NAMIC Wiki - User contributions [en]

NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation

2008-06-27T13:27:42Z

Yiwei: /* Key Investigators */

{|
|[[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:Nirep.JPG|thumb|320px|NIREP program]]
|}
__NOTOC__
===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 <kate@spicybrains.org> (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="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
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 style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

We plan to do the following tasks to improve the NIREP software package:
surfaces, etc. into a composite image.
*<strike>Use CPack to package the NIREP program.</strike>
*<strike>Setup and use a DART Dashboard at Iowa</strike>
*Select a license for the software.
*<strike>Redesign the Database Manager and investigate how database managers are implemented in other tools.</strike>
*<strike>Learn about setting up data distribution via Xnat.</strike>
*<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 style="width: 40%; float: right">

<h1>Progress</h1>
* CDash/Dashboard
** Dashboard is [http://dashboard.nirep.org installed] on the server
** Configured and uploading
** Need to talk to Julien about CDash/CTest/CMake issues (space in name, SITE_NAME, BUILD)
* 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
uoload 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>

<br style="clear: both;" />

</div>

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

* [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://idm.univ-rennes1.fr/VMIP/SPIE2007_gb.html SPIE Medical Imaging: Validation in Medical Image Registration Workshop, Feb. 18, 2007]
* [http://ieeexplore.ieee.org/xpl/tocresult.jsp?isYear=2006&isnumber=36137&Submit32=Go+To+Issues IEEE Transactions on Medical Imaging, Special Issue on Validation in Medical Image Processing 25(11), Nov. 2006 (need access to IEEE explore to view papers) ]
* [http://ieeexplore.ieee.org/iel5/42/27515/01225846.pdf P. Hellier, C. Barillot, I. Corouge, B. Gibaud, G. Le Goualher, D. L. Collins, A. Evans, G. Malandain, N. Ayache, G. E. Christensen, and H. J. Johnson, Retrospective Evaluation of Intersubject Brain Registration, IEEE Transactions on Medical Imaging, 22(9) 2003, pp. 1120-1130 (need access to IEEE explore to view paper) ]
* [http://idm.univ-rennes1.fr/VMIP/ressourcesgb.html P. Jannin, C. Grova, C.R. Maurer, Model for defining and reporting reference-based validation protocols in medical image processing, International Journal of Computer Assisted Radiology and Surgery, 1(2), August 2006. ]
* [http://idm.univ-rennes1.fr/VMIP/ressourcesgb.html P. Jannin, M. Fitzpatrick, D. Hawkes, X. Pennec, R. Shahidi, and M.W. Vannier, Editorial: Validation of Medical Image Processing in Image-Guided Therapy, IEEE Transactions on Medical Imaging, 21(11), 2002, pp. 1445-1449. ]

NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation

2008-06-27T13:26:27Z

Yiwei: /* Key Investigators */

{|
|[[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:Nirep.JPG|thumb|320px|NIREP program]]
|}
__NOTOC__
===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 <kate@spicybrains.org> (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="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
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 style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

We plan to do the following tasks to improve the NIREP software package:
surfaces, etc. into a composite image.
*<strike>Use CPack to package the NIREP program.</strike>
*<strike>Setup and use a DART Dashboard at Iowa</strike>
*Select a license for the software.
*<strike>Redesign the Database Manager and investigate how database managers are implemented in other tools.</strike>
*<strike>Learn about setting up data distribution via Xnat.</strike>
*<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 style="width: 40%; float: right">

<h1>Progress</h1>
* CDash/Dashboard
** Dashboard is [http://dashboard.nirep.org installed] on the server
** Configured and uploading
** Need to talk to Julien about CDash/CTest/CMake issues (space in name, SITE_NAME, BUILD)
* 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 with every managed file, and distribute to others(other desktop users, file repository servers and XNAT Enterprise archives).
** 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
uoload 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>

<br style="clear: both;" />

</div>

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

* [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://idm.univ-rennes1.fr/VMIP/SPIE2007_gb.html SPIE Medical Imaging: Validation in Medical Image Registration Workshop, Feb. 18, 2007]
* [http://ieeexplore.ieee.org/xpl/tocresult.jsp?isYear=2006&isnumber=36137&Submit32=Go+To+Issues IEEE Transactions on Medical Imaging, Special Issue on Validation in Medical Image Processing 25(11), Nov. 2006 (need access to IEEE explore to view papers) ]
* [http://ieeexplore.ieee.org/iel5/42/27515/01225846.pdf P. Hellier, C. Barillot, I. Corouge, B. Gibaud, G. Le Goualher, D. L. Collins, A. Evans, G. Malandain, N. Ayache, G. E. Christensen, and H. J. Johnson, Retrospective Evaluation of Intersubject Brain Registration, IEEE Transactions on Medical Imaging, 22(9) 2003, pp. 1120-1130 (need access to IEEE explore to view paper) ]
* [http://idm.univ-rennes1.fr/VMIP/ressourcesgb.html P. Jannin, C. Grova, C.R. Maurer, Model for defining and reporting reference-based validation protocols in medical image processing, International Journal of Computer Assisted Radiology and Surgery, 1(2), August 2006. ]
* [http://idm.univ-rennes1.fr/VMIP/ressourcesgb.html P. Jannin, M. Fitzpatrick, D. Hawkes, X. Pennec, R. Shahidi, and M.W. Vannier, Editorial: Validation of Medical Image Processing in Image-Guided Therapy, IEEE Transactions on Medical Imaging, 21(11), 2002, pp. 1445-1449. ]

NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation

2008-06-27T13:17:40Z

Yiwei: /* Key Investigators */

{|
|[[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:Nirep.JPG|thumb|320px|NIREP program]]
|}
__NOTOC__
===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 <kate@spicybrains.org> (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="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
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 style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

We plan to do the following tasks to improve the NIREP software package:
surfaces, etc. into a composite image.
*<strike>Use CPack to package the NIREP program.</strike>
*<strike>Setup and use a DART Dashboard at Iowa</strike>
*Select a license for the software.
*<strike>Redesign the Database Manager and investigate how database managers are implemented in other tools.</strike>
*<strike>Learn about setting up data distribution via Xnat.</strike>
*<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 style="width: 40%; float: right">

<h1>Progress</h1>
* CDash/Dashboard
** Dashboard is [http://dashboard.nirep.org installed] on the server
** Configured and uploading
** Need to talk to Julien about CDash/CTest/CMake issues (space in name, SITE_NAME, BUILD)
* 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 with every managed file, and distribute to others.
*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>

<br style="clear: both;" />

</div>

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

* [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://idm.univ-rennes1.fr/VMIP/SPIE2007_gb.html SPIE Medical Imaging: Validation in Medical Image Registration Workshop, Feb. 18, 2007]
* [http://ieeexplore.ieee.org/xpl/tocresult.jsp?isYear=2006&isnumber=36137&Submit32=Go+To+Issues IEEE Transactions on Medical Imaging, Special Issue on Validation in Medical Image Processing 25(11), Nov. 2006 (need access to IEEE explore to view papers) ]
* [http://ieeexplore.ieee.org/iel5/42/27515/01225846.pdf P. Hellier, C. Barillot, I. Corouge, B. Gibaud, G. Le Goualher, D. L. Collins, A. Evans, G. Malandain, N. Ayache, G. E. Christensen, and H. J. Johnson, Retrospective Evaluation of Intersubject Brain Registration, IEEE Transactions on Medical Imaging, 22(9) 2003, pp. 1120-1130 (need access to IEEE explore to view paper) ]
* [http://idm.univ-rennes1.fr/VMIP/ressourcesgb.html P. Jannin, C. Grova, C.R. Maurer, Model for defining and reporting reference-based validation protocols in medical image processing, International Journal of Computer Assisted Radiology and Surgery, 1(2), August 2006. ]
* [http://idm.univ-rennes1.fr/VMIP/ressourcesgb.html P. Jannin, M. Fitzpatrick, D. Hawkes, X. Pennec, R. Shahidi, and M.W. Vannier, Editorial: Validation of Medical Image Processing in Image-Guided Therapy, IEEE Transactions on Medical Imaging, 21(11), 2002, pp. 1445-1449. ]