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

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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:genuFA.jpg|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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* Iowa: Kent Williams, Hans Johnson
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* Utah: Tom Fletcher, Ross Whitaker
 
  
 
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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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Revise and refactor the DicomToNrrd program to build properly with ITK 4.1.  Enhance it to accept a wider variety of DICOM Diffusion Weighted Images.
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The program needs to be compliant with DCMTK version that will be in future Slicer versions.
  
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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Starting from the original DIcomToNrrd program (as it exists in the Slicer3/Slicer4 source code),
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modify the program to satisfy the following goals:
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Make it compatible with ITK 4.  The old version made direct calls to GDCM version 1 APIs, and ITK 4 incorporates GDCM 2, which is not compatible.
  
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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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Re-write the existing code to be more readable and maintainable.
  
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Our plan for the project week is to first try out <bar>,...
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Add more regression tests, incorporating new test images that were not readable with the old version of DicomToNRRD.
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Prepare for DCMTK integration by using system version of DCMTK
  
 
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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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Intial goals for this project are complete.
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* The program successfully reads all test images as the earlier ITK3-only version of DicomToNrrd.
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* It can also handle several image 'flavors' that caused the earlier version to fail.
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* Test images contributed by the Slicer community have been added to the testing data corpus, which is stored on MIDAS (http://midas.kitware.com)
  
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New goals have made progress, but have not been finalized
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* ITK integration with new DCMTK is located at: http://review.source.kitware.com/#/c/5989/12
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* http://git.dcmtk.org/dcmtk.git.rt tag "f2b71c92461085718f3bccd1c7415382d3e11e3a"
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* Verified that DICOM-RT version of DCMTK builds without obvious errors.
  
 
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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)
 
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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#ITK Module
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#ITK Module - NO
 
#Slicer Module
 
#Slicer Module
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##Built-in
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##Built-in - NO
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##Extension -- commandline
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##Extension -- commandline - YES
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##Extension -- loadable
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##Extension -- loadable - NO
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#Other (Please specify)
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#Other
  
 
==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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* 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 .
 
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Latest revision as of 20:59, 21 June 2012

Home < 2012 Summer Project Week:DicomToNrrd

Key Investigators

  • Iowa: Kent Williams, Hans Johnson

Objective

Revise and refactor the DicomToNrrd program to build properly with ITK 4.1. Enhance it to accept a wider variety of DICOM Diffusion Weighted Images.

The program needs to be compliant with DCMTK version that will be in future Slicer versions.

Approach, Plan

Starting from the original DIcomToNrrd program (as it exists in the Slicer3/Slicer4 source code), modify the program to satisfy the following goals:

Make it compatible with ITK 4. The old version made direct calls to GDCM version 1 APIs, and ITK 4 incorporates GDCM 2, which is not compatible.

Re-write the existing code to be more readable and maintainable.

Add more regression tests, incorporating new test images that were not readable with the old version of DicomToNRRD.

Prepare for DCMTK integration by using system version of DCMTK

Progress

Intial goals for this project are complete.

  • The program successfully reads all test images as the earlier ITK3-only version of DicomToNrrd.
  • It can also handle several image 'flavors' that caused the earlier version to fail.
  • Test images contributed by the Slicer community have been added to the testing data corpus, which is stored on MIDAS (http://midas.kitware.com)

New goals have made progress, but have not been finalized

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 - NO
  2. Slicer Module
    1. Built-in - NO
    2. Extension -- commandline - YES
    3. Extension -- loadable - NO
  3. Other

References

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