Difference between revisions of "2013 Summer Project Week:Airway Inspector Porting"

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(Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.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-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2013.png|[[2013_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:EmphysemaGUI.png|Emphysema Analysis Tool
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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:AIScreenshot.png|Airway Analysis Tool
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Image:CIPArchitecture.png|Chest Imaging Platform Architecture
 
</gallery>
 
</gallery>
  
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==Instructions for Use of this Template==
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==Key Investigators==
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#Please create a new wiki page with an appropriate title for your project using the convention 2013_Summer_Project_Week:<Project Name>
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* BWH: Raul San Jose, Demian Wassermann, Rola Harmouche, James Ross
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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
 
  
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==Key Investigators==
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<h3>Background</h3>
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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Airway Inspector (www.airwayinspector.org) is a tool for CT-based image quantitative analysis of the lung to allow the  exploration of  airway morphology and desitometric characteristics [1]. Airway Inspector is based on Slicer2.
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* Utah: Tom Fletcher, Ross Whitaker
 
  
 
<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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Port the capabilities of Airway Inspector to Slicer4.
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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This goal will be achieved by creating  extension module with two components:
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* Emphysema Analysis Sub-Module
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** Port Chest structure segmentation using VTK
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** Creation of loadable module
  
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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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* Airway Analysis Sub-Module
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** Port airway measurement VTK classes
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Our plan for the project week is to first try out <bar>,...
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** Creation of a loadable module
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</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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The  main libraries for lung and airway wall segmentation tools have been developed using C++ and VTK and have been validated and used in multiple clinical works.
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We have created an extension to support this porting. We have developed two CLI to support the emphysema analsyis sub-module. A scripted python module is under development to encapsulate the logic.
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The Airway Analysis Sub-module still is in the design phase.
  
  
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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  
  
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#ITK Module
 
 
#Slicer Module
 
#Slicer Module
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##Built-in
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##Extension — loadable modules
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##Extension -- commandline
 
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##Extension -- loadable
 
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#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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* San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302. Available on-line: www.lulu.com/content/3507981.
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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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* 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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* 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 .
 

Latest revision as of 14:58, 21 June 2013

Home < 2013 Summer Project Week:Airway Inspector Porting

  • Emphysema Analysis Tool

  • Airway Analysis Tool

  • Chest Imaging Platform Architecture

Key Investigators

  • BWH: Raul San Jose, Demian Wassermann, Rola Harmouche, James Ross

Background

Airway Inspector (www.airwayinspector.org) is a tool for CT-based image quantitative analysis of the lung to allow the exploration of airway morphology and desitometric characteristics [1]. Airway Inspector is based on Slicer2.

Objective

Port the capabilities of Airway Inspector to Slicer4.

Approach, Plan

This goal will be achieved by creating extension module with two components:

  • Emphysema Analysis Sub-Module
    • Port Chest structure segmentation using VTK
    • Creation of loadable module
  • Airway Analysis Sub-Module
    • Port airway measurement VTK classes
    • Creation of a loadable module

Progress

The main libraries for lung and airway wall segmentation tools have been developed using C++ and VTK and have been validated and used in multiple clinical works.

We have created an extension to support this porting. We have developed two CLI to support the emphysema analsyis sub-module. A scripted python module is under development to encapsulate the logic.

The Airway Analysis Sub-module still is in the design phase.


Delivery Mechanism

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

  1. Slicer Module
    1. Extension — loadable modules

References

  • San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302. Available on-line: www.lulu.com/content/3507981.
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