Interactive computation and visualization of structural connectomes in real-time

Structural networks contain high dimensional data that raise huge computational and visualization problems, especially when attempting to characterise them using graph theory. As a result, it can be non-intuitive to grasp the contribution of each edge within a graph, both at a local and global scale. Here, we introduce a new platform that enables tractography-based networks to be explored in a highly interactive real-time fashion. The framework allows one to interactively tune graph-related parameters on the fly, as opposed to conventional visualization softwares that rely on pre-computed connectivity matrices. From a neurosurgical perspective, the method also provides enhanced understanding regarding the potential removal of a specific node or transection of an edge from the network, allowing surgeons and clinicians to discern the value of each node

A generative network model of neurodevelopmental diversity in structural brain organization.

The formation of large-scale brain networks, and their continual refinement, represent crucial developmental processes that can drive individual differences in cognition and which are associated with multiple neurodevelopmental conditions. But how does this organization arise, and what mechanisms drive diversity in organization? We use generative network modeling to provide a computational framework for understanding neurodevelopmental diversity. Within this framework macroscopic brain organization, complete with spatial embedding of its organization, is an emergent property of a generative wiring equation that optimizes its connectivity by renegotiating its biological costs and topological values continuously over time. The rules that govern these iterative wiring properties are controlled by a set of tightly framed parameters, with subtle differences in these parameters steering network growth towards different neurodiverse outcomes. Regional expression of genes associated with the simulations converge on biological processes and cellular components predominantly involved in synaptic signaling, neuronal projection, catabolic intracellular processes and protein transport. Together, this provides a unifying computational framework for conceptualizing the mechanisms and diversity in neurodevelopment, capable of integrating different levels of analysis-from genes to cognition

A Tool for Interactive Data Visualization: Application to Over 10,000 Brain Imaging and Phantom MRI Data Sets

In this paper we propose a web-based approach for quick visualization of big data from brain magnetic resonance imaging (MRI) scans using a combination of an automated image capture and processing system, nonlinear embedding, and interactive data visualization tools. We draw upon thousands of MRI scans captured via the COllaborative Imaging and Neuroinformatics Suite (COINS). We then interface the output of several analysis pipelines based on structural and functional data to a t-distributed stochastic neighbor embedding (t-SNE) algorithm which reduces the number of dimensions for each scan in the input data set to two dimensions while preserving the local structure of data sets. Finally, we interactively display the output of this approach via a web-page, based on data driven documents (D3) JavaScript library. Two distinct approaches were used to visualize the data. In the first approach, we computed multiple quality control (QC) values from pre-processed data, which were used as inputs to the t-SNE algorithm. This approach helps in assessing the quality of each data set relative to others. In the second case, computed variables of interest (e.g., brain volume or voxel values from segmented gray matter images) were used as inputs to the t-SNE algorithm. This approach helps in identifying interesting patterns in the data sets. We demonstrate these approaches using multiple examples from over 10,000 data sets including (1) quality control measures calculated from phantom data over time, (2) quality control data from human functional MRI data across various studies, scanners, sites, (3) volumetric and density measures from human structural MRI data across various studies, scanners and sites. Results from (1) and (2) show the potential of our approach to combine t-SNE data reduction with interactive color coding of variables of interest to quickly identify visually unique clusters of data (i.e., data sets with poor QC, clustering of data by site) quickly. Results from (3) demonstrate interesting patterns of gray matter and volume, and evaluate how they map onto variables including scanners, age, and gender. In sum, the proposed approach allows researchers to rapidly identify and extract meaningful information from big data sets. Such tools are becoming increasingly important as datasets grow larger

Enhancing studies of the connectome in autism using the autism brain imaging data exchange II

The second iteration of the Autism Brain Imaging Data Exchange (ABIDE II) aims to enhance the scope of brain connectomics research in Autism Spectrum Disorder (ASD). Consistent with the initial ABIDE effort (ABIDE I), that released 1112 datasets in 2012, this new multisite open-data resource is an aggregate of resting state functional magnetic resonance imaging (MRI) and corresponding structural MRI and phenotypic datasets. ABIDE II includes datasets from an additional 487 individuals with ASD and 557 controls previously collected across 16 international institutions. The combination of ABIDE I and ABIDE II provides investigators with 2156 unique cross-sectional datasets allowing selection of samples for discovery and/or replication. This sample size can also facilitate the identification of neurobiological subgroups, as well as preliminary examinations of sex differences in ASD. Additionally, ABIDE II includes a range of psychiatric variables to inform our understanding of the neural correlates of co-occurring psychopathology; 284 diffusion imaging datasets are also included. It is anticipated that these enhancements will contribute to unraveling key sources of ASD heterogeneity

The Intrinsic Connectome of the Rat Amygdala

The connectomes of nervous systems or parts there of are becoming important subjects of study as the amount of connectivity data increases. Because most tract-tracing studies are performed on the rat, we conducted a comprehensive analysis of the amygdala connectome of this species resulting in a meta-study. The data were imported into the neuroVIISAS system, where regions of the connectome are organized in a controlled ontology and network analysis can be performed. A weighted digraph represents the bilateral intrinsic (connections of regions of the amygdala) and extrinsic (connections of regions of the amygdala to non-amygdaloid regions) connectome of the amygdala. Its structure as well as its local and global network parameters depend on the arrangement of neuronal entities in the ontology. The intrinsic amygdala connectome is a small-world and scale-free network. The anterior cortical nucleus (72 in- and out-going edges), the posterior nucleus (45), and the anterior basomedial nucleus (44) are the nuclear regions that posses most in- and outdegrees. The posterior nucleus turns out to be the most important nucleus of the intrinsic amygdala network since its Shapley rate is minimal. Within the intrinsic amygdala, regions were determined that are essential for network integrity. These regions are important for behavioral (processing of emotions and motivation) and functional (memory) performances of the amygdala as reported in other studies

Scalable Machine Learning Methods for Massive Biomedical Data Analysis.

Modern data acquisition techniques have enabled biomedical researchers to collect and analyze datasets of substantial size and complexity. The massive size of these datasets allows us to comprehensively study the biological system of interest at an unprecedented level of detail, which may lead to the discovery of clinically relevant biomarkers. Nonetheless, the dimensionality of these datasets presents critical computational and statistical challenges, as traditional statistical methods break down when the number of predictors dominates the number of observations, a setting frequently encountered in biomedical data analysis. This difficulty is compounded by the fact that biological data tend to be noisy and often possess complex correlation patterns among the predictors. The central goal of this dissertation is to develop a computationally tractable machine learning framework that allows us to extract scientifically meaningful information from these massive and highly complex biomedical datasets. We motivate the scope of our study by considering two important problems with clinical relevance: (1) uncertainty analysis for biomedical image registration, and (2) psychiatric disease prediction based on functional connectomes, which are high dimensional correlation maps generated from resting state functional MRI.PhDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111354/1/takanori_1.pd

Lead-OR: A multimodal platform for deep brain stimulation surgery

Background: Deep brain stimulation (DBS) electrode implant trajectories are stereotactically defined using preoperative neuroimaging. To validate the correct trajectory, microelectrode recordings (MERs) or local field potential recordings can be used to extend neuroanatomical information (defined by MRI) with neurophysiological activity patterns recorded from micro- and macroelectrodes probing the surgical target site. Currently, these two sources of information (imaging vs. electrophysiology) are analyzed separately, while means to fuse both data streams have not been introduced. Methods: Here, we present a tool that integrates resources from stereotactic planning, neuroimaging, MER, and high-resolution atlas data to create a real-time visualization of the implant trajectory. We validate the tool based on a retrospective cohort of DBS patients (N = 52) offline and present single-use cases of the real-time platform. Results: We establish an open-source software tool for multimodal data visualization and analysis during DBS surgery. We show a general correspondence between features derived from neuroimaging and electrophysiological recordings and present examples that demonstrate the functionality of the tool. Conclusions: This novel software platform for multimodal data visualization and analysis bears translational potential to improve accuracy of DBS surgery. The toolbox is made openly available and is extendable to integrate with additional software packages