Difference between revisions of "2011 Summer Project Week SlicerVmtk4"

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(Created page with '__NOTOC__ <gallery> Image:PW-MIT2011.png|Projects List Image:notfound.png|Interesting picture to be added... </gallery> '''The Vascular Mo…')
 
 
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<gallery>
 
<gallery>
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
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Image:notfound.png|Interesting picture to be added...  
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Image:Vesselnes.png|The Vesselness modules in Slicer3 (left) and Slicer4 (right)
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Image:Levelset.png|The Level Set Segmentation modules in Slicer3 (left) and Slicer4 (right)
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Image:Centerline.png|The Centerlines modules in Slicer3 (left) and Slicer4 (right)
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Image:Slicervmtk4.png|The VMTK extension in the Slicer4 extension wizard
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Image:slicervmtkdashboard.png|The Slicer4 Dashboard showing the VMTK extension.
 
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</gallery>
  
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==Key Investigators==
 
==Key Investigators==
 
* University of Pennsylvania: Daniel Haehn
 
* University of Pennsylvania: Daniel Haehn
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* University of Pennsylvania: Kilian Pohl
 
* Orobix Inc.: Luca Antiga
 
* Orobix Inc.: Luca Antiga
 
* Isomics Inc.: Steve Pieper
 
* Isomics Inc.: Steve Pieper
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* SPL: Ron Kikinis
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
  
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<!-- What you plan to achieve during project week goes here -->
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The Vascular Modeling Toolkit (VMTK) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.
  
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Main goal of the incorporation effort for the upcoming 3D Slicer version 4 is the enhancement of the modules' usability and in particular the focus on reducing the required user-interaction.
  
 
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<!-- What specific things you will be doing during the week: writing code?  trying code on specific datasets?  talking with other attendees?  All of the above? -->
 
<!-- What specific things you will be doing during the week: writing code?  trying code on specific datasets?  talking with other attendees?  All of the above? -->
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One single extension bundle called '''SlicerVmtk4''' will provide a package of all VMTK libraries and modules. We want to use the 3D Slicer4 extension infrastructure for distribution and will try to achieve this during the project week.
  
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In terms of usability each module now has a preview mode which displays results in less than 10 seconds. Also, beside seed points, only max. one parameter is required. If desired, more parameters are available in an advanced mode.
  
 
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<!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
 
<!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
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The SlicerVmtk4 extension uses the Superbuild mechanism to download the VMTK libraries. This was not supported by the extension infrastructure yet so we worked on that during the project week with Slicer4 Core Developers. We are very close to finish it and then this extension will be included in the Slicer4 Nightly builds.
  
 
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==References==
 
==References==
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http://slicer.vmtk.org <br>
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* The project website: http://slicer.vmtk.org  
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* VMTK in 3D Slicer4 in action: Lung CT - http://www.youtube.com/watch?v=DJ2032yo5Co
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<!-- Add links here to background material: where can we download the data?  where is the source code repository?  what papers or web sites will help someone quickly learn what the outstanding issues are? -->
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* Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
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* D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
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* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010. Available online at http://www.spl.harvard.edu/publications/item/view/1957.
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* Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.
  
 
==Delivery Mechanism==
 
==Delivery Mechanism==

Latest revision as of 15:38, 24 June 2011

Home < 2011 Summer Project Week SlicerVmtk4

  • The Vesselness modules in Slicer3 (left) and Slicer4 (right)

  • The Level Set Segmentation modules in Slicer3 (left) and Slicer4 (right)

  • The Centerlines modules in Slicer3 (left) and Slicer4 (right)

  • The VMTK extension in the Slicer4 extension wizard

  • The Slicer4 Dashboard showing the VMTK extension.

The Vascular Modeling Toolkit in 3D Slicer 4

Key Investigators

  • University of Pennsylvania: Daniel Haehn
  • University of Pennsylvania: Kilian Pohl
  • Orobix Inc.: Luca Antiga
  • Isomics Inc.: Steve Pieper
  • SPL: Ron Kikinis

Objective

The Vascular Modeling Toolkit (VMTK) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

Main goal of the incorporation effort for the upcoming 3D Slicer version 4 is the enhancement of the modules' usability and in particular the focus on reducing the required user-interaction.

Approach, Plan

One single extension bundle called SlicerVmtk4 will provide a package of all VMTK libraries and modules. We want to use the 3D Slicer4 extension infrastructure for distribution and will try to achieve this during the project week.

In terms of usability each module now has a preview mode which displays results in less than 10 seconds. Also, beside seed points, only max. one parameter is required. If desired, more parameters are available in an advanced mode.

Progress

The SlicerVmtk4 extension uses the Superbuild mechanism to download the VMTK libraries. This was not supported by the extension infrastructure yet so we worked on that during the project week with Slicer4 Core Developers. We are very close to finish it and then this extension will be included in the Slicer4 Nightly builds.

References


  • Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
  • D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
  • D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010. Available online at http://www.spl.harvard.edu/publications/item/view/1957.
  • Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.

Delivery Mechanism

This work will be delivered to the NAMIC Kit as a

  1. Slicer Module
    1. Built-in:
    2. Extension -- commandline:
    3. Extension -- loadable: [X]
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