Difference between revisions of "NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation"

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|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
 
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
 
|[[Image:Logo2skull.jpg|thumb|320px|NIREP application splash screen]]
 
|[[Image:Logo2skull.jpg|thumb|320px|NIREP application splash screen]]
 +
|[[Image:Nirep.JPG|thumb|320px|NIREP program]]
 
|}
 
|}
 
__NOTOC__
 
__NOTOC__
 
===Key Investigators===
 
===Key Investigators===
−
*Gary Christensen, Iowa (NIREP principal investigator)
+
*Gary Christensen, Iowa <gary-christensen@uiowa.edu> (NIREP PI)
−
*Jeffrey Hawley (NIREP software developer)
+
*Jeffrey Hawley <woofton_9@eaglescrag.net> (NIREP software developer)
−
*Ying Wei (NIREP software developer)
+
*Ying Wei <wywendy2000@gmail.com> (NIREP software developer)
−
*Kate Rasing (NIREP software developer)
+
*Kate Rasing (NIREP software developer)
−
 
+
*Julien Jomier, Kitware
−
 
+
*Bill Hoffman
 +
*Sebastien Barre, Kitware
 +
*Jim Miller
 +
*Luis Ibanez, Kitware (image registration regression testing, Cpack, and ITK)
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
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We have started the Non-rigid Image Registration Evaluation Project (NIREP) to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria.  
 
We have started the Non-rigid Image Registration Evaluation Project (NIREP) to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria.  
  
 +
The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms.
  
 
</div>
 
</div>
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
−
The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms.
 
  
−
Our goal for this week is to further the prototype software package that was created last year with help in these areas:
+
We plan to do the following tasks to improve the NIREP software package:
−
*The best way to break the VTK pipeline
+
surfaces, etc. into a composite image.
−
*Learn more about streaming images
+
*<strike>Use CPack to package the NIREP program.</strike>
−
*Learn how other tools combine images, landmarks, contours, surfaces, etc. into a composite image.
+
*<strike>Setup and use a DART Dashboard at Iowa</strike>
−
*Discuss design of the Database Manager and investigate how database managers are implemented in other tools.
+
*Select a license for the software.
−
*CPack
+
*<strike>Redesign the Database Manager and investigate how database managers are implemented in other tools.</strike>
−
*DART Dashboard
+
*<strike>Learn about setting up data distribution via Xnat.</strike>
−
*wxWidgets support
+
*<strike>Learn about distributing tools with NSIS.</strike>
 +
*<strike>Learn the best way to break the VTK & ITK pipelines</strike>
 +
*Implement streaming of images in NIREP software
 +
*Learn how other tools combine images, landmarks, contours,
 +
 
  
 +
*Investigate integration of wxWidgets with ITK and VTK.
  
 
</div>
 
</div>
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<h1>Progress</h1>
 
<h1>Progress</h1>
−
 
+
* CMake/CTest/CDash/CPack
 +
** Dashboard is [http://dashboard.nirep.org installed] on the server
 +
** Configured and uploading
 +
** Submitted CDash bug
 +
** Talked with Julien Jomier, Sebastien Barre, and Bill Hoffman about CDash/CTest/CMake/CPack issues & got the CMake/CTest written correctly, CPack/CDash working
 +
* XNAT
 +
** Talked with Hans about common XNAT server
 +
** Started installing on transform
 +
** Uploaded and organized NIREP initial evaluation database NA0 to XNAT central.
 +
** Talked with Mikhail and Tim about how to organize local files(NIREP database) in XNAT Deaktop(XND), store text metadata, and distribute to others.
 +
** Fixed certain problems with XNAT Desktop and XNAT central, and still need to ask Tim and Mikhail more to see how to better organize and upload database both local and website and if it can be more convenient. 
 +
*Talked with Hans about breaking the pipelines and started implementation
 +
*Talked with Bill Hoffman and got NIREP packaged with CPack (which uses NSIS)
 +
*Talked with Steve Pieper about MRML and other methods used in Slicer that could help us with our Database Manager
 
</div>
 
</div>
  
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This work was supported in part by NIH grants EB004126, CA096679 and HL64368.
 
This work was supported in part by NIH grants EB004126, CA096679 and HL64368.
  
−
* [http://www.nirep.org/architecture.htm Link to NIREP web site: ]
+
* [http://www.nirep.org Link to NIREP web site: ]
 
* [http://www.consort-statement.org/Initiatives/newstard.htm The STARD Initiative -- Towards Complete and Accurate Reporting of Studies on Diagnostic Accuracy ]  
 
* [http://www.consort-statement.org/Initiatives/newstard.htm The STARD Initiative -- Towards Complete and Accurate Reporting of Studies on Diagnostic Accuracy ]  
 
* [http://idm.univ-rennes1.fr/VMIP/SPIE2007_gb.html SPIE Medical Imaging: Validation in Medical Image Registration Workshop, Feb. 18, 2007]  
 
* [http://idm.univ-rennes1.fr/VMIP/SPIE2007_gb.html SPIE Medical Imaging: Validation in Medical Image Registration Workshop, Feb. 18, 2007]  

Latest revision as of 17:48, 28 October 2008

Home < NA-MIC < Projects < Collaboration < NIREP: Non-rigid Image Registration Evaluation
Return to Project Week Main Page
NIREP application splash screen
NIREP program

Key Investigators

  • Gary Christensen, Iowa <gary-christensen@uiowa.edu> (NIREP PI)
  • Jeffrey Hawley <woofton_9@eaglescrag.net> (NIREP software developer)
  • Ying Wei <wywendy2000@gmail.com> (NIREP software developer)
  • Kate Rasing (NIREP software developer)
  • Julien Jomier, Kitware
  • Bill Hoffman
  • Sebastien Barre, Kitware
  • Jim Miller
  • Luis Ibanez, Kitware (image registration regression testing, Cpack, and ITK)

Objective

We have started the Non-rigid Image Registration Evaluation Project (NIREP) to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria.

The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms.

Approach, Plan

We plan to do the following tasks to improve the NIREP software package: surfaces, etc. into a composite image.

  • Use CPack to package the NIREP program.
  • Setup and use a DART Dashboard at Iowa
  • Select a license for the software.
  • Redesign the Database Manager and investigate how database managers are implemented in other tools.
  • Learn about setting up data distribution via Xnat.
  • Learn about distributing tools with NSIS.
  • Learn the best way to break the VTK & ITK pipelines
  • Implement streaming of images in NIREP software
  • Learn how other tools combine images, landmarks, contours,


  • Investigate integration of wxWidgets with ITK and VTK.

Progress

  • CMake/CTest/CDash/CPack
    • Dashboard is installed on the server
    • Configured and uploading
    • Submitted CDash bug
    • Talked with Julien Jomier, Sebastien Barre, and Bill Hoffman about CDash/CTest/CMake/CPack issues & got the CMake/CTest written correctly, CPack/CDash working
  • XNAT
    • Talked with Hans about common XNAT server
    • Started installing on transform
    • Uploaded and organized NIREP initial evaluation database NA0 to XNAT central.
    • Talked with Mikhail and Tim about how to organize local files(NIREP database) in XNAT Deaktop(XND), store text metadata, and distribute to others.
    • Fixed certain problems with XNAT Desktop and XNAT central, and still need to ask Tim and Mikhail more to see how to better organize and upload database both local and website and if it can be more convenient.
  • Talked with Hans about breaking the pipelines and started implementation
  • Talked with Bill Hoffman and got NIREP packaged with CPack (which uses NSIS)
  • Talked with Steve Pieper about MRML and other methods used in Slicer that could help us with our Database Manager


References

This work was supported in part by NIH grants EB004126, CA096679 and HL64368.

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