an appropriate analytic model, it can lead to a misinterpretation of the role of each outcome metric in the graph's structure and thus misinterpretation of FC results. We show that failing to account for either SC or the inter-relation between outcome measures can lead to inflated false positives (FP) and/or false negatives (FN) in inter- or intra-resting state network connectivity results (defined, respectively, as a positive or negative result in network connectivity that is present when not accounting for SC and/or outcome measure inter-relation, but becomes not significant when accounting for all variables). Overall, we find that unconscious patients have lower rates of FP and FN for within cortical connectivity, lower rates of FN for cortico-subcortical connectivity, and lower rates of FP for within subcortical connectivity. These lower rates in unconscious patients may reflect differences in their triadic closure and SC metrics, which bias the interpretations of the inter- or intra-resting state network connectivity if the SC metrics and triadic closure are not modeled. We suggest that future studies of functional connectivity in DOC patients (i) incorporate where possible SC metrics and (ii) properly account for the intercorrelated nature of outcome variables.

Network Analysis in Disorders of Consciousness: Four Problems and One Proposed Solution (Exponential Random Graph Models)

In recent years, the study of the neural basis of consciousness, particularly in the context of patients recovering from severe brain injury, has greatly benefited from the application of sophisticated network analysis techniques to functional brain data. Yet, current graph theoretic approaches, as employed in the neuroimaging literature, suffer from four important shortcomings. First, they require arbitrary fixing of the number of connections (i.e., density) across networks which are likely to have different "natural" (i.e., stable) density (e.g., patients vs. controls, vegetative state vs. minimally conscious state patients). Second, when describing networks, they do not control for the fact that many characteristics are interrelated, particularly some of the most popular metrics employed (e.g., nodal degree, clustering coefficient)-which can lead to spurious results. Third, in the clinical domain of disorders of consciousness, there currently are no methods for incorporating structural connectivity in the characterization of functional networks which clouds the interpretation of functional differences across groups with different underlying pathology as well as in longitudinal approaches where structural reorganization processes might be operating. Finally, current methods do not allow assessing the dynamics of network change over time. We present a different framework for network analysis, based on Exponential Random Graph Models, which overcomes the above limitations and is thus particularly well suited for clinical populations with disorders of consciousness. We demonstrate this approach in the context of the longitudinal study of recovery from coma. First, our data show that throughout recovery from coma, brain graphs vary in their natural level of connectivity (from 10.4 to 14.5%), which conflicts with the standard approach of imposing arbitrary and equal density thresholds across networks (e.g., time-points, subjects, groups). Second, we show that failure to consider the interrelation between network measures does lead to spurious characterization of both inter- and intra-regional brain connectivity. Finally, we show that Separable Temporal ERGM can be employed to describe network dynamics over time revealing the specific pattern of formation and dissolution of connectivity that accompany recovery from coma.

Mapping population-based structural connectomes

Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a large number of individuals. This article develops a population-based structural connectome (PSC) mapping framework to address these challenges. PSC simultaneously characterizes a large number of white matter bundles within and across different subjects by registering different subjects' brains based on coarse cortical parcellations, compressing the bundles of each connection, and extracting novel connection weights. A robust tractography algorithm and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness of the extracted structural connectomes. The developed PSC framework can be used to reproducibly extract binary networks, weighted networks and streamline-based brain connectomes. We apply the PSC to Human Connectome Project data to illustrate its application in characterizing normal variations and heritability of structural connectomes in healthy subjects.