Realtime Visualization of the Connectome in the Browser using WebGL
Daniel Ginsburg (Children's Hospital Boston), Stephan Gerhard (Ecole Polytechnique Fédérale de Lausanne), Rudolph Pienaar (Children's Hospital Boston)
Recent advances in browser technology along with the widespread proliferation of Graphics Processing Units (GPUs) have enabled new visualization capabilities in the browser. Analyzing the connectome requires intensive preprocessing along with realtime visualization for results exploration. The introduction of WebGL  has made exploration of such data possible in the browser, enabling visualizations across a range of devices without any client-side software requirements other than a WebGL-enabled browser. This poster introduces several visualization techniques that were developed for exploration of connectome data.
The publicly available Connectome Mapper  provides a pipeline to automatically generate structural networks from raw diffusion MRI data for the human brain. In the segmentation stage, T1 MPRAGE MRI is processed by Freesurfer  producing gray / white matter segmentations. The Diffusion Toolkit  is used for reconstruction, and a deterministic streamline algorithm  is used for tractography, generating fiber tracts of the same subject. A parcellation is generated for cortical and subcortical regions-of-interest. These datasets are then coregistered, and a network is generated weighting the connectivity between regions based on the fiber tracts.
Figure 1 shows a screenshot of the WebGL-based visualization. The visualization is composed of the pial surface colored with the per-vertex mean curvature, fiber tracts colored by direction, regions-of-interest rendered with cubes, and lines between regions denoting connectivity. The connectivity lines are colored based on the mean fiber tract length connecting the two regions-of-interest. The visualization can be tuned interactively and contains user interface elements that allow for display of pial or white matter surface, selection of curvature overlay, restriction of fiber tract length, and selection of connectivity regions-of-interest.
We presented a realtime visual exploration of the connectome data including FreeSurfer structural reconstruction, tractography, and network data all within the browser. This project establishes the capability of WebGL as a viable visualization platform for structural connectivity data and provides a means for rapidly exploring and validating the results of Connectome Mapper pipeline. WebGL is underpinned by OpenGL ES 2.0, a graphics standard already supported by a wide range of GPUs on handheld devices including the iPhone, iPad, and numerous Android phones. As WebGL proliferates to such devices, techniques such as those demonstrated in our poster will be enabled across a range of devices.
 WebGL Specification, http://www.khronos.org/registry/webgl/specs/latest/
 Connectome Mapping Toolkit, http://www.cmtk.org/
 Freesurfer, http://surfer.nmr.mgh.harvard.edu/
 Diffusion Toolkit, http://trackvis.org/dtk/