Difference between revisions of "2011 Winter Project Week:StenosisDetector"

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<gallery>
 
<gallery>
 
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2011.png|[[2011_Winter_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:step1.png|StensosisDetector Step1
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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:step2.png|StensosisDetector Step2
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Image:step3.png|StensosisDetector Step3
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Image:step4.png|StensosisDetector Step4
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Image:step5.png|StensosisDetector Step5
 
</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 Project/<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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* University of Heidelberg, Germany: Suares Tamekue
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* Utah: Tom Fletcher, Ross Whitaker
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* UPenn: Daniel Haehn
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* [http://www.orobix.com Orobix], Italy: Luca Antiga
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* SPL: Ron Kikinis
  
 
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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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We are developing a stenosis detector based on VMTK in Slicer 4. The goal is to be able to visualize stenosis after a vessel segmentation using a wizard-based interface.
  
  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
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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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Our approach for developing the stenosis detector is: first vessel enhancement, level-set segmentation, network extraction and then quantification and visualization of stenosis.
  
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Our plan for the project week is to first try out <bar>,...
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The tool will be evaluated on datasets.
  
 
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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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A prototyp of the graphical user interface has been designed and implemented.
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'''Project Week Update:'''
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The week was very productive. We got a lot of feedback from the Kitware guys. Specially on the wizard interface which is based on the CTK library. We also had to clarify an issue concerning the area of the wizard content and the way the different wizard steps interact with each other and with the logic.
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##Built-in
 
##Built-in
 
##Extension -- commandline
 
##Extension -- commandline
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##Extension -- loadable
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##Extension -- loadable [X]
 
#Other (Please specify)
 
#Other (Please specify)
  
 
==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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* 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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* 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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* 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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* 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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* 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.
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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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* 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.
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</div>
 
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Latest revision as of 17:22, 14 January 2011

Home < 2011 Winter Project Week:StenosisDetector

  • StensosisDetector Step1

  • StensosisDetector Step2

  • StensosisDetector Step3

  • StensosisDetector Step4

  • StensosisDetector Step5

Key Investigators

  • University of Heidelberg, Germany: Suares Tamekue
  • UPenn: Daniel Haehn
  • Orobix, Italy: Luca Antiga
  • SPL: Ron Kikinis

Objective

We are developing a stenosis detector based on VMTK in Slicer 4. The goal is to be able to visualize stenosis after a vessel segmentation using a wizard-based interface.




Approach, Plan

Our approach for developing the stenosis detector is: first vessel enhancement, level-set segmentation, network extraction and then quantification and visualization of stenosis.

The tool will be evaluated on datasets.

Progress

A prototyp of the graphical user interface has been designed and implemented.

Project Week Update: The week was very productive. We got a lot of feedback from the Kitware guys. Specially on the wizard interface which is based on the CTK library. We also had to clarify an issue concerning the area of the wizard content and the way the different wizard steps interact with each other and with the logic.


Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

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

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.
  • 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.
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