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

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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:|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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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:|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
 
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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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* UIowa: David Welch, Hans Johnson
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* Utah: Tom Fletcher, Ross Whitaker
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* Utah: Clement Vachet, Sylvian Gouttard
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* UNC: Guido Gerig, Mahshid Farzinfar, Martin Styner
  
 
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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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DTIPrep is a useful tool for automated QA of DWI images, but it has areas where improvement and increased usability could be achieved. We will identify ways to improve user interaction and experience, as well as address any architectural decisions that affect future development. Specific goals are:
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# Fix the behavior of the '--outputFolder' flag to something more intuitive or add alternative method and document current behavior
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# Fix the xml reporting scheme for batch processing mode and make it conform to the interactive mode
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#*; Example : [[Media:DTIPrepMisimatchingTXT.txt]] [[Media:DTIPrepMismatchingXML.xml]]
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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We will meet with the main developers of DTIPrep and discuss user experiences and ways to improve the interface.    We will also address any additional enhancements and solutions that is needed for the tool.
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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 plan for the project week is to first try out <bar>,...
 
  
 
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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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N/A
  
  
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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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* Z. Liu et al., [http://www.nitrc.org/docman/view.php/283/753/spie2010-dwi-qc.pdf| "Quality control of diffusion weighted images"] Proc. SPIE 2010, vol. 1, no. 1, p. 76280J-76280J-9.
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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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[http://www.nitrc.org/docman/view.php/283/754/1050_Thu_7628-17_Zhexing_Liu.ppt| Powerpoint presentation]
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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 .
 
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Latest revision as of 16:39, 18 June 2012

Home < 2012 Summer Project Week:DTIPrep

Key Investigators

  • UIowa: David Welch, Hans Johnson
  • Utah: Clement Vachet, Sylvian Gouttard
  • UNC: Guido Gerig, Mahshid Farzinfar, Martin Styner

Objective

DTIPrep is a useful tool for automated QA of DWI images, but it has areas where improvement and increased usability could be achieved. We will identify ways to improve user interaction and experience, as well as address any architectural decisions that affect future development. Specific goals are:

  1. Fix the behavior of the '--outputFolder' flag to something more intuitive or add alternative method and document current behavior
  2. Fix the xml reporting scheme for batch processing mode and make it conform to the interactive mode


Approach, Plan

We will meet with the main developers of DTIPrep and discuss user experiences and ways to improve the interface. We will also address any additional enhancements and solutions that is needed for the tool.

Progress

N/A


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
  3. Other (Please specify)

References

Powerpoint presentation

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