NAMIC Wiki - User contributions [en]

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

2008-10-28T17:48:52Z

Krasing:

{|
|[[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 (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>
* 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>

<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

2008-06-27T14:35:00Z

Krasing: /* 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>
* 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>

<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

2008-06-27T14:27:01Z

Krasing:

{|
|[[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
** Submitted CDash bug
** Talked with Julien and Bill Hoffman 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 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>

<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

2008-06-25T19:54:19Z

Krasing:

{|
|[[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.
*Use CPack to package the NIREP program.
*<strike>Setup and use a DART Dashboard at Iowa</strike>
*Select a license for the software.
*Redesign the Database Manager and investigate how database managers are implemented in other tools.
*<strike>Learn about setting up data distribution via Xnat.</strike>
*Learn about distributing tools with NIRIC.
*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.

</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
*Talked with Hans about breaking the pipelines and started implementation
</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

2008-06-25T04:31:19Z

Krasing: /* 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.
*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.
*Set up distributing data via Xnat.
*Learn about distributing tools with NIRIC.
*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.

</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 for Kate, not for Jeff.
** 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
</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

2008-06-25T04:29:58Z

Krasing:

{|
|[[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.
*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.
*Set up distributing data via Xnet.
*Learn about distributing tools with NIRIC.
*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.

</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 for Kate, not for Jeff.
** Need to talk to Julien about CDash/CTest/CMake issues (space in name, SITE_NAME, BUILD)
</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/Lung Atlas

2008-06-24T15:04:21Z

Krasing: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]
|}

__NOTOC__

===Key Investigators===
* Gary Christensen, Iowa
* Nathan Fritze, Iowa
* Nathan Burnette, Iowa
*Bill Hoffman
*Sebastien Barre, Kitware
*Katie Hayes, BWH
*Jim Miller
*Luis Ibanez, Kitware (image registration regression testing, Cpack, and ITK)
*Will Schroeder, Kitware (license issues)

<div style="margin: 20px;">

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

<h1>Objective</h1>

Develop a software tool for visualizing and querying an electronic lung airway atlas. We are developing atlases of the human lung R01 HL64368, the rat lung R01HL073598, and the mouse lung R01 HL080285. We want to make a common software tool that can be customized for specific atlases. The image data and semantic information will be stored in a database and will be indexed through a graphical user interface.

</div>

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

<h1>Approach, Plan</h1>

Our plan for the project week is to
*Reduce bottlenecks for the atlas application
*Setup CMake, CPack, and Dashboard for project.
*Select a license for software
*Look at atlases developed in Slicer3.
*Compare and contrast the performance of Kwwidgets and wxWidgets
*Discuss ideas for a data manager object that is used to read, organize, and manage memory issues for the atlas.
*Learn the best ways to visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software
*Refine user interface for displaying atlas statistics, images, labels, coloring.
*Discuss registration methods for matching airway trees.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...
* Set up Dashboard project& made it work.

</div>

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

</div>

===References===

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

2008-06-23T17:43:25Z

Krasing:

{|
|[[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.
*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.
*Set up distributing data via Xnet.
*Learn about distributing tools with NIRIC.
*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.

</div>

<div style="width: 40%; float: right">

<h1>Progress</h1>
* CDash/Dashboard
** Dashboard is [http://dashboard.nirep.org installed] on the server
** The installation needs to be tested with CDashTest -- the project appears to be misconfigured.
</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

2008-06-23T17:15:09Z

Krasing: /* 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.
*Redesign the Database Manager and investigate how database managers are implemented in other tools.
*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,
*Use CPack to package the NIREP program.
*Setup and use a DART Dashboard at Iowa
*Investigate integration of wxWidgets with ITK and VTK.

</div>

<div style="width: 40%; float: right">

<h1>Progress</h1>
* CDash/Dashboard
** 6/12: Dashboard is [http://dashboard.nirep.org installed] on the server
*** The installation needs to be tested with CDashTest -- the project appears to be misconfigured.
*** 6/13: The NIREP web server is offline (floods)
** 6/19: php modules added to secondary server, CDash installed
*** CMake needs to be installed
</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

2008-06-14T23:34:10Z

Krasing: /* 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]]
|}
__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:
*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, surfaces, etc. into a composite image.
*Discuss design of the Database Manager and investigate how database managers are implemented in other tools.
*Use CPack to package the NIREP program.
*Setup and use a DART Dashboard at Iowa
*Investigate integration of wxWidgets with ITK and VTK.

</div>

<div style="width: 40%; float: right">

<h1>Progress</h1>
* 6/12
** Dashboard is [http://dashboard.nirep.org installed] on the server
*** The installation needs to be tested with CDashTest -- the project appears to be misconfigured.
* 6/13
** The NIREP web server seems to be offline
</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

2008-06-14T23:33:34Z

Krasing: /* 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]]
|}
__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:
*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, surfaces, etc. into a composite image.
*Discuss design of the Database Manager and investigate how database managers are implemented in other tools.
*Use CPack to package the NIREP program.
*Setup and use a DART Dashboard at Iowa
*Investigate integration of wxWidgets with ITK and VTK.

</div>

<div style="width: 40%; float: right">

<h1>Progress</h1>
* 6/12
** Dashboard is [http://dashboard.nirep.org installed] on the server
*** The installation needs to be tested with CDashTest -- the project appears to be misconfigured.
* 6/13
* The NIREP web server seems to be offline
</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

2008-06-13T16:09:02Z

Krasing: /* 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]]
|}
__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:
*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, surfaces, etc. into a composite image.
*Discuss design of the Database Manager and investigate how database managers are implemented in other tools.
*Use CPack to package the NIREP program.
*Setup and use a DART Dashboard at Iowa
*Investigate integration of wxWidgets with ITK and VTK.

</div>

<div style="width: 40%; float: right">

<h1>Progress</h1>
* Dashboard is [http://dashboard.nirep.org installed] on the server
** needs to be tested with CDashTest yet
</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. ]