Difference between revisions of "2012 Summer Project Week:XTK"

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(Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…')
 
 
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<gallery>
 
<gallery>
 
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:Xfibers.png|Tractography rendered with XTK in 5 lines of JavaScript code, here the [http://lessons.goxtk.com/06/ live version].
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:Xvolume.png|MRI volume + label map rendered with XTK, here the [http://lessons.goxtk.com/13/ live version].
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Image:Xtkabdom.png|The SPL Abdominal Atlas. ''Left'': In 3D Slicer version 4, ''Right'': In a web browser exported using the '''WebGL Export''' module.
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Image:Xtkbrain.png|The NAC Brain Atlas: ''Left'': In Slicer, ''Right'': In a web browser.
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Image:Xtkblack.png|An example WebGL export with black background color and a caption tooltip. ''Left'': In Slicer, ''Right'': In a web browser.
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Image:webgl_export_template.png|Template at the end of the summer project week [[Media:Progress_webglexport.mov]]
 
</gallery>
 
</gallery>
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==Instructions for Use of this Template==
 
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#Please create a new wiki page with an appropriate title for your project using the convention 2012_Winter_Project_Week:<Project Name>
 
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#Copy the entire text of this page into the page created above
 
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#Link the created page into the list of projects for the project event
 
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#Delete this section from the created page
 
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
==Key Investigators==
 
==Key Investigators==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* Boston Children's Hospital: Daniel Haehn, Nicolas Rannous, Rudolph Pienaar
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* Utah: Tom Fletcher, Ross Whitaker
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* Isomics Inc.: Steve Pieper
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
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<h3>Objective</h3>
 
<h3>Objective</h3>
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We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
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XTK is a WebGL framework providing an easy-to-use API to visualize scientific data on the web. No background or knowledge in Computer Graphics is required and a [https://github.com/xtk/X/wiki/X:Fileformats variety of file formats] can be natively read and visualized with very little JavaScript code.<br><br>Nevertheless, some researchers want to share their data without writing any code so we propose a '''one-click WebGL export module''' for 3D Slicer 4.
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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The '''WebGL Export''' module should enable the export of ''Surface Models'', ''Fiber Tracks'' and ''Volumes in 2D and 3D (including Volume Rendering)'' from 3D Slicer 4 to the web.
  
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Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
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First step of further development is to update the currently existing '''WebGL Export''' module to a new XTK version. Additionally, a TrackVis file format (.TRK) writer should be implemented for 3D Slicer 4 since XTK natively supports this format for Tractography.  
  
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Our plan for the project week is to first try out <bar>,...
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Also, it should be interesting to investigate if Slicer Data Bundles or Scene Views can be exported.
  
 
</div>
 
</div>
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<h3>Progress</h3>
 
<h3>Progress</h3>
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Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
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*Progress:
 +
** A first version of the '''WebGL Export''' module is part of the latest 3D Slicer 4 release. Currently, it supports the export of ''Surface Models'' to a website (see [http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf tutorial]).
 +
** Feedback for the tutorial.
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** HTML/JAVASCRIPT/CSS Template for exported scene.
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** Identify new requirements in XTK (vtk tensors, etc.)
 +
** Fixes in XTK (resize web browser)
  
 +
* Next:
 +
** Finish the template (design + connections)
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** Export the whole slicer scene in new HTML template
  
 
</div>
 
</div>
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==Delivery Mechanism==
 
==Delivery Mechanism==
  
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This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
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This work will be delivered to the NA-MIC Kit as a
  
 
#ITK Module
 
#ITK Module
 
#Slicer Module
 
#Slicer Module
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##Built-in
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##Built-in '''YES'''
 
##Extension -- commandline
 
##Extension -- commandline
 
##Extension -- loadable
 
##Extension -- loadable
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==References==
 
==References==
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*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
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* [http://goXTK.com The XTK website] including lessons, demos etc.
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* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
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* [https://github.com/xtk/SlicerWebGLExport Github Project Page] for the 3D Slicer WebGL Export module
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* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
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* '''WebGL for Baby Brains: Neuroimaging in the Browser''' at the WebGL Camp Orlando 2012, [http://www.youtube.com/watch?v=SQuH-xpdlbc Video]
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* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
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* '''Science!''' featuring XTK, [http://creativejs.com/2012/04/science/ CreativeJS.com]
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* '''The X Toolkit for Scientific Visualization''' on [http://www.webgl.com/2012/03/webgl-demo-the-x-toolkit-for-scientific-visualization/ WebGL.com]
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* D. Haehn, N. Rannou, B. Ahtam, E. Grant, R. Pienaar: '''Neuroimaging in the Browser using the X Toolkit''', INCF Neuroinformatics 2012, [http://www.neuroinformatics2012.org/abstracts/neuroimaging-in-the-browser-using-the-x-toolkit Abstract]
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* A. Klein, N. Nichols, D. Haehn: '''Mindboggle 2 interface: online visualization of extracted brain features with XTK''', INCF Neuroinformatics 2012, [http://www.neuroinformatics2012.org/abstracts/mindboggle-2-interface-online-visualization-of-extracted-brain-features-with-xtk Abstract]

Latest revision as of 14:55, 22 June 2012

Home < 2012 Summer Project Week:XTK

  • Tractography rendered with XTK in 5 lines of JavaScript code, here the live version.

  • MRI volume + label map rendered with XTK, here the live version.

  • The SPL Abdominal Atlas. Left: In 3D Slicer version 4, Right: In a web browser exported using the WebGL Export module.

  • The NAC Brain Atlas: Left: In Slicer, Right: In a web browser.

  • An example WebGL export with black background color and a caption tooltip. Left: In Slicer, Right: In a web browser.

  • Template at the end of the summer project week Media:Progress_webglexport.mov

Key Investigators

  • Boston Children's Hospital: Daniel Haehn, Nicolas Rannous, Rudolph Pienaar
  • Isomics Inc.: Steve Pieper

Objective

XTK is a WebGL framework providing an easy-to-use API to visualize scientific data on the web. No background or knowledge in Computer Graphics is required and a variety of file formats can be natively read and visualized with very little JavaScript code.

Nevertheless, some researchers want to share their data without writing any code so we propose a one-click WebGL export module for 3D Slicer 4.


Approach, Plan

The WebGL Export module should enable the export of Surface Models, Fiber Tracks and Volumes in 2D and 3D (including Volume Rendering) from 3D Slicer 4 to the web.

First step of further development is to update the currently existing WebGL Export module to a new XTK version. Additionally, a TrackVis file format (.TRK) writer should be implemented for 3D Slicer 4 since XTK natively supports this format for Tractography.

Also, it should be interesting to investigate if Slicer Data Bundles or Scene Views can be exported.

Progress

  • Progress:
    • A first version of the WebGL Export module is part of the latest 3D Slicer 4 release. Currently, it supports the export of Surface Models to a website (see tutorial).
    • Feedback for the tutorial.
    • HTML/JAVASCRIPT/CSS Template for exported scene.
    • Identify new requirements in XTK (vtk tensors, etc.)
    • Fixes in XTK (resize web browser)
  • Next:
    • Finish the template (design + connections)
    • Export the whole slicer scene in new HTML template

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a

  1. ITK Module
  2. Slicer Module
    1. Built-in YES
    2. Extension -- commandline
    3. Extension -- loadable
  3. Other (Please specify)

References

  • The XTK website including lessons, demos etc.
  • Github Project Page for the 3D Slicer WebGL Export module
  • WebGL for Baby Brains: Neuroimaging in the Browser at the WebGL Camp Orlando 2012, Video
  • Science! featuring XTK, CreativeJS.com
  • The X Toolkit for Scientific Visualization on WebGL.com
  • D. Haehn, N. Rannou, B. Ahtam, E. Grant, R. Pienaar: Neuroimaging in the Browser using the X Toolkit, INCF Neuroinformatics 2012, Abstract
  • A. Klein, N. Nichols, D. Haehn: Mindboggle 2 interface: online visualization of extracted brain features with XTK, INCF Neuroinformatics 2012, Abstract
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