Difference between revisions of "2012 Summer Project Week:ITKv4 Integration"

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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:ITKv4Integration-screenshot.png| Screenshot
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
 
 
</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 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: Hans Johnson, Kent Williams
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* Utah: Tom Fletcher, Ross Whitaker
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* GE: Jim Miller
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* SPL: Steve Pieper
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* Kitware: JC, Julien
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* NLM (C): Bradley Lowekamp
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* NoWare: Bill Lorensen
  
 
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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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# Move Slicer build from ITKv3 to ITKv4
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## Complete build from scratch with packaging
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## Build against ITKv4
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## Build with SimpleITK
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# Pass Rule 1 and Rule 2 of "Rons Rules for tools"
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## You make it, I break it. [1]
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## Your tool does not exist, until it works on my laptop with my data. [2]
  
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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Figure out how to get packaging working when building with ITKv4
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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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* Basic building is working (Has been for a long time).
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* Compiler propagation to submodules needed
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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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*
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During Project Week we resolved the packaging issues.
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# ITKv4 now supports runtime only installs. (Thanks Bill Lorensen)
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## This required changes to both Slicer and ITKv4 (for complete compliance).
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### The Slicer changes are checked into the repo.
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### The ITKv4 changes are tested and merged into master branch of ITKv4
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### BRAINSTools was cleaned up to support the COMPONENT Runtime Install
  
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# Clean build process
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## Remove configuration warnings about unnecessary/unused configuration commands
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## Fix shared library linking for python on Mac for creating successful install
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## Complete build success tested to respect superbuild requested compiler (set default CC=/dev/null and CXX=/dev/null to force errors)
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##
 
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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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As part of the CMake build system
  
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#ITK Module
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==References==
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#Slicer Module
 
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##Built-in
 
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##Extension -- commandline
 
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##Extension -- loadable
 
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#Other (Please specify)
 
  
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==References==
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http://www.na-mic.org/Bug/view.php?id=2007
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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 .
 
  
 
</div>
 
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Latest revision as of 13:49, 22 June 2012

Home < 2012 Summer Project Week:ITKv4 Integration

Key Investigators

  • Iowa: Hans Johnson, Kent Williams
  • GE: Jim Miller
  • SPL: Steve Pieper
  • Kitware: JC, Julien
  • NLM (C): Bradley Lowekamp
  • NoWare: Bill Lorensen

Objective

  1. Move Slicer build from ITKv3 to ITKv4
    1. Complete build from scratch with packaging
    2. Build against ITKv4
    3. Build with SimpleITK
  2. Pass Rule 1 and Rule 2 of "Rons Rules for tools"
    1. You make it, I break it. [1]
    2. Your tool does not exist, until it works on my laptop with my data. [2]

Approach, Plan

Figure out how to get packaging working when building with ITKv4

  • Basic building is working (Has been for a long time).
  • Compiler propagation to submodules needed

Progress

During Project Week we resolved the packaging issues.

  1. ITKv4 now supports runtime only installs. (Thanks Bill Lorensen)
    1. This required changes to both Slicer and ITKv4 (for complete compliance).
      1. The Slicer changes are checked into the repo.
      2. The ITKv4 changes are tested and merged into master branch of ITKv4
      3. BRAINSTools was cleaned up to support the COMPONENT Runtime Install
  1. Clean build process
    1. Remove configuration warnings about unnecessary/unused configuration commands
    2. Fix shared library linking for python on Mac for creating successful install
    3. Complete build success tested to respect superbuild requested compiler (set default CC=/dev/null and CXX=/dev/null to force errors)

Delivery Mechanism

As part of the CMake build system

References

http://www.na-mic.org/Bug/view.php?id=2007

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