NAMIC Wiki - User contributions [en]

File:2008MITDay4-016.jpg

2008-07-02T01:15:27Z

Hawle:

Photo taken by Jeffrey Hawley. [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 For more photos]

File:2008MITDay3-106.jpg

2008-07-02T01:15:15Z

Hawle:

Photo taken by Jeffrey Hawley. [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 For more photos]

File:2008MITDay3-080.jpg

2008-07-02T01:14:59Z

Hawle:

Photo taken by Jeffrey Hawley. [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 For more photos]

File:2008MITDay3-089.jpg

2008-07-02T01:14:51Z

Hawle:

Photo taken by Jeffrey Hawley. [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 For more photos]

File:2008MITDay3-038.jpg

2008-07-02T01:14:43Z

Hawle:

Photo taken by Jeffrey Hawley. [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 For more photos]

File:2008MITDay3-030.jpg

2008-07-02T01:14:34Z

Hawle:

Photo taken by Jeffrey Hawley. [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 For more photos]

File:2008MITDay1-349.jpg

2008-07-02T01:14:27Z

Hawle:

Photo taken by Jeffrey Hawley. [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 For more photos]

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

2008-06-27T13:54:34Z

Hawle: /* 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
** <strike>Need to talk to Julien about CDash/CTest/CMake issues (space in name, SITE_NAME, BUILD)</strike>
* 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

2008-06-27T13:53:47Z

Hawle: /* 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 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

2008-06-27T13:53:13Z

Hawle: /* 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
**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

2008-06-26T19:27:58Z

Hawle: /* 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
*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

2008-06-26T19:23:42Z

Hawle:

{|
|[[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.
*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.
*<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
*Talked with Hans about breaking the pipelines and started implementation
*Talked with Bill Hoffman and got NIREP packaged with CPack
</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

2008-06-26T14:16:08Z

Hawle: /* 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.
*<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.
*<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
*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

2008-06-25T17:07:37Z

Hawle: /* 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
** 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

2008-06-25T17:07:07Z

Hawle:

{|
|[[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
** 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
</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

2008-06-25T17:05:33Z

Hawle:

{|
|[[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
** 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. ]

2008 Summer Project Week

2008-06-25T12:19:32Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==
*'''Dates:''' June 23-27, 2008
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. If you are attending for one day only, the registration fee is not required.
*'''Registration Method''' The event is full. [[User:Tkapur|Tkapur]] 18:12, 17 June 2008 (UTC)
*'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2008 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
*Next Project Week in Utah -- January 5-9, 2009

==Introduction to NA-MIC Project Week==
Please read an introduction about these events [[Project_Events#Introduction|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: [[2008-Project-Week-Welcome|Welcome]] (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 10-10:30am [http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 Slicer 3.2 Update] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Jackson Room 38-466) (Ron Kikinis)
** noon lunch
** 1pm: [[2008-Project-Week-SVN-Change|Cut over to a new version of the NA-MIC SVN]].
** 1:00-4:00pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Stata 32-D451) (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Stata Kiva Conference Room) (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stata Kiva Conference Room) (Stephen Aylward)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Stata 32 D-451) (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** Noon: Lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[2008_Summer_Project_Week:DWIRegistrationOMT|DWI Registration using Optimal Mass Transport]] (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##[[2008_Summer_Project_Week:LobeParcellation| Parcellation of 3T MR data]](Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##[[2008_Summer_Project_Week:GMLongDistanceTractography|GM Long Distance Tractography]] (John Melonakos GATech, Marek Kubicki BWH)
##[[2008_Summer_Project_Week:PopulationDTIApplication|Group Analysis of DTI]] (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[2008_Summer_Project_Week:RegionalCorticalThicknessTool|Work Flow Tool for regional cortical thickness pipeline]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:NITRCRegistration|NITRC registration of cortical thickness modules]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:DWI-DTI_PrepTools|DWI DTI Prep Tools]] (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Lesion Classification Module]] (Mark Scully MIND)
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration and time course analyses in white matter lesions]] (Mark Scully and Jeremy Bockholt, MIND)
##[[DBP2:MIND:BeyondLesionsProject|Enhancements and extension of white matter lesion classification using DTI scalars]] (Jeremy Bockholt, MIND)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[2008_Summer_Project_Week:TransRectal_Prostate_Biopsy_Module|Trans-Rectal Prostate Biopsy module]] (David Gobbi, Gabor Fichtinger, Queens/JHU)
##[[2008_Summer_Project_Week:ProstateSegReg|Prostate Segmentation and Registration]] (Yi Gao GATech, Gabor Fichtinger JHU)
##[[2008_Summer_Project_Week:PerkStation|Hardware/software overlay for percutaneous intervention (PERK Station)]] (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#[[2008_Summer_Project_Week:GroupwiseBSplineForDTI| Integraton of groupwise b-spline registration into atlas building]] (Casey Goodlett, Serdar Balci)
#[[2008_Summer_Project_Week:GroupwisePortingToNamicKit| Porting groupwise registration project into NAMIC-kit]] (Serdar Balci, Brad Davis)
# [[2008_Summer_Project_Week:CVS_SVN_Synchronization|CVS / SVN auto synchronization]] (Sebastien, Steve, Jim, Will, Bill)
# [[2008_Summer_Project_Week:3DWidgetsInSlicer|3D Widgets in Slicer]] (Nicole Aucoin, Will Schroeder)
## Issues with existing widgets
## Design of new widgets
# [[2008_Summer_Project_Week:Batch_Processing|Batch processing in the NAMIC Kit]] (Julien, Marco, Steve, Jim)
#[[2008_Summer_Project_Week:ModuleChaining|Module Chaining]] (Marco, Jim, Steve, Dan B., Luca)
# [[2008_Summer_Project_Week:Nonlinear transforms | Nonlinear transforms]] (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# [[2008_Summer_Project_Week:XNATandXCEDE| Slicer3, XNAT integration and XCEDE Web Services ]] (Dan M., Wendy, Steve, Julien, Dan B.)
## Review and enrich use cases [[Media: XCEDE-Use-Cases-2008-06-25.ppt | (developing use case ppt)]]
# [[2008_Summer_Project_Week:PythonInSlicer| Python in Slicer]] (Dan B., Michael Halle, Steve, Luca)
# [[2008_Summer_Project_Week:PerformanceTuningFiducials|Performance Tuning of Fiducials]] using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
# [[2008_Summer_Project_Week:FocusedGUIRefinement|Focused GUI Refinement and Strategies for Consistency]] (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)
# [[2008_Summer_Project_Week:AtlasFreeSegmentation|Atlas free Segmentation]] (Tammy Riklin-Raviv, MIT)
#[[NA-MIC/Projects/Collaboration/EM Bias Field Correction | New Bias Field Correction in EM]] (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
# [[2008_Summer_Project_Week:FluidMechanicsTractographyUCLA|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman, UCLA)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Grand Joldes)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Non-rigid image registration]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#[[FMA (Protege) links to Slicer]] (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga, Dan Blezek, Mike Halle, Steve Pieper)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC]] (Dana Peters Group)
#[[NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3]] (Junichi, Haiying and Noby - SPL, David and Siddharth - Queen's, Danielle - Robarts)
#[[NA-MIC/Projects/Collaboration/MGH RadOnc]] (Greg Sharp, MGH)
#[[NA-MIC/Projects/External Collaboration/W&M CRTC]] Non-rigid registration for neurosurgery (Nikos Chrisochoides, Andriy Fedorov, College of William&Mary)
#[[NA-MIC/Projects/Collaboration/SBIA UPenn]] DTI and HARDI Analysis tools(Ragini Verma, SBIA Upenn)
#[[Projects/Diffusion/2008 Project Week DiffusionMRI QBall]] Diffusion QBall framework integration( Demian Wassermann, Rachid Deriche, Odyssée INRIA, CF Westin, LMI
#[[IGT_Projects_Discussion]]

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

==Attendee List==
# Jack Blevins Acoustic Med
# Pratik Patel Brainlab
# Mark Anderson BWH
# Nicole Aucoin BWH
# Sylvain Bouix BWH
# Michael Halle BWH
# Nobuhiko Hata BWH
# Katie Hayes BWH
# Scott Hoge BWH
# Marianna Jakab BWH
# Tina Kapur BWH
# Ron Kikinis BWH
# Jacek Kukluk BWH
# Haying Liu BWH
# Bjoern Menze BWH
# Wendy Plesniak BWH
# Kilian Pohl BWH
# Sonia Pujol BWH
# Carlos Sánchez Mendoza BWH
# Priya Srinivasan BWH
# Junichi Tokuda BWH
# Demian Wassermann BWH (INRIA)
# C-F Westin BWH
# Xiaodong Tao GE
# Dirk Padfield GE
# Jim Miller GE
# Surprise Guest from EAB
# Viswanath Avasarala GE
# John Melonakos GA Tech
# Yi Gao GA Tech
# Tauseef Rehman GA Tech
# Sean Megason Harvard Med
# Alex Gouaillard Harvard Med
# Kishore Mosaliganti Harvard Med
# Arnaud Gelas Harvard Med
# Dana Peters Harvard Med
# Jason Taclas Harvard Med
# Douglas Alan Harvard
# Toru Higaki Hiroshima U
# Daniel Blezek Isomics
# Curtis Lisle Isomics
# Steve Pieper Isomics
# Alex Yarmarkovich Isomics
# Csaba Csoma JHU
# Peter Kazanzides JHU
# Will Schroeder Kitware
# Sebastien Barre Kitware
# Julien Jomier Kitware
# Bill Hoffman Kitware
# Luis Ibanez Kitware
# Luca Antiga Mario Negri Inst
# Randy Gollub MGH
# Silas Mann MGH
# Greg Sharp MGH
# Marta Peroni MGH
# Serdar Balci MIT
# Bryce Kim MIT
# Clare Poynton MIT
# Tammy Riklin Raviv MIT
# Polina Golland MIT
# Jeremy Bockholt MRN Lupus DBP
# Mark Scully MRN Lupus DBP
# Gabor Fichtinger Queen's
# David Gobbi Queen's
# Purang Abolmaesumi Queen's
# Siddharth Vikal Queen's
# Zhen Qian Rutgers
# Jinghao Zhou Rutgers
# Jeffrey Grethe UCSD
# Marco Ruiz UCSD
# Chris Churas UCSD
# Nathan Hageman UCLA
# Keith Gunderson U Iowa
# Gary Christensen U Iowa
# Jeffrey Hawley U Iowa
# Kate Raising U Iowa
# Nathan Fritze U Iowa
# Paul Song U Iowa
# Cheng Zhang U Iowa
# Ying Wei U Iowa
# Nathan Burnette U Iowa
# Hans Johnson U Iowa
# Vincent Magnotta U Iowa
# Clement Vachet UNC
# Zhexing Liu UNC
# Ragini Verma U Penn
# Luke Bloy U Penn
# Yang Li U Penn
# Ran Tao Utah
# Marcel Prastawa Utah
# Casey Goodlett Utah
# Ross Whitaker Utah
# John Hale U Tulsa
# Cody Pollet U Tulsa
# Nikeisha Schimke U Tulsa
# Adam Wittek Western Australia
# Grand Joldes Western Australia
# Jamie Berger Western Australia
# Carling Cheung Western Ontario
# Danielle Pace Western Ontario
# Vidya Rajagopalan VA Tech
# Nikos Chrisochoides William and Mary
# Andriy Fedorov William and Mary
# Dan Marcus Washington U
# Tim Olsen Washington U
# Kevin Archie Washington U
# Misha Milchenko Washington U
# Xenophon Papademetris Yale U
# John Onofrey Yale U
# Yifeng Jiang Yale U
# Dustin Scheinost Yale U
#* Please note that Registration is closed. Do not add names here. [[User:Tkapur|Tkapur]] 18:19, 19 June 2008 (UTC)

==Pictures==
<gallery perrow="3" widths="150px">
Image:NA-MIC-ProjectWeek1.JPG|Lunch
Image:NA-MIC-ProjectWeek2.JPG|Day 1
</gallery>
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 PICTURES!] taken by Jeffrey Hawley

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

2008-06-20T04:30:14Z

Hawle:

{|
|[[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>
* 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

2008-06-20T04:29:13Z

Hawle:

{|
|[[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>
* 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. ]

File:Nirep.JPG

2008-06-20T04:27:59Z

Hawle: A print screen of the NIREP project as of 06/19/2008.

A print screen of the NIREP project as of 06/19/2008.

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

2008-06-12T21:23:33Z

Hawle:

{|
|[[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-chrsitensen@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>

</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. ]

2008 Summer Project Week

2008-06-11T22:04:48Z

Hawle: /* External Collaborations */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.]This rate is good only through June 1.

Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Ron Kikinis)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stephen Aylward)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[2008_Summer_Project_Week:RegionalCorticalThicknessTool|Work Flow Tool for regional cortical thickness pipeline]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:NITRCRegistration|NITRC registration of cortical thickness modules]] (Clement Vachet UNC)
##DTI tools for a) DWI preparation and b) DTI atlas building (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[2008_Summer_Project_Week:TransRectal_Prostate_Biopsy_Module|Trans-Rectal Prostate Biopsy module]] (David Gobbi, Gabor Fichtinger, Queens/JHU)
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration]] (Yi Gao GATech, Gabor Fichtinger JHU)
##[[2008_Summer_Project_Week:PerkStation|Hardware/software overlay for percutaneous intervention (PERK Station)]] (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)
# [[2008_Summer_Project_Week:AtlasFreeSegmentation|Atlas free Segmentation]] (Tammy Riklin-Raviv, MIT)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Non-rigid image registration]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC]] (Dana Peters Group)
#[[NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3]] (Junichi, Haiying and Noby - SPL, David - Queen's), Danielle - Robarts) )

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 3
# David Gobbi, Queen's, Core 3
# Purang Abolmaesumi, Queen's, Core 3, June 23-25
# Siddharth Vikal, Queen's, Core 3
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 3
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University (Monday - Wednesday)
# Tim Olsen, Washington University (Monday - Wednesday)
# Kevin Archie, Washington University (Monday - Wednesday)
# Misha Milchenko, Washington University (Monday - Wednesday)
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT
# Peter Kazanzides, JHU, Collaborator (June 24)
# Scott Hoge, BWH, (Wed, Jun 25)
#*WE HAVE REACHED CAPACITY. REGISTRATION IS CLOSED. [[User:Tkapur|Tkapur]] 19:42, 6 June 2008 (UTC)

==Pictures==

2008 Summer Project Week

2008-06-10T15:02:49Z

Hawle: /* External Collaborations */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.]This rate is good only through June 1.

Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##Work Flow Tool for regional cortical thickness pipeline (Clement Vachet UNC)
##NITRC registration of cortical thickness modules (Clement Vachet UNC)
##DTI tools for a) DWI preparation and b) DTI atlas building (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[DBP2:JHU:Roadmap|Trans-Rectal Prostate Biopsy module (David Gobbi, Gabor Fichtinger, Queens/JHU)]]
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)]]
##Hardware/software overlay for percutaneous intervention (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 3
# David Gobbi, Queen's, Core 3
# Purang Abolmaesumi, Queen's, Core 3
# Siddharth Vikal, Queen's, Core 3
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 3
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University
# Tim Olsen, Washington University
# Kevin Archie, Washington University
# Misha Milchenko, Washington University
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT
# Peter Kazanzides, JHU, Collaborator
# Scott Hoge, BWH, (Wed, Jun 25)
#*WE HAVE REACHED CAPACITY. REGISTRATION IS CLOSED. [[User:Tkapur|Tkapur]] 19:42, 6 June 2008 (UTC)

==Pictures==

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

2008-06-09T18:00:10Z

Hawle:

{|
|[[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 (NIREP principal investigator)
*Jeffrey Hawley (NIREP software developer)
*Ying Wei (NIREP software developer)
*Kate Rasing (NIREP software developer)

<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.

</div>

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

<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:
*The best way to break the VTK pipeline
*Streaming Images
*Revisit Object Overlays
*Seeing ways to do Database Managers
*CPack
*DART Dashboard
*wxWidgets support

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
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.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

2008-06-09T17:59:10Z

Hawle: New page: {| |Project Week Main Page ]] |} __NOTOC__ ===Key Investigators=== *Gary Christensen, Iowa (NIREP principal ...

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|}
__NOTOC__
===Key Investigators===
*Gary Christensen, Iowa (NIREP principal investigator)
*Jeffrey Hawley (NIREP software developer)
*Ying Wei (NIREP software developer)
*Kate Rasing (NIREP software developer)

<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.

</div>

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

<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:
*The best way to break the VTK pipeline
*Streaming Images
*Revisit Object Overlays
*Seeing ways to do Database Managers
*CPack
*DART Dashboard
*wxWidgets support

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
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.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. ]

2008 Summer Project Week

2008-06-09T17:51:28Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.]This rate is good only through June 1.

Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##Work Flow Tool for regional cortical thickness pipeline (Clement Vachet UNC)
##NITRC registration of cortical thickness modules (Clement Vachet UNC)
##DTI tools for a) DWI preparation and b) DTI atlas building (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[DBP2:JHU:Roadmap|Trans-Rectal Prostate Biopsy module (David Gobbi, Gabor Fichtinger, Queens/JHU)]]
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)]]
##Hardware/software overlay for percutaneous intervention (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#Lung Atlas (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 3
# David Gobbi, Queen's, Core 3
# Purang Abolmaesumi, Queen's, Core 3
# Siddharth Vikal, Queen's, Core 3
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 3
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University
# Tim Olsen, Washington University
# Kevin Archie, Washington University
# Misha Milchenko, Washington University
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT
# Peter Kazanzides, JHU, Collaborator
# Scott Hoge, BWH, (Wed, Jun 25)
#*WE HAVE REACHED CAPACITY. REGISTRATION IS CLOSED. [[User:Tkapur|Tkapur]] 19:42, 6 June 2008 (UTC)

==Pictures==

2007 Programming/Project Week MIT

2007-11-05T17:19:43Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007 -- [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=3945 PICTURES!] taken by Jeffrey Hawley ]]
==Summary==
{|-
[[Image:Mit.jpg|thumb|right|400px|Photo taken by Jeffrey Hawley]]
|}
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.

Statistics at a glance:
* 85 Registered Attendees: 35 NA-MIC participants, 46 collaborators, 2 EAB+NIH
** 37 NA-MIC Participants breakdown by cores: Core 1 (7), Core 2 (14), Core 3 (10), Core 4-5-6-7 (4)
** 46 Collaborators: Acoustic Med (2), BWH (19), Caltech (2), GE (1), Harvard IIC (1), JHU (1), Kitware (1), Knowledge Vis (1), Mario Negri (1), MGH (2), NWU (4), UIowa(12), Virginia Tech (1)
* 41 Projects: DBP-II(6), Structural Analysis (2), Diffusion Image Analysis (7), NA-MIC Kit (14), External Collaborations (12)

== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
* Monday June 25
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
** 3:30-4:30pm: [[Special topic breakout: Atlases]]
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)
# [[Projects/Diffusion/2007_Project_Week_Glyphed_Visualization_For_Volume_Data|Sliced Multiple Glyphed Visualization for Volume Data]] (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)

===Calibration/Validation===
This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5
#[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Ross Whitaker, Guido Gerig, Randy Gollub)

===NA-MIC Kit - Slicer 3===
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_Lightbox|Lightbox]] (James, Jim, Wendy, Alex)
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Curt, Nicole, Alex, Steve, Will, Vince)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Katie, Steve, Bill Hoffman)
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)
# [[Projects/Slicer3/2007_Project_Week_Lego Mindstorms dissemination for IGT | Lego Mindstorms Dissemination for IGT]] (Danielle Pace)
# [[Projects/Slicer3/2007_Project_Week_EdgeDetection | Edge Detection in Slicer3]] (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
# MIND Clinical Imaging Study: [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)

===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
===Core1===
#John Melonakos, Georgia Tech, Core 1
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1
#Serdar K Balci, MIT, Core 1
#Elliot Uvero, MIT, Core 1
#Ran Tao, Utah, Core 1
#Kevin Teich, MGH, Core 1
===Core2===
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jeffrey Grethe, UCSD, Core 2
#Marco Ruiz, UCSD, Core 2
#Neil Jones, UCSD, Core 2
#Jim Miller, GE Core 2
#Dan Blezek, GE Core 2
#Steve Pieper, Isomics, Core 2
#Alex Yarmarkovich, Isomics, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2 (Mon, Tue)
#Nathan Hageman, UCLA, Core 2 (Tue, Wed)

===Core3-I&II===
#Sylvain Bouix, BWH, Core 3
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Marek Kubicki, BWH, Core 3 (II) (One-day)
#Clement Vachet, UNC Core 3 (II)
#David Gobbi, Queen's University, Core 3 (II)
#Csaba Csoma, Johns Hopkins University, Core 3 (II)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II)
#Mark Scully, The MIND Institute, Core 3 (II)
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01
===Core 4,5,6,7===
#Zack Galbreath, Kitware, Core 4 (Mon, Tue)
#Randy Gollub, MGH, COre 5
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
===Collaborators===
#Chris Wyatt, Virginia Tech, Collaborator R01
#Vincent Magnotta, University of Iowa, Collaborator R01
#Kiran Shivanna, University of Iowa, Collaborator R01
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeffrey Hawley, University of Iowa, Gary's student
#Luca Antiga, Mario Negri Institute, Collaborator
#Stephen Aylward, Kitware, Collaborator
#Peter Kazanzides, JHU, Collaborator (One-day)
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator
#Greg Sharp, MGH, Collaborator
#Lilla Zollei, MGH, Collaborator (One-day)
#James Ross, GE, Collaborator
#Alex Gouaillard, CEGS Caltech, Collaborator
#Sean Megason, CEGS caltech, Collaborator
#Clif Burdette, Acousticmed, Collaborator
#Jack Blevins, Acousticmed, Collaborator
#Curtis Lisle, KnowledgeVis, Collaborator
#Douglas Alan, Harvard IIC, Collaborator
#Michael Halle, BWH/IIC, Collaborator
#Katie Hayes, BWH, Core 2
#Nicole Aucoin, BWH, Core 2
#Wendy Plesniak, BWH, Collaborator
#Kilian Pohl, BWH Collaborator
#Raimundo Sierra, BWH, Collaborator
#Lauren O'Donnell, BWH, Collaborator
#Raul San Jose, BWH, Collaborator
#C-F Westin, BWH, Collaborator
#Demian Wassermann, BWH/INRIA , Collaborator
#Danielle Pace, BWH , Summer Intern
#Sandy Wells, BWH, Collaborator
#Haiying Liu, BWH Collaborator
#Clare Tempany, BWH Collaborator (One-day)
#Noby Hata, BWH Collaborator (One-day)
#Hong Xiang, BWH Collaborator (One-day)
#Kim Lawson, BWH Collaborator (One-day)
#Junichi Tokuda, BWH Collaborator (One-day)
#Robert Cormack, BWH Collaborator (One-day)

===NIH, EAB===
#Zohara Cohen, NIH (One-day)
#Bill Lorensen, EAB (One-day)

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

==Pictures==
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=3945 PICTURES!] taken by Jeffrey Hawley

File:Mit.jpg

2007-11-05T17:19:08Z

Hawle:

A wide angle picture of the Grier Conference room, taken by Jeffrey Hawley on Friday, June 29th, 2007.
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=3945 For more photos]

2007 Programming/Project Week MIT

2007-07-17T18:56:40Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007 -- [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=2783 PICTURES!] taken by Jeffrey Hawley ]]
==Summary==
{|-
[[Image:Mit.jpg|thumb|right|400px|Photo taken by Jeffrey Hawley]]
|}
The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 46 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.

Statistics at a glance:
* 85 Registered Attendees: 35 NA-MIC participants, 46 collaborators, 2 EAB+NIH
** 37 NA-MIC Participants breakdown by cores: Core 1 (7), Core 2 (14), Core 3 (10), Core 4-5-6-7 (4)
** 46 Collaborators: Acoustic Med (2), BWH (19), Caltech (2), GE (1), Harvard IIC (1), JHU (1), Kitware (1), Knowledge Vis (1), Mario Negri (1), MGH (2), NWU (4), UIowa(12), Virginia Tech (1)
* 41 Projects: DBP-II(6), Structural Analysis (2), Diffusion Image Analysis (7), NA-MIC Kit (14), External Collaborations (12)

== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
* Monday June 25
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
** 3:30-4:30pm: [[Special topic breakout: Atlases]]
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)
# [[Projects/Diffusion/2007_Project_Week_Glyphed_Visualization_For_Volume_Data|Sliced Multiple Glyphed Visualization for Volume Data]] (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)

===Calibration/Validation===
This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5
#[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Ross Whitaker, Guido Gerig, Randy Gollub)

===NA-MIC Kit - Slicer 3===
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_Lightbox|Lightbox]] (James, Jim, Wendy, Alex)
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Curt, Nicole, Alex, Steve, Will, Vince)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Katie, Steve, Bill Hoffman)
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)
# [[Projects/Slicer3/2007_Project_Week_Lego Mindstorms dissemination for IGT | Lego Mindstorms Dissemination for IGT]] (Danielle Pace)
# [[Projects/Slicer3/2007_Project_Week_EdgeDetection | Edge Detection in Slicer3]] (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
# MIND Clinical Imaging Study: [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)

===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
===Core1===
#John Melonakos, Georgia Tech, Core 1
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1
#Serdar K Balci, MIT, Core 1
#Elliot Uvero, MIT, Core 1
#Ran Tao, Utah, Core 1
#Kevin Teich, MGH, Core 1
===Core2===
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jeffrey Grethe, UCSD, Core 2
#Marco Ruiz, UCSD, Core 2
#Neil Jones, UCSD, Core 2
#Jim Miller, GE Core 2
#Dan Blezek, GE Core 2
#Steve Pieper, Isomics, Core 2
#Alex Yarmarkovich, Isomics, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2 (Mon, Tue)
#Nathan Hageman, UCLA, Core 2 (Tue, Wed)

===Core3-I&II===
#Sylvain Bouix, BWH, Core 3
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Marek Kubicki, BWH, Core 3 (II) (One-day)
#Clement Vachet, UNC Core 3 (II)
#David Gobbi, Queen's University, Core 3 (II)
#Csaba Csoma, Johns Hopkins University, Core 3 (II)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II)
#Mark Scully, The MIND Institute, Core 3 (II)
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01
===Core 4,5,6,7===
#Zack Galbreath, Kitware, Core 4 (Mon, Tue)
#Randy Gollub, MGH, COre 5
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
===Collaborators===
#Chris Wyatt, Virginia Tech, Collaborator R01
#Vincent Magnotta, University of Iowa, Collaborator R01
#Kiran Shivanna, University of Iowa, Collaborator R01
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeffrey Hawley, University of Iowa, Gary's student
#Luca Antiga, Mario Negri Institute, Collaborator
#Stephen Aylward, Kitware, Collaborator
#Peter Kazanzides, JHU, Collaborator (One-day)
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator
#Greg Sharp, MGH, Collaborator
#Lilla Zollei, MGH, Collaborator (One-day)
#James Ross, GE, Collaborator
#Alex Gouaillard, CEGS Caltech, Collaborator
#Sean Megason, CEGS caltech, Collaborator
#Clif Burdette, Acousticmed, Collaborator
#Jack Blevins, Acousticmed, Collaborator
#Curtis Lisle, KnowledgeVis, Collaborator
#Douglas Alan, Harvard IIC, Collaborator
#Michael Halle, BWH/IIC, Collaborator
#Katie Hayes, BWH, Core 2
#Nicole Aucoin, BWH, Core 2
#Wendy Plesniak, BWH, Collaborator
#Kilian Pohl, BWH Collaborator
#Raimundo Sierra, BWH, Collaborator
#Lauren O'Donnell, BWH, Collaborator
#Raul San Jose, BWH, Collaborator
#C-F Westin, BWH, Collaborator
#Demian Wassermann, BWH/INRIA , Collaborator
#Danielle Pace, BWH , Summer Intern
#Sandy Wells, BWH, Collaborator
#Haiying Liu, BWH Collaborator
#Clare Tempany, BWH Collaborator (One-day)
#Noby Hata, BWH Collaborator (One-day)
#Hong Xiang, BWH Collaborator (One-day)
#Kim Lawson, BWH Collaborator (One-day)
#Junichi Tokuda, BWH Collaborator (One-day)
#Robert Cormack, BWH Collaborator (One-day)

===NIH, EAB===
#Zohara Cohen, NIH (One-day)
#Bill Lorensen, EAB (One-day)

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

==Pictures==
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=2783 PICTURES!] taken by Jeffrey Hawley

File:Mit.jpg

2007-07-05T14:54:30Z

Hawle:

A wide angle picture of the Grier Conference room, taken by Jeffrey Hawley on Friday, June 29th, 2007.
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=2783 For more photos]

2007 Programming/Project Week MIT

2007-07-05T14:53:37Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007 -- [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=2783 PICTURES!] taken by Jeffrey Hawley ]]
==Summary==

{|-
[[Image:Mit.jpg|thumb|center|500px|Photo taken by Jeffrey Hawley]]
|}

The fifth NA-MIC Programming/Project event was concluded at MIT on June 29, 2007.

Some statistics:

* This was the largest hands-on project event in the three year history of NA-MIC with peak attendance of 90 on Tuesday.
* 85 Registered Attendees: 35 NA-MIC participants, 46 collaborators, 2 EAB+NIH
** 37 NA-MIC Participants breakdown by cores: Core 1 (7), Core 2 (14), Core 3 (10), Core 4-5-6-7 (4)
** 46 Collaborators: Acoustic Med (2), BWH (19), Caltech (2), GE (1), Harvard IIC (1), JHU (1), Kitware (1), Knowledge Vis (1), Mario Negri (1), MGH (2), NWU (4), UIowa(12), Virginia Tech (1)
* 41 Projects: DBP-II(6), Structural Analysis (2), Diffusion Image Analysis (7), NA-MIC Kit (14), External Collaborations (12)

== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
* Monday June 25
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
** 3:30-4:30pm: [[Special topic breakout: Atlases]]
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Doug Markant, Doug Terry, Lauren O'Donnell, Katharina Quintus, Jorge Alvarado Harvard)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)
# [[Projects/Diffusion/2007_Project_Week_Glyphed_Visualization_For_Volume_Data|Sliced Multiple Glyphed Visualization for Volume Data]] (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)

===NA-MIC Kit - Slicer 3===
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_Lightbox|Lightbox]] (James, Jim, Wendy, Alex)
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Curt, Nicole, Alex, Steve, Will, Vince)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Katie, Steve, Bill Hoffman)
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)
# [[Projects/Slicer3/2007_Project_Week_Lego Mindstorms dissemination for IGT | Lego Mindstorms Dissemination for IGT]] (Danielle Pace)
# [[Projects/Slicer3/2007_Project_Week_EdgeDetection | Edge Detection in Slicer3]] (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
# MIND Clinical Imaging Study: [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)

===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
===Core1===
#John Melonakos, Georgia Tech, Core 1
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1
#Serdar K Balci, MIT, Core 1
#Elliot Uvero, MIT, Core 1
#Ran Tao, Utah, Core 1
#Kevin Teich, MGH, Core 1
===Core2===
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jeffrey Grethe, UCSD, Core 2
#Marco Ruiz, UCSD, Core 2
#Neil Jones, UCSD, Core 2
#Jim Miller, GE Core 2
#Dan Blezek, GE Core 2
#Steve Pieper, Isomics, Core 2
#Alex Yarmarkovich, Isomics, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2 (Mon, Tue)
#Nathan Hageman, UCLA, Core 2 (Tue, Wed)

===Core3-I&II===
#Sylvain Bouix, BWH, Core 3
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Marek Kubicki, BWH, Core 3 (II) (One-day)
#Clement Vachet, UNC Core 3 (II)
#David Gobbi, Queen's University, Core 3 (II)
#Csaba Csoma, Johns Hopkins University, Core 3 (II)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II)
#Mark Scully, The MIND Institute, Core 3 (II)
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01
===Core 4,5,6,7===
#Zack Galbreath, Kitware, Core 4 (Mon, Tue)
#Randy Gollub, MGH, COre 5
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
===Collaborators===
#Chris Wyatt, Virginia Tech, Collaborator R01
#Vincent Magnotta, University of Iowa, Collaborator R01
#Kiran Shivanna, University of Iowa, Collaborator R01
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Luca Antiga, Mario Negri Institute, Collaborator
#Stephen Aylward, Kitware, Collaborator
#Peter Kazanzides, JHU, Collaborator (One-day)
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator
#Greg Sharp, MGH, Collaborator
#Lilla Zollei, MGH, Collaborator (One-day)
#James Ross, GE, Collaborator
#Alex Gouaillard, CEGS Caltech, Collaborator
#Sean Megason, CEGS caltech, Collaborator
#Clif Burdette, Acousticmed, Collaborator
#Jack Blevins, Acousticmed, Collaborator
#Curtis Lisle, KnowledgeVis, Collaborator
#Douglas Alan, Harvard IIC, Collaborator
#Michael Halle, BWH/IIC, Collaborator
#Katie Hayes, BWH, Core 2
#Nicole Aucoin, BWH, Core 2
#Wendy Plesniak, BWH, Collaborator
#Kilian Pohl, BWH Collaborator
#Raimundo Sierra, BWH, Collaborator
#Lauren O'Donnell, BWH, Collaborator
#Raul San Jose, BWH, Collaborator
#C-F Westin, BWH, Collaborator
#Demian Wassermann, BWH/INRIA , Collaborator
#Danielle Pace, BWH , Summer Intern
#Sandy Wells, BWH, Collaborator
#Haiying Liu, BWH Collaborator
#Clare Tempany, BWH Collaborator (One-day)
#Noby Hata, BWH Collaborator (One-day)
#Hong Xiang, BWH Collaborator (One-day)
#Kim Lawson, BWH Collaborator (One-day)
#Junichi Tokuda, BWH Collaborator (One-day)
#Robert Cormack, BWH Collaborator (One-day)

===NIH, EAB===
#Zohara Cohen, NIH (One-day)
#Bill Lorensen, EAB (One-day)

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

==Pictures==
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=2783 PICTURES!] taken by Jeffrey Hawley

File:Mit.jpg

2007-07-02T18:55:45Z

Hawle:

A wide angle picture of the Grier Conference room, taken by Jeffrey Hawley on Friday, June 29th, 2007.
[http://woofton.rivendel.net/gallery2/main.php For more photos]

2007 Programming/Project Week MIT

2007-07-01T03:19:11Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007 -- [http://woofton.rivendel.net/gallery2 PICTURES!] taken by Jeffrey Hawley ]]
==Summary==

Participation: 90 on peak day (Tuesday), 50 on trough (Friday afternoon, and Wednesday 5pm).

[[Image:Mit.jpg|thumb|320px|Photo taken by Jeffrey Hawley]]

== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
* Monday June 25
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
** 3:30-4:30pm: [[Special topic breakout: Atlases]]
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Doug Markant, Doug Terry, Lauren O'Donnell, Katharina Quintus, Jorge Alvarado Harvard)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)
# [[Projects/Diffusion/2007_Project_Week_Glyphed_Visualization_For_Volume_Data|Sliced Multiple Glyphed Visualization for Volume Data]] (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)

===NA-MIC Kit - Slicer 3===
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_Lightbox|Lightbox]] (James, Jim, Wendy, Alex)
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Curt, Nicole, Alex, Steve, Will, Vince)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Katie, Steve, Bill Hoffman)
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)
# [[Projects/Slicer3/2007_Project_Week_Lego Mindstorms dissemination for IGT | Lego Mindstorms Dissemination for IGT]] (Danielle Pace)
# [[Projects/Slicer3/2007_Project_Week_EdgeDetection | Edge Detection in Slicer3]] (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
# MIND Clinical Imaging Study
## [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)

===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
===Full Week===
#John Melonakos, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Tauseef Rehman, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Casey Goodlett, UNC, Core 1 (Registration Fee: Received by DK at MIT)
#Serdar K Balci, MIT, Core 1 (Registration Fee: )
#Elliot Uvero, MIT, Core 1 (Registration Fee: )
#Ran Tao, Utah, Core 1 (Registration Fee: )
#Kevin Teich, MGH, Core 1 (Registration Fee: )
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Registration Fee: )
#Jeffrey Grethe, UCSD, Core 2 (Registration Fee: )
#Marco Ruiz, UCSD, Core 2 (Registration Fee: )
#Neil Jones, UCSD, Core 2 (Registration Fee: Received by DK at MIT)
#Jim Miller, GE Core 2 (Registration Fee: )
#Dan Blezek, GE Core 2 (Registration Fee: Received by DK at MIT)
#Steve Pieper, Isomics, Core 2 (Registration Fee: )
#Alex Yarmarkovich, Isomics, Core 2 (Registration Fee: Received by DK at MIT)
#Katie Hayes, BWH, Core 2 (Registration Fee: BWH Check Attendee 1) - confirmed by Ron
#Nicole Aucoin, BWH, Core 2 (Registration Fee: BWH Check Attendee 2) - confirmed by Ron
#Will Schroeder, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 1)
#Yumin Yuan, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 2)
#Brad Davis, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 3)
#Luis Ibanez, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 4)
#Bill Hoffman, Kitware, Core 2 (Mon, Tue) (Registration Fee: Kitware Check Attendee 5)
#Sylvain Bouix, BWH, Core 3 (Registration Fee: ) - to be paid by personal check and reimbursed by MS
#Katharina Quintus, BWH, Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Marc Niethammer, BWH. Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Clement Vachet, UNC Core 3 (II) (Registration Fee: )
#David Gobbi, Queen's University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#Csaba Csoma, Johns Hopkins University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II) (Registration Fee: )
#Mark Scully, The MIND Institute, Core 3 (II) (Registration Fee: )
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01 (Registration Fee: )
#Zack Galbreath, Kitware, Core 4 (Mon, Tue) (Registration Fee: )
#Tina Kapur, BWH, Core 6 (Registration Fee: BWH Check Attendee 3)- confirmed by Ron
#Ron Kikinis, Core 7, PI (Registration Fee: BWH Check Attendee 4)- confirmed by Ron
#Chris Wyatt, Virginia Tech, Collaborator R01 (Registration Fee: Received by DK at MIT)
#Vincent Magnotta, University of Iowa, Collaborator R01 (Registration Fee: )
#Kiran Shivanna, University of Iowa, Collaborator R01 (Registration Fee: )
#Luca Antiga, Mario Negri Institute, Collaborator (Registration Fee: )
#Stephen Aylward, Kitware, Collaborator (Registration Fee: Kitware CHeck Attendee 6)
#Douglas Alan, Harvard IIC, Collaborator (Registration Fee: )
#Michael Halle, BWH/IIC, Collaborator (Registration Fee: BWH Check Attendee 5 ) - confirmed by Ron
#Wendy Plesniak, BWH, Collaborator (Registration Fee: BWH Check Attendee 6)- confirmed by Ron
#Kilian Pohl, BWH Collaborator (Registration Fee: BWH Check Attendee 7)- confirmed by Ron
#Raimundo Sierra, BWH, Collaborator (Registration Fee: BWH Check Attendee 8)- confirmed by Ron
#Lauren O'Donnell, BWH, Collaborator (Registration Fee: BWH Check Attendee 9)- confirmed by Ron
#Raul San Jose, BWH, Collaborator (Registration Fee: BWH Check Attendee 10)- confirmed by Ron
#Haiying Liu, BWH Collaborator (Registration Fee: BWH Check Attendee 11)- confirmed by Ron
#Hans Johnson, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Gary E. Christensen, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Joo Hyun (Paul) Song, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Xiujuan Geng, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jake Nickel, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Nick Kiguta, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kunlin Cao, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#James Harris, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kai Ding, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jeff Hawley, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Skip Talbot, Northwestern University, Collaborator (Registration Fee: )
#Alex Kogan, Northwestern University, Collaborator (Registration Fee: )
#Vladimir Kleper, Northwestern University, Collaborator (Registration Fee: )
#Pat Mongkolwat, Northwestern University, Collaborator (Registration Fee: )
#Greg Sharp, MGH, Collaborator (Registration Fee: )
#James Ross, GE, Collaborator (Registration Fee: )
#Alex Gouaillard, CEGS Caltech, Collaborator (Registration Fee: )
#Sean Megason, CEGS caltech, Collaborator (Registration Fee: )
#Clif Burdette, Acousticmed, Collaborator (Registration Fee: )
#Jack Blevins, Acousticmed, Collaborator (Registration Fee: )
#Curtis Lisle, KnowledgeVis, Collaborator (Registration Fee: )
#C-F Westin, BWH, Collaborator (Registration Fee: BWH Check Attendee 12)- confirmed by Ron
#Demian Wassermann, BWH/INRIA , Collaborator (Registration Fee: BWH Check Attendee 13)
#Danielle Pace, BWH , Summer Intern (Registration Fee: BWH Check Attendee 14)
#Sandy Wells, BWH, Collaborator (Registration Fee: BWH Check Attendee 15)

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

===One Day===
#Marek Kubicki, BWH, Core 3 (Monday) (Registration Fee: 0)
#Clare Tempany, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Noby Hata, BWH Collaborator (Monday) (Registration Fee: 0)
#Peter Kazanzides, JHU, Collaborator (Wednesday) (Registration Fee: 0)
#Lilla Zollei, MGH, Collaborator (Tuesday) (Registration Fee: 0)
#Hong Xiang, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Kim Lawson, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Junichi Tokuda, BWH Collaborator (Tuesday) (Registration Fee: 0)

==Pictures==
[http://woofton.rivendel.net/gallery2 PICTURES!] taken by Jeffrey Hawley

File:Mit.jpg

2007-07-01T03:10:22Z

Hawle: A wide angle picture of the Grier Conference room, taken by Jeffrey Hawley on Friday, June 29th, 2007.

A wide angle picture of the Grier Conference room, taken by Jeffrey Hawley on Friday, June 29th, 2007.

2007 Programming/Project Week MIT

2007-06-29T05:25:20Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
* Monday June 25
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
** 3:30-4:30pm: [[Special topic breakout: Atlases]]
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Doug Markant, Doug Terry, Lauren O'Donnell, Katharina Quintus, Jorge Alvarado Harvard)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Polina Golland)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)
# [[Projects/Diffusion/2007_Project_Week_Glyphed_Visualization_For_Volume_Data|Sliced Multiple Glyphed Visualization for Volume Data]] (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)

===NA-MIC Kit - Slicer 3===
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt, Will)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)
# [[Projects/Slicer3/2007_Project_Week_Lego Mindstorms dissemination for IGT | Lego Mindstorms Dissemination for IGT]] (Danielle Pace)
# [[Projects/Slicer3/2007_Project_Week_EdgeDetection | Edge Detection in Slicer3]] (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
# MIND Clinical Imaging Study
## [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)

===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
===Full Week===
#John Melonakos, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Tauseef Rehman, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Casey Goodlett, UNC, Core 1 (Registration Fee: Received by DK at MIT)
#Serdar K Balci, MIT, Core 1 (Registration Fee: )
#Elliot Uvero, MIT, Core 1 (Registration Fee: )
#Ran Tao, Utah, Core 1 (Registration Fee: )
#Kevin Teich, MGH, Core 1 (Registration Fee: )
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Registration Fee: )
#Jeffrey Grethe, UCSD, Core 2 (Registration Fee: )
#Marco Ruiz, UCSD, Core 2 (Registration Fee: )
#Neil Jones, UCSD, Core 2 (Registration Fee: Received by DK at MIT)
#Jim Miller, GE Core 2 (Registration Fee: )
#Dan Blezek, GE Core 2 (Registration Fee: Received by DK at MIT)
#Steve Pieper, Isomics, Core 2 (Registration Fee: )
#Alex Yarmarkovich, Isomics, Core 2 (Registration Fee: Received by DK at MIT)
#Katie Hayes, BWH, Core 2 (Registration Fee: BWH Check Attendee 1) - confirmed by Ron
#Nicole Aucoin, BWH, Core 2 (Registration Fee: BWH Check Attendee 2) - confirmed by Ron
#Will Schroeder, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 1)
#Yumin Yuan, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 2)
#Brad Davis, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 3)
#Luis Ibanez, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 4)
#Bill Hoffman, Kitware, Core 2 (Mon, Tue) (Registration Fee: Kitware Check Attendee 5)
#Sylvain Bouix, BWH, Core 3 (Registration Fee: ) - to be paid by personal check and reimbursed by MS
#Katharina Quintus, BWH, Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Marc Niethammer, BWH. Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Clement Vachet, UNC Core 3 (II) (Registration Fee: )
#David Gobbi, Queen's University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#Csaba Csoma, Johns Hopkins University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II) (Registration Fee: )
#Mark Scully, The MIND Institute, Core 3 (II) (Registration Fee: )
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01 (Registration Fee: )
#Zack Galbreath, Kitware, Core 4 (Mon, Tue) (Registration Fee: )
#Tina Kapur, BWH, Core 6 (Registration Fee: BWH Check Attendee 3)- confirmed by Ron
#Ron Kikinis, Core 7, PI (Registration Fee: BWH Check Attendee 4)- confirmed by Ron
#Chris Wyatt, Virginia Tech, Collaborator R01 (Registration Fee: Received by DK at MIT)
#Vincent Magnotta, University of Iowa, Collaborator R01 (Registration Fee: )
#Kiran Shivanna, University of Iowa, Collaborator R01 (Registration Fee: )
#Luca Antiga, Mario Negri Institute, Collaborator (Registration Fee: )
#Stephen Aylward, Kitware, Collaborator (Registration Fee: Kitware CHeck Attendee 6)
#Douglas Alan, Harvard IIC, Collaborator (Registration Fee: )
#Michael Halle, BWH/IIC, Collaborator (Registration Fee: BWH Check Attendee 5 ) - confirmed by Ron
#Wendy Plesniak, BWH, Collaborator (Registration Fee: BWH Check Attendee 6)- confirmed by Ron
#Kilian Pohl, BWH Collaborator (Registration Fee: BWH Check Attendee 7)- confirmed by Ron
#Raimundo Sierra, BWH, Collaborator (Registration Fee: BWH Check Attendee 8)- confirmed by Ron
#Lauren O'Donnell, BWH, Collaborator (Registration Fee: BWH Check Attendee 9)- confirmed by Ron
#Raul San Jose, BWH, Collaborator (Registration Fee: BWH Check Attendee 10)- confirmed by Ron
#Haiying Liu, BWH Collaborator (Registration Fee: BWH Check Attendee 11)- confirmed by Ron
#Hans Johnson, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Gary E. Christensen, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Joo Hyun (Paul) Song, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Xiujuan Geng, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jake Nickel, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Nick Kiguta, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kunlin Cao, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#James Harris, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kai Ding, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jeff Hawley, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Skip Talbot, Northwestern University, Collaborator (Registration Fee: )
#Alex Kogan, Northwestern University, Collaborator (Registration Fee: )
#Vladimir Kleper, Northwestern University, Collaborator (Registration Fee: )
#Pat Mongkolwat, Northwestern University, Collaborator (Registration Fee: )
#Greg Sharp, MGH, Collaborator (Registration Fee: )
#James Ross, GE, Collaborator (Registration Fee: )
#Alex Gouaillard, CEGS Caltech, Collaborator (Registration Fee: )
#Sean Megason, CEGS caltech, Collaborator (Registration Fee: )
#Clif Burdette, Acousticmed, Collaborator (Registration Fee: )
#Jack Blevins, Acousticmed, Collaborator (Registration Fee: )
#Curtis Lisle, KnowledgeVis, Collaborator (Registration Fee: )
#C-F Westin, BWH, Collaborator (Registration Fee: BWH Check Attendee 12)- confirmed by Ron
#Demian Wassermann, BWH/INRIA , Collaborator (Registration Fee: BWH Check Attendee 13)
#Danielle Pace, BWH , Summer Intern (Registration Fee: BWH Check Attendee 14)
#Sandy Wells, BWH, Collaborator (Registration Fee: BWH Check Attendee 15)

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

===One Day===
#Marek Kubicki, BWH, Core 3 (Monday) (Registration Fee: 0)
#Clare Tempany, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Noby Hata, BWH Collaborator (Monday) (Registration Fee: 0)
#Peter Kazanzides, JHU, Collaborator (Wednesday) (Registration Fee: 0)
#Lilla Zollei, MGH, Collaborator (Tuesday) (Registration Fee: 0)
#Hong Xiang, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Kim Lawson, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Junichi Tokuda, BWH Collaborator (Tuesday) (Registration Fee: 0)

==Pictures==
[http://woofton.rivendel.net/gallery2 PICTURES!] taken by Jeffrey Hawley

2007 Programming/Project Week MIT

2007-06-28T21:29:27Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
* Monday June 25
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
** 3:30-4:30pm: [[Special topic breakout: Atlases]]
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Doug Markant, Doug Terry, Lauren O'Donnell, Katharina Quintus, Jorge Alvarado Harvard)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Polina Golland)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)

===NA-MIC Kit - Slicer 3===
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt, Will)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
# MIND Clinical Imaging Study
## [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)

===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
===Full Week===
#John Melonakos, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Tauseef Rehman, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Casey Goodlett, UNC, Core 1 (Registration Fee: Received by DK at MIT)
#Serdar K Balci, MIT, Core 1 (Registration Fee: )
#Elliot Uvero, MIT, Core 1 (Registration Fee: )
#Ran Tao, Utah, Core 1 (Registration Fee: )
#Kevin Teich, MGH, Core 1 (Registration Fee: )
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Registration Fee: )
#Jeffrey Grethe, UCSD, Core 2 (Registration Fee: )
#Marco Ruiz, UCSD, Core 2 (Registration Fee: )
#Neil Jones, UCSD, Core 2 (Registration Fee: Received by DK at MIT)
#Jim Miller, GE Core 2 (Registration Fee: )
#Dan Blezek, GE Core 2 (Registration Fee: Received by DK at MIT)
#Steve Pieper, Isomics, Core 2 (Registration Fee: )
#Alex Yarmarkovich, Isomics, Core 2 (Registration Fee: Received by DK at MIT)
#Katie Hayes, BWH, Core 2 (Registration Fee: BWH Check Attendee 1) - confirmed by Ron
#Nicole Aucoin, BWH, Core 2 (Registration Fee: BWH Check Attendee 2) - confirmed by Ron
#Will Schroeder, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 1)
#Yumin Yuan, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 2)
#Brad Davis, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 3)
#Luis Ibanez, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 4)
#Bill Hoffman, Kitware, Core 2 (Mon, Tue) (Registration Fee: Kitware Check Attendee 5)
#Sylvain Bouix, BWH, Core 3 (Registration Fee: ) - to be paid by personal check and reimbursed by MS
#Katharina Quintus, BWH, Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Marc Niethammer, BWH. Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Clement Vachet, UNC Core 3 (II) (Registration Fee: )
#David Gobbi, Queen's University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#Csaba Csoma, Johns Hopkins University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II) (Registration Fee: )
#Mark Scully, The MIND Institute, Core 3 (II) (Registration Fee: )
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01 (Registration Fee: )
#Zack Galbreath, Kitware, Core 4 (Mon, Tue) (Registration Fee: )
#Tina Kapur, BWH, Core 6 (Registration Fee: BWH Check Attendee 3)- confirmed by Ron
#Ron Kikinis, Core 7, PI (Registration Fee: BWH Check Attendee 4)- confirmed by Ron
#Chris Wyatt, Virginia Tech, Collaborator R01 (Registration Fee: Received by DK at MIT)
#Vincent Magnotta, University of Iowa, Collaborator R01 (Registration Fee: )
#Kiran Shivanna, University of Iowa, Collaborator R01 (Registration Fee: )
#Luca Antiga, Mario Negri Institute, Collaborator (Registration Fee: )
#Stephen Aylward, Kitware, Collaborator (Registration Fee: Kitware CHeck Attendee 6)
#Douglas Alan, Harvard IIC, Collaborator (Registration Fee: )
#Michael Halle, BWH/IIC, Collaborator (Registration Fee: BWH Check Attendee 5 ) - confirmed by Ron
#Wendy Plesniak, BWH, Collaborator (Registration Fee: BWH Check Attendee 6)- confirmed by Ron
#Kilian Pohl, BWH Collaborator (Registration Fee: BWH Check Attendee 7)- confirmed by Ron
#Raimundo Sierra, BWH, Collaborator (Registration Fee: BWH Check Attendee 8)- confirmed by Ron
#Lauren O'Donnell, BWH, Collaborator (Registration Fee: BWH Check Attendee 9)- confirmed by Ron
#Raul San Jose, BWH, Collaborator (Registration Fee: BWH Check Attendee 10)- confirmed by Ron
#Haiying Liu, BWH Collaborator (Registration Fee: BWH Check Attendee 11)- confirmed by Ron
#Hans Johnson, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Gary E. Christensen, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Joo Hyun (Paul) Song, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Xiujuan Geng, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jake Nickel, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Nick Kiguta, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kunlin Cao, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#James Harris, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kai Ding, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jeff Hawley, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Skip Talbot, Northwestern University, Collaborator (Registration Fee: )
#Alex Kogan, Northwestern University, Collaborator (Registration Fee: )
#Vladimir Kleper, Northwestern University, Collaborator (Registration Fee: )
#Pat Mongkolwat, Northwestern University, Collaborator (Registration Fee: )
#Greg Sharp, MGH, Collaborator (Registration Fee: )
#James Ross, GE, Collaborator (Registration Fee: )
#Alex Gouaillard, CEGS Caltech, Collaborator (Registration Fee: )
#Sean Megason, CEGS caltech, Collaborator (Registration Fee: )
#Clif Burdette, Acousticmed, Collaborator (Registration Fee: )
#Jack Blevins, Acousticmed, Collaborator (Registration Fee: )
#Curtis Lisle, KnowledgeVis, Collaborator (Registration Fee: )
#C-F Westin, BWH, Collaborator (Registration Fee: BWH Check Attendee 12)- confirmed by Ron
#Demian Wassermann, BWH/INRIA , Collaborator (Registration Fee: BWH Check Attendee 13)
#Danielle Pace, BWH , Summer Intern (Registration Fee: BWH Check Attendee 14)
#Sandy Wells, BWH, Collaborator (Registration Fee: BWH Check Attendee 15)

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

===One Day===
#Marek Kubicki, BWH, Core 3 (Monday) (Registration Fee: 0)
#Clare Tempany, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Noby Hata, BWH Collaborator (Monday) (Registration Fee: 0)
#Peter Kazanzides, JHU, Collaborator (Wednesday) (Registration Fee: 0)
#Lilla Zollei, MGH, Collaborator (Tuesday) (Registration Fee: 0)
#Hong Xiang, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Kim Lawson, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Junichi Tokuda, BWH Collaborator (Tuesday) (Registration Fee: 0)

[http://woofton.rivendel.net/gallery2 PICTURES!] taken by Jeffrey Hawley

2007 Programming/Project Week MIT

2007-06-28T21:28:57Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
* Monday June 25
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
** 3:30-4:30pm: [[Special topic breakout: Atlases]]
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Doug Markant, Doug Terry, Lauren O'Donnell, Katharina Quintus, Jorge Alvarado Harvard)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Polina Golland)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)

===NA-MIC Kit - Slicer 3===
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt, Will)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
# MIND Clinical Imaging Study
## [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)

===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
===Full Week===
#John Melonakos, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Tauseef Rehman, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Casey Goodlett, UNC, Core 1 (Registration Fee: Received by DK at MIT)
#Serdar K Balci, MIT, Core 1 (Registration Fee: )
#Elliot Uvero, MIT, Core 1 (Registration Fee: )
#Ran Tao, Utah, Core 1 (Registration Fee: )
#Kevin Teich, MGH, Core 1 (Registration Fee: )
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Registration Fee: )
#Jeffrey Grethe, UCSD, Core 2 (Registration Fee: )
#Marco Ruiz, UCSD, Core 2 (Registration Fee: )
#Neil Jones, UCSD, Core 2 (Registration Fee: Received by DK at MIT)
#Jim Miller, GE Core 2 (Registration Fee: )
#Dan Blezek, GE Core 2 (Registration Fee: Received by DK at MIT)
#Steve Pieper, Isomics, Core 2 (Registration Fee: )
#Alex Yarmarkovich, Isomics, Core 2 (Registration Fee: Received by DK at MIT)
#Katie Hayes, BWH, Core 2 (Registration Fee: BWH Check Attendee 1) - confirmed by Ron
#Nicole Aucoin, BWH, Core 2 (Registration Fee: BWH Check Attendee 2) - confirmed by Ron
#Will Schroeder, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 1)
#Yumin Yuan, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 2)
#Brad Davis, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 3)
#Luis Ibanez, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 4)
#Bill Hoffman, Kitware, Core 2 (Mon, Tue) (Registration Fee: Kitware Check Attendee 5)
#Sylvain Bouix, BWH, Core 3 (Registration Fee: ) - to be paid by personal check and reimbursed by MS
#Katharina Quintus, BWH, Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Marc Niethammer, BWH. Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Clement Vachet, UNC Core 3 (II) (Registration Fee: )
#David Gobbi, Queen's University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#Csaba Csoma, Johns Hopkins University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II) (Registration Fee: )
#Mark Scully, The MIND Institute, Core 3 (II) (Registration Fee: )
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01 (Registration Fee: )
#Zack Galbreath, Kitware, Core 4 (Mon, Tue) (Registration Fee: )
#Tina Kapur, BWH, Core 6 (Registration Fee: BWH Check Attendee 3)- confirmed by Ron
#Ron Kikinis, Core 7, PI (Registration Fee: BWH Check Attendee 4)- confirmed by Ron
#Chris Wyatt, Virginia Tech, Collaborator R01 (Registration Fee: Received by DK at MIT)
#Vincent Magnotta, University of Iowa, Collaborator R01 (Registration Fee: )
#Kiran Shivanna, University of Iowa, Collaborator R01 (Registration Fee: )
#Luca Antiga, Mario Negri Institute, Collaborator (Registration Fee: )
#Stephen Aylward, Kitware, Collaborator (Registration Fee: Kitware CHeck Attendee 6)
#Douglas Alan, Harvard IIC, Collaborator (Registration Fee: )
#Michael Halle, BWH/IIC, Collaborator (Registration Fee: BWH Check Attendee 5 ) - confirmed by Ron
#Wendy Plesniak, BWH, Collaborator (Registration Fee: BWH Check Attendee 6)- confirmed by Ron
#Kilian Pohl, BWH Collaborator (Registration Fee: BWH Check Attendee 7)- confirmed by Ron
#Raimundo Sierra, BWH, Collaborator (Registration Fee: BWH Check Attendee 8)- confirmed by Ron
#Lauren O'Donnell, BWH, Collaborator (Registration Fee: BWH Check Attendee 9)- confirmed by Ron
#Raul San Jose, BWH, Collaborator (Registration Fee: BWH Check Attendee 10)- confirmed by Ron
#Haiying Liu, BWH Collaborator (Registration Fee: BWH Check Attendee 11)- confirmed by Ron
#Hans Johnson, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Gary E. Christensen, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Joo Hyun (Paul) Song, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Xiujuan Geng, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jake Nickel, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Nick Kiguta, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kunlin Cao, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#James Harris, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kai Ding, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jeff Hawley, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Skip Talbot, Northwestern University, Collaborator (Registration Fee: )
#Alex Kogan, Northwestern University, Collaborator (Registration Fee: )
#Vladimir Kleper, Northwestern University, Collaborator (Registration Fee: )
#Pat Mongkolwat, Northwestern University, Collaborator (Registration Fee: )
#Greg Sharp, MGH, Collaborator (Registration Fee: )
#James Ross, GE, Collaborator (Registration Fee: )
#Alex Gouaillard, CEGS Caltech, Collaborator (Registration Fee: )
#Sean Megason, CEGS caltech, Collaborator (Registration Fee: )
#Clif Burdette, Acousticmed, Collaborator (Registration Fee: )
#Jack Blevins, Acousticmed, Collaborator (Registration Fee: )
#Curtis Lisle, KnowledgeVis, Collaborator (Registration Fee: )
#C-F Westin, BWH, Collaborator (Registration Fee: BWH Check Attendee 12)- confirmed by Ron
#Demian Wassermann, BWH/INRIA , Collaborator (Registration Fee: BWH Check Attendee 13)
#Danielle Pace, BWH , Summer Intern (Registration Fee: BWH Check Attendee 14)
#Sandy Wells, BWH, Collaborator (Registration Fee: BWH Check Attendee 15)

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

===One Day===
#Marek Kubicki, BWH, Core 3 (Monday) (Registration Fee: 0)
#Clare Tempany, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Noby Hata, BWH Collaborator (Monday) (Registration Fee: 0)
#Peter Kazanzides, JHU, Collaborator (Wednesday) (Registration Fee: 0)
#Lilla Zollei, MGH, Collaborator (Tuesday) (Registration Fee: 0)
#Hong Xiang, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Kim Lawson, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Junichi Tokuda, BWH Collaborator (Tuesday) (Registration Fee: 0)

==[http://woofton.rivendel.net/gallery2 PICTURES!]== taken by Jeffrey Hawley

2007 Programming/Project Week MIT

2007-06-28T21:28:16Z

Hawle:

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
* Monday June 25
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
** 3:30-4:30pm: [[Special topic breakout: Atlases]]
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Doug Markant, Doug Terry, Lauren O'Donnell, Katharina Quintus, Jorge Alvarado Harvard)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Polina Golland)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)

===NA-MIC Kit - Slicer 3===
#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt, Will)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
# MIND Clinical Imaging Study
## [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)

===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
===Full Week===
#John Melonakos, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Tauseef Rehman, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Casey Goodlett, UNC, Core 1 (Registration Fee: Received by DK at MIT)
#Serdar K Balci, MIT, Core 1 (Registration Fee: )
#Elliot Uvero, MIT, Core 1 (Registration Fee: )
#Ran Tao, Utah, Core 1 (Registration Fee: )
#Kevin Teich, MGH, Core 1 (Registration Fee: )
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Registration Fee: )
#Jeffrey Grethe, UCSD, Core 2 (Registration Fee: )
#Marco Ruiz, UCSD, Core 2 (Registration Fee: )
#Neil Jones, UCSD, Core 2 (Registration Fee: Received by DK at MIT)
#Jim Miller, GE Core 2 (Registration Fee: )
#Dan Blezek, GE Core 2 (Registration Fee: Received by DK at MIT)
#Steve Pieper, Isomics, Core 2 (Registration Fee: )
#Alex Yarmarkovich, Isomics, Core 2 (Registration Fee: Received by DK at MIT)
#Katie Hayes, BWH, Core 2 (Registration Fee: BWH Check Attendee 1) - confirmed by Ron
#Nicole Aucoin, BWH, Core 2 (Registration Fee: BWH Check Attendee 2) - confirmed by Ron
#Will Schroeder, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 1)
#Yumin Yuan, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 2)
#Brad Davis, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 3)
#Luis Ibanez, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 4)
#Bill Hoffman, Kitware, Core 2 (Mon, Tue) (Registration Fee: Kitware Check Attendee 5)
#Sylvain Bouix, BWH, Core 3 (Registration Fee: ) - to be paid by personal check and reimbursed by MS
#Katharina Quintus, BWH, Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Marc Niethammer, BWH. Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Clement Vachet, UNC Core 3 (II) (Registration Fee: )
#David Gobbi, Queen's University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#Csaba Csoma, Johns Hopkins University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II) (Registration Fee: )
#Mark Scully, The MIND Institute, Core 3 (II) (Registration Fee: )
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01 (Registration Fee: )
#Zack Galbreath, Kitware, Core 4 (Mon, Tue) (Registration Fee: )
#Tina Kapur, BWH, Core 6 (Registration Fee: BWH Check Attendee 3)- confirmed by Ron
#Ron Kikinis, Core 7, PI (Registration Fee: BWH Check Attendee 4)- confirmed by Ron
#Chris Wyatt, Virginia Tech, Collaborator R01 (Registration Fee: Received by DK at MIT)
#Vincent Magnotta, University of Iowa, Collaborator R01 (Registration Fee: )
#Kiran Shivanna, University of Iowa, Collaborator R01 (Registration Fee: )
#Luca Antiga, Mario Negri Institute, Collaborator (Registration Fee: )
#Stephen Aylward, Kitware, Collaborator (Registration Fee: Kitware CHeck Attendee 6)
#Douglas Alan, Harvard IIC, Collaborator (Registration Fee: )
#Michael Halle, BWH/IIC, Collaborator (Registration Fee: BWH Check Attendee 5 ) - confirmed by Ron
#Wendy Plesniak, BWH, Collaborator (Registration Fee: BWH Check Attendee 6)- confirmed by Ron
#Kilian Pohl, BWH Collaborator (Registration Fee: BWH Check Attendee 7)- confirmed by Ron
#Raimundo Sierra, BWH, Collaborator (Registration Fee: BWH Check Attendee 8)- confirmed by Ron
#Lauren O'Donnell, BWH, Collaborator (Registration Fee: BWH Check Attendee 9)- confirmed by Ron
#Raul San Jose, BWH, Collaborator (Registration Fee: BWH Check Attendee 10)- confirmed by Ron
#Haiying Liu, BWH Collaborator (Registration Fee: BWH Check Attendee 11)- confirmed by Ron
#Hans Johnson, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Gary E. Christensen, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Joo Hyun (Paul) Song, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Xiujuan Geng, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jake Nickel, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Nick Kiguta, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kunlin Cao, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#James Harris, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kai Ding, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jeff Hawley, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Skip Talbot, Northwestern University, Collaborator (Registration Fee: )
#Alex Kogan, Northwestern University, Collaborator (Registration Fee: )
#Vladimir Kleper, Northwestern University, Collaborator (Registration Fee: )
#Pat Mongkolwat, Northwestern University, Collaborator (Registration Fee: )
#Greg Sharp, MGH, Collaborator (Registration Fee: )
#James Ross, GE, Collaborator (Registration Fee: )
#Alex Gouaillard, CEGS Caltech, Collaborator (Registration Fee: )
#Sean Megason, CEGS caltech, Collaborator (Registration Fee: )
#Clif Burdette, Acousticmed, Collaborator (Registration Fee: )
#Jack Blevins, Acousticmed, Collaborator (Registration Fee: )
#Curtis Lisle, KnowledgeVis, Collaborator (Registration Fee: )
#C-F Westin, BWH, Collaborator (Registration Fee: BWH Check Attendee 12)- confirmed by Ron
#Demian Wassermann, BWH/INRIA , Collaborator (Registration Fee: BWH Check Attendee 13)
#Danielle Pace, BWH , Summer Intern (Registration Fee: BWH Check Attendee 14)
#Sandy Wells, BWH, Collaborator (Registration Fee: BWH Check Attendee 15)

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

===One Day===
#Marek Kubicki, BWH, Core 3 (Monday) (Registration Fee: 0)
#Clare Tempany, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Noby Hata, BWH Collaborator (Monday) (Registration Fee: 0)
#Peter Kazanzides, JHU, Collaborator (Wednesday) (Registration Fee: 0)
#Lilla Zollei, MGH, Collaborator (Tuesday) (Registration Fee: 0)
#Hong Xiang, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Kim Lawson, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Junichi Tokuda, BWH Collaborator (Tuesday) (Registration Fee: 0)

[http://woofton.rivendel.net/gallery2 PICTURES!] taken by Jeffrey Hawley