text: Visually comparing brain networks, or connectomes, is an essential task in the field of neuroscience. Especially relevant to the field of clinical neuroscience, group studies that examine differences between populations or changes over time within a population enable neuroscientists to reason about effective diagnoses and treatments for a range of neuropsychiatric disorders. In this paper, we specifically explore how visual analytics tools can be used to facilitate various clinical neuroscience tasks, in which observation and analysis of meaningful patterns in the connectome can support patient diagnosis and treatment. We conduct a survey of visualization tasks that enable clinical neuroscience activities, and further explore how existing connectome visualization tools support or fail to support these tasks. Based on our investigation of these tasks, we introduce a novel visualization tool, NeuroCave, to support group studies analyses. We discuss how our design decisions (the use of immersive visualization, the use of hierarchical clustering and dimensionality reduction techniques, and the choice of visual encodings) are motivated by these tasks. We evaluate NeuroCave through two use cases that illustrate the utility of interactive connectome visualization in clinical neuroscience contexts. In the first use case, we study sex differences using functional connectomes and discover hidden connectome patterns associated with well-known cognitive differences in spatial and verbal abilities. In the second use case, we show how the utility of visualizing the brain in different topological space coupled with clustering information can reveal the brain's intrinsic structure.
  @cite_4: This project demonstrates real-time rendering and sharing of standard medical data formats between WebGL-enabled browsers across multiple devices. Any linked browser can interact with and update the display, which propogates to all other linked browsers.
  @cite_9: Effective visualization is central to the exploration and comprehension of brain imaging data. While MRI data are acquired in three-dimensional space, the methods for visualizing such data have rarely taken advantage of three-dimensional stereoscopic technologies. We present here results of stereoscopic visualization of clinical data, as well as an atlas of whole-brain functional connectivity. In comparison with traditional 3D rendering techniques, we demonstrate the utility of stereoscopic visualizations to provide an intuitive description of the exact location and the relative sizes of various brain landmarks, structures and lesions. In the case of resting state fMRI, stereoscopic 3D visualization facilitated comprehension of the anatomical position of complex large-scale functional connectivity patterns. Overall, stereoscopic visualization improves the intuitive visual comprehension of image contents, and brings increased dimensionality to visualization of traditional MRI data, as well as patterns of functional connectivity.
  @cite_53: 
  @cite_52: Electroencephalography (EEG) and magnetoencephalography (MEG) provide insight into neuronal processes in the brain in a real-time scale. Brain activity can be modeled in terms of a source distribution found by solving the bioelectromagnetic inverse problem, e.g. using linear source reconstruction methods. Such methods are particularly suitable to be used on modern highly parallel processing systems, such as widely available graphic processing units (GPUs). The utilization of these capabilities paves the way for online neuroelectromagnetic source imaging. We present a system that, according to its modular scheme, can be configured in a very flexible way using graphical building blocks. It allows to use different preprocessing algorithms together with a linear source reconstruction method. The algorithms use both CPU and GPU resources.
  @cite_6: It has been known for some time that larger graphs can be interpreted if laid out in 3D and displayed with stereo and or motion depth cues to support spatial perception. However, prior studies were carried out using displays that provided a level of detail far short of what the human visual system is capable of resolving. Therefore, we undertook a graph comprehension study using a very high resolution stereoscopic display. In our first experiment, we examined the effect of stereoscopic display, kinetic depth, and using 3D tubes versus lines to display the links. The results showed a much greater benefit for 3D viewing than previous studies. For example, with both motion and stereoscopic depth cues, unskilled observers could see paths between nodes in 333 node graphs with less than a 10p error rate. Skilled observers could see up to a 1000-node graph with less than a 10p error rate. This represented an order of magnitude increase over 2D display. In our second experiment, we varied both nodes and links to understand the constraints on the number of links and the size of graph that can be reliably traced. We found the difference between number of links and number of nodes to best account for error rates and suggest that this is evidence for a “perceptual phase transition.” These findings are discussed in terms of their implications for information display.
  @cite_0: In this paper we present a new technique and prototype graph visualization system, stereoscopic highlighting, to help answer accessibility and adjacency queries when interacting with a node-link diagram. Our technique utilizes stereoscopic depth to highlight regions of interest in a 2D graph by projecting these parts onto a plane closer to the viewpoint of the user. This technique aims to isolate and magnify specific portions of the graph that need to be explored in detail without resorting to other highlighting techniques like color or motion, which can then be reserved to encode other data attributes. This mechanism of stereoscopic highlighting also enables focus+context views by juxtaposing a detailed image of a region of interest with the overall graph, which is visualized at a further depth with correspondingly less detail. In order to validate our technique, we ran a controlled experiment with 16 subjects comparing static visual highlighting to stereoscopic highlighting on 2D and 3D graph layouts for a range of tasks. Our results show that while for most tasks the difference in performance between stereoscopic highlighting alone and static visual highlighting is not statistically significant, users performed better when both highlighting methods were used concurrently. In more complicated tasks, 3D layout with static visual highlighting outperformed 2D layouts with a single highlighting method. However, it did not outperform the 2D layout utilizing both highlighting techniques simultaneously. Based on these results, we conclude that stereoscopic highlighting is a promising technique that can significantly enhance graph visualizations for certain use cases.
  @cite_15: Abstract Independent component analysis (ICA) has become an increasingly utilized approach for analyzing brain imaging data. In contrast to the widely used general linear model (GLM) that requires the user to parameterize the data (e.g. the brain’s response to stimuli), ICA, by relying upon a general assumption of independence, allows the user to be agnostic regarding the exact form of the response. In addition, ICA is intrinsically a multivariate approach, and hence each component provides a grouping of brain activity into regions that share the same response pattern thus providing a natural measure of functional connectivity. There are a wide variety of ICA approaches that have been proposed, in this paper we focus upon two distinct methods. The first part of this paper reviews the use of ICA for making group inferences from fMRI data. We provide an overview of current approaches for utilizing ICA to make group inferences with a focus upon the group ICA approach implemented in the GIFT software. In the next part of this paper, we provide an overview of the use of ICA to combine or fuse multimodal data. ICA has proven particularly useful for data fusion of multiple tasks or data modalities such as single nucleotide polymorphism (SNP) data or event-related potentials. As demonstrated by a number of examples in this paper, ICA is a powerful and versatile data-driven approach for studying the brain.
summary: While most commonly used visualization tools are dedicated desktop applications, web-based implementations, such as @cite_4 or @cite_15 , free the user from being attached to a specific operating system @cite_52 . is also a web-based application and runs in any modern browser. The use of stereoscopic techniques can provide a more immersive way to explore brain imaging data @cite_9 , H "a find that healthcare professionals perceive the increased dimensionality provided by stereoscopy as beneficial for understanding depth in the displayed scenery @cite_53 . Moreover, Ware and Mitchell find that the use of stereographic visualizations reduces the perception error rate in graph perception for large graphs with more than 500 nodes @cite_6 , and @cite_0 observed that, when coupled with highlighting, stereoscopic representations of 3D graphs outperformed their non-immersive counterpart. lets the user move between desktop and VR environments for interactively exploring 3D connectomes.