NAMIC Wiki - User contributions [en]

File:Screen shot 2010-06-25 at 10.21.41 AM.png

2010-06-25T14:23:54Z

Chamel69:

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-25T13:49:18Z

Chamel69: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis SPHARM-PDM Overview]
Image:Slicer1.png|Quality Control within Slicer.
Image:Spharm-correspondance.jpg‎|Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.
</gallery>

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is to make ShapeAnalysisModule directly available as a 3D Slicer extension <bar>,...

</div>

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

<h3>Progress</h3>

This week, I developed a quality control based on MRML scene for our statistic tool shapeAnalysisMANCOVA.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-16T16:06:25Z

Chamel69: uploaded a new version of "File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf"

Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer TutorialContestSummer2010

2010-06-16T16:05:28Z

Chamel69:

This is the page for the tutorial materials for Automatic SPHARM Shape Analysis in 3D Slicer

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.ppt PPT: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.ppt]

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf PDF: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip Data: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer TutorialContestSummer2010

2010-06-16T16:04:43Z

Chamel69:

This is the page for the tutorial materials for Automatic SPHARM Shape Analysis in 3D Slicer

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.ppt PPT: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.ppt]

[http://wiki.na-mic.org/Wiki/index.php/File:`AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf PDF: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip Data: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer TutorialContestSummer2010

2010-06-16T16:03:49Z

Chamel69:

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.ppt

2010-06-16T16:02:12Z

Chamel69:

Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer TutorialContestSummer2010

2010-06-16T16:00:30Z

Chamel69:

This is the page for the tutorial materials for Automatic SPHARM Shape Analysis in 3D Slicer

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.ppt PPT: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.ppt]

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip Data: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-16T15:58:44Z

Chamel69: uploaded a new version of "File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf"

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-16T15:57:22Z

Chamel69: uploaded a new version of "File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf"

Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer TutorialContestSummer2010

2010-06-16T15:55:50Z

Chamel69:

This is the page for the tutorial materials for Automatic SPHARM Shape Analysis in 3D Slicer

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf PPT: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.ppt]

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip Data: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-16T15:43:31Z

Chamel69: uploaded a new version of "File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf"

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-16T15:42:02Z

Chamel69: uploaded a new version of "File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf"

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-16T15:36:49Z

Chamel69: uploaded a new version of "File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf"

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-16T15:31:31Z

Chamel69: uploaded a new version of "File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf"

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:31:46Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis SPHARM-PDM Overview]
Image:Slicer1.png|Quality Control within Slicer.
Image:Spharm-correspondance.jpg‎|Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.
</gallery>

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is to make ShapeAnalysisModule directly available as a 3D Slicer extension <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:31:27Z

Chamel69: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis SPHARM-PDM Overview]
Image:Slicer1.png|Quality Control within Slicer.
Image:Spharm-correspondance.jpg‎|Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.
</gallery>

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is to make ShapeAnalysisModule directly available as a 3D Slicer extension <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>
[[Media:Example.ogg]]

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:30:48Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis SPHARM-PDM Overview]
Image:Slicer1.png|Quality Control within Slicer.
Image:Spharm-correspondance.jpg‎|Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.
</gallery>

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is to make ShapeAnalysisModule directly available as a 3D Slicer extension <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>
[[Media:Example.ogg]]

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:29:22Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis SPHARM-PDM Overview]
Image:Slicer1.png|Quality Control within Slicer.
Image:Spharm-correspondance.jpg‎|Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.
</gallery>

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>
[[Media:Example.ogg]]

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:29:13Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis SPHARM-PDM Overview]
Image:Slicer1.png|Quality Control within Slicer.
Image:Spharm-correspodance.jpg‎|Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.
</gallery>

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>
[[Media:Example.ogg]]

File:Spharm-correspondance.jpg

2010-06-16T14:28:17Z

Chamel69:

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:26:45Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis SPHARM-PDM Overview]
Image:Slicer1.png|Quality Control within Slicer
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>
[[Media:Example.ogg]]

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:25:35Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis ARCTIC: Automatic Regional Cortical ThICkness]
Image:Slicer1.png|Sucal depth on genus-zero cortical surface
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>
[[Media:Example.ogg]]

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:24:56Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis ARCTIC: Automatic Regional Cortical ThICkness]
Image:[[File:Slicer1.png]]
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>
[[Media:Example.ogg]]

File:Slicer1.png

2010-06-16T14:24:22Z

Chamel69:

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:14:01Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis ARCTIC: Automatic Regional Cortical ThICkness]
Image:[[File:blablajpg]]
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:11:42Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis ARCTIC: Automatic Regional Cortical ThICkness]
Image:[[File:Example.jpg]]
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:10:24Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis ARCTIC: Automatic Regional Cortical ThICkness]
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:08:05Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image: http://www.na-mic.org/Wiki/index.php/File:UNCShape_OverviewAnalysis_MICCAI06.gif| Shape Analysis Overview.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>

Automatic SPHARM Shape Analysis in 3D Slicer

2010-06-16T14:07:46Z

Chamel69: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List Image:http://www.na-mic.org/Wiki/index.php/File:UNCShape_OverviewAnalysis_MICCAI06.gi…'

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:http://www.na-mic.org/Wiki/index.php/File:UNCShape_OverviewAnalysis_MICCAI06.gif| Shape Analysis Overview.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.

</div>

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

<h3>Approach, Plan</h3>

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is make this module as part of Slicer3 <bar>,...

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable YES
#Other (Please specify)

</div>

2010 Summer Project Week

2010-06-16T13:49:06Z

Chamel69: /* Shape Analysis */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*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.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#Intraoperative Brain Shift Monitoring Using Shear Model Transcranial Ultrasound (Jason White, Steve Pieper?, Pratik Patel?)
#Prostate Intervention(Junichi, Sam Song, Tamas Ungi)
# Liver Ablation (Haiying Liu)
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#Module Inventory (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]]Superbuild (David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/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 17, 2010: 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. XNAT/MIDAS). 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Anderson Peter , GE Navigation (Retired)
# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Bowers Michael , Johns Hopkins University
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Ding Liya , The Ohio State University
# Eckbo Ryan , BWH
# Ersoy Ilker , University of Missouri Columbia
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Fritscher Karl , UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# Gorgolewski Chris , SPL
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Grama Kedar , Rensselaer Polytechnic Institute
# Haehn Daniel , University of Pennsylvania
# Hafiane Adel , ENSI-Bourges
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Halle Michael , BWH/SPL
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Jagadeesan Jayender , SPL
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Lee Joohwi , UNC Chapel Hill
# Li Rui , MGH
# Lienhard Stefan , LMI
# Lisle Curtis , KnowledgeVis, LLC
# Liu Felix , Beth Israel Deaconess Medical Center
# Liu Yanling , SAIC-Frederick, Inc.
# Liu Haiying , Brigham and Women's Hospital
# Lowekamp Bradley , Lockheed Martin
# machiraju raghu , The Ohio State University
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Marks William , Focused Ultrasound Lab, BWH, HMS
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Olson Beck , UCSF
# Onofrey John , Yale University
# Padmanabhan Raghav , RPI
# Palaniappan Kannappan , university of Missouri
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Patel Pratik , Brainlab Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# PECOT Thierry , Ohio State University
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Singh Shantanu , The Ohio State University
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , BWH
# Tao Xiaodong , GE Research
# Tokuda Junichi , Brigham and Women's Hospital
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Weinrich Adam , Nokia
# Wells Sandy , BWH
# White Phillip , BWH/HMS
# Wu Guorong , University of North Carolina at Chapel Hill
# Yamada Atsushi , Nagoya Institute of Technology
# Yarmarkovich Alexander , ISOMICS
# Zaitsev Alexander , Brigham and Womens Hospital

2010 Summer Project Week

2010-06-16T13:48:48Z

Chamel69: /* Analysis */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*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.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#Intraoperative Brain Shift Monitoring Using Shear Model Transcranial Ultrasound (Jason White, Steve Pieper?, Pratik Patel?)
#Prostate Intervention(Junichi, Sam Song, Tamas Ungi)
# Liver Ablation (Haiying Liu)
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#Module Inventory (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]]Superbuild (David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/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 17, 2010: 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. XNAT/MIDAS). 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Anderson Peter , GE Navigation (Retired)
# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Bowers Michael , Johns Hopkins University
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Ding Liya , The Ohio State University
# Eckbo Ryan , BWH
# Ersoy Ilker , University of Missouri Columbia
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Fritscher Karl , UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# Gorgolewski Chris , SPL
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Grama Kedar , Rensselaer Polytechnic Institute
# Haehn Daniel , University of Pennsylvania
# Hafiane Adel , ENSI-Bourges
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Halle Michael , BWH/SPL
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Jagadeesan Jayender , SPL
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Lee Joohwi , UNC Chapel Hill
# Li Rui , MGH
# Lienhard Stefan , LMI
# Lisle Curtis , KnowledgeVis, LLC
# Liu Felix , Beth Israel Deaconess Medical Center
# Liu Yanling , SAIC-Frederick, Inc.
# Liu Haiying , Brigham and Women's Hospital
# Lowekamp Bradley , Lockheed Martin
# machiraju raghu , The Ohio State University
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Marks William , Focused Ultrasound Lab, BWH, HMS
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Olson Beck , UCSF
# Onofrey John , Yale University
# Padmanabhan Raghav , RPI
# Palaniappan Kannappan , university of Missouri
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Patel Pratik , Brainlab Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# PECOT Thierry , Ohio State University
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Singh Shantanu , The Ohio State University
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , BWH
# Tao Xiaodong , GE Research
# Tokuda Junichi , Brigham and Women's Hospital
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Weinrich Adam , Nokia
# Wells Sandy , BWH
# White Phillip , BWH/HMS
# Wu Guorong , University of North Carolina at Chapel Hill
# Yamada Atsushi , Nagoya Institute of Technology
# Yarmarkovich Alexander , ISOMICS
# Zaitsev Alexander , Brigham and Womens Hospital

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-15T19:47:56Z

Chamel69: uploaded a new version of "File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf"

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.pdf

2010-06-15T04:05:15Z

Chamel69:

File:AutomaticSPHARMShapeAnalysis TutorialContestSummer2010.zip

2010-06-14T21:47:29Z

Chamel69:

File:Fiducials TutorialContestSummer2010.zip

2010-06-14T21:40:30Z

Chamel69: uploaded a new version of "File:Fiducials TutorialContestSummer2010.zip": Reverted to version as of 01:00, 12 June 2010

Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer TutorialContestSummer2010

2010-06-14T21:38:30Z

Chamel69:

This is the page for the tutorial materials for Automatic SPHARM Shape Analysis in 3D Slicer

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf PDF: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip Data: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

File:Fiducials TutorialContestSummer2010.zip

2010-06-14T21:13:00Z

Chamel69: uploaded a new version of "File:Fiducials TutorialContestSummer2010.zip"

Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer TutorialContestSummer2010

2010-06-14T21:10:59Z

Chamel69:

This is the page for the tutorial materials for Automatic SPHARM Shape Analysis in 3D Slicer

[http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.pdf PDF: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Data: AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.zip]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer TutorialContestSummer2010

2010-06-14T21:08:29Z

Chamel69: Created page with 'This is the page for the tutorial materials for Automatic SPHARM Shape Analysis in 3D Slicer [http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialCon…'

This is the page for the tutorial materials for Automatic SPHARM Shape Analysis in 3D Slicer

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysis_TutorialContestSummer2010.pdf pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:AutomaticSPHARMShapeAnalysisData_TutorialContestSummer2010.zip Data]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

Summer 2010 Tutorial Contest

2010-06-14T21:04:47Z

Chamel69: /* List of submitted tutorials */

'''Organizational Telephone Call May 13th at 3pm Eastern Time (part of standard NA-MIC Engineering tcon)'''

=Background=

[http://www.slicer.org Slicer3] is used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer. Our current portfolio of tutorials as well as tutorials that were developed in past contests are posted on the [http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training#Software_tutorials| NA-MIC training compendium].

=Tutorial Contest Goal=
The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups.

There will be three categories:
#'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least:
#*materials about the scientific and application background and motivation,
#*step-by-step guides, and
#*sample data
#*Examples: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARCTIC (Automatic Regional Cortical Thickness) Tutorial]] , [[IGT:ToolKit/Neurosurgical-Planning|Neurosurgical Planning for Image Guided Therapy using Slicer3]]
#'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:
#*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment
#*step-by-step guides, and
#*at least two different sample data sets from two different institutions
#*Examples: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]], [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|Automatic Segmentation Tutorial ]]
# '''METHODOLOGY TUTORIAL'''. Application-level tutorials for users and developers.
<br>

=Rules=
*Tutorial must be based on the '''Slicer3.6 release'''
*To enter the contest, you must provide '''a version of the tutorial that works on at least one platform'''.
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Tutorial must include contact information of the primary author (e-mail and phone number)
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template.ppt‎| tutorial template]].
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules
*Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission.

=Submission Dead-line and Presentation=

* '''<span style="background-color: yellow"> Submission dead-line: Monday June 14, 2010'''</span>
* Presentation: all tutorials will be presented by the authors during the Summer 2010 Project Week, on '''Tuesday June 22 from 3:00 pm to 5:30 pm'''. Each tutorial presentation should be 10 minutes long.
* If you wish to participate in the contest, please follow the three steps below:
**1. Create a wiki page for your tutorial
**2. Upload your slides and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestSummer2010.pdf' and 'TutorialData_TutorialContestSummer2010.zip'
**3. Add a link to the uploaded tutorial and datasets on your tutorial page.
**4. Add a link to your tutorial page in the list below.

= List of submitted tutorials=

[[Slicer3:Fiducials_TutorialContestSummer2010 | Fiducials]]

[[Slicer3:RSS_TutorialContestSummer2010 | RSS (Robust Statistics Segmenter)]]

[[Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer_TutorialContestSummer2010 | Automatic SPHARM Shape Analysis in 3D Slicer]]

Summer 2010 Tutorial Contest

2010-06-14T21:03:30Z

Chamel69: /* List of submitted tutorials */

'''Organizational Telephone Call May 13th at 3pm Eastern Time (part of standard NA-MIC Engineering tcon)'''

=Background=

[http://www.slicer.org Slicer3] is used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer. Our current portfolio of tutorials as well as tutorials that were developed in past contests are posted on the [http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training#Software_tutorials| NA-MIC training compendium].

=Tutorial Contest Goal=
The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups.

There will be three categories:
#'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least:
#*materials about the scientific and application background and motivation,
#*step-by-step guides, and
#*sample data
#*Examples: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARCTIC (Automatic Regional Cortical Thickness) Tutorial]] , [[IGT:ToolKit/Neurosurgical-Planning|Neurosurgical Planning for Image Guided Therapy using Slicer3]]
#'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:
#*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment
#*step-by-step guides, and
#*at least two different sample data sets from two different institutions
#*Examples: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]], [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|Automatic Segmentation Tutorial ]]
# '''METHODOLOGY TUTORIAL'''. Application-level tutorials for users and developers.
<br>

=Rules=
*Tutorial must be based on the '''Slicer3.6 release'''
*To enter the contest, you must provide '''a version of the tutorial that works on at least one platform'''.
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Tutorial must include contact information of the primary author (e-mail and phone number)
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template.ppt‎| tutorial template]].
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules
*Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission.

=Submission Dead-line and Presentation=

* '''<span style="background-color: yellow"> Submission dead-line: Monday June 14, 2010'''</span>
* Presentation: all tutorials will be presented by the authors during the Summer 2010 Project Week, on '''Tuesday June 22 from 3:00 pm to 5:30 pm'''. Each tutorial presentation should be 10 minutes long.
* If you wish to participate in the contest, please follow the three steps below:
**1. Create a wiki page for your tutorial
**2. Upload your slides and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestSummer2010.pdf' and 'TutorialData_TutorialContestSummer2010.zip'
**3. Add a link to the uploaded tutorial and datasets on your tutorial page.
**4. Add a link to your tutorial page in the list below.

= List of submitted tutorials=

[[Slicer3:Fiducials_TutorialContestSummer2010 | Fiducials]]

[[Slicer3:RSS_TutorialContestSummer2010 | RSS (Robust Statistics Segmenter)]]

[[Slicer3:RSS_TutorialContestSummer2010 | Automatic SPHARM Shape Analysis in 3D Slicer]]

2010 Summer Project Week

2010-06-03T18:25:10Z

Chamel69: /* Analysis */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*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.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanesz)
**3-4pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, ?)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo)

=== IGT ===
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, will, Schroeder, Nicole, Ron)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/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 17, 2010: 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. XNAT/MIDAS). 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

#Aucoin, Nicole, BWH
#Audette, Michel, Kitware
#Aylward, Stephen, Kitware, Inc
#Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories
#Bouix, Sylvain, BWH
#Budin, Francois, UNC
#Burdette, Everette, Acoustic MedSystems, Inc.
#Chen, Min, Johns Hopkins University
#Datar, Manasi, SCI Institute
#Eckbo, Ryan, BWH
#Fedorov, Andriy, Surgical Planning Lab
#Fillion-Robin, Jean-Christophe, Kitware Inc.
#Finet, Julien, Kitware Inc
#Fishbaugh, James, SCI Institute
#Gao, Yi, Gerogia Tech
#GELAS, Arnaud, Harvard Medical School
#gouaillard, alexandre, CoSMo Software
#Gouttard, Sylvain, SCI Institute
#Haehn, Daniel, University of Pennsylvania
#Hageman, Nathan
#Hahn, Dieter, University Erlangen
#Hamel, Corentin, UNC Chapel Hill
#Hata, Nobuhiko, Brigham and Women's Hospital
#Hayes, Kathryn, Brigham and Women's Hospital
#Holton, Leslie, Medtronic Navigation
#Ibanez, Luis, KITWARE Inc.
#Johnson, Hans, University of Iowa
#Kapur, Tina, Brigham and Women's Hospital
#Kikinis, Ron, Brigham and Women's Hospital
#Kim, Minjeong, UNC-Chapel Hill
#Kolesov, Ivan, Georgia Institute of Technology
#Larson, Garrett, UNC-CH
#Li, Rui, MGH
#Lisle, Curtis, KnowledgeVis, LLC
#Liu, Haiying, Brigham and Women's Hospital
#Liu, Yanling, SAIC-Frederick, Inc.
#Magnotta, Vincent, The University of Iowa
#malaterre, mathieu, CoSMo Software
#Mastrogiacomo, Katie, Brigham and Women's Hospital
#Matsui, Joy, University
#Megason, Sean, Harvard Medical School
#Meier, Dominik, BWH, Boston MA
#menze, bjoern, CSAIL MIT
#Mosaliganti, Kishore, Harvard Medical School
#Niethammer, Marc, UNC Chapel Hill
#Norton, Isaiah, BWH Neurosurgery
#Paniagua, Beatriz, University of North Caolina at Chapel Hill
#Papademetris, Xenophon, Yale University
#Partyka, David, Kitware Inc
#Pathak, Sudhir, Univeristy Of Pittsburgh
#Peroni, Marta, Politecnico di Milano
#Perrot-Audet, Antonin, Harvard Medical School
#Pieper, Steve, Isomics, Inc.
#Plesniak, Wendy, BWH
#Pohl, Kilian, IBM
#Pujol, Sonia, Brigham and Women's Hospital
#Rannou, Nicolas, Harvard Medical School
#Riklin Raviv, Tammy, MIT, CSAIL
#Ruiz, Marco, UCSD
#Schroeder, William, Kitware
#Scully, Mark, The Mind Research Network
#Sharp, Greg, MGH
#Shi, Yundi, UNC Chapel Hill
#Shusharina, Nadya, MGH
#Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)
#Souhait, Lydie, Harvard Medical School
#Spinczyk, Dominik, Silesian University of Technology
#Srinivasan, Padmapriya
#Tao, Xiaodong, GE Research
#Ungi, Tamas, Queen's University
#Vachet, Clement, UNC Chapel Hill
#Veni, Gopalkrishna, SCI Institute
#Wassermann, Demian, SPL/LMI/PNL
#Wells, Sandy, BWH
#Wu, Guorong, University of North Carolina at Chapel Hill

2010 WinterProject Week XNATUseforPopulationAnalysis

2010-01-08T17:24:28Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Corentin Hamel, Martin Styner, Clement Vachet
* Dan Marcus, Tim Olsen, John Paulett, Wendy Plesniak, Julien Jomier

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing a Slicer module for population analysis. The module will take as an input a file with all the files needed for the population analysis.
Actually all the files will be download with FetchMI from XNAT.

</div>

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

<h3>Approach, Plan</h3>

Our approach for the project week is to first try out to download not only A MRML scene but any file we need. Then retrieve this files and send them to another module for processing.

</div>

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

<h3>Progress</h3>
We had two meetings this week with people from XNAT and BatchMake who help us define a new approach to perform population analysis. A slicer Qt widget will be create to select some data from XNAT. After that BatchMake will use an xcat file as an input and to dowload the related datas and perform the shape analysis problem.

</div>
</div>

<div style="width: 97%; float: left;">

==References==
<div>
[http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies]

</div>

2010 WinterProject Week XNATUseforPopulationAnalysis

2010-01-08T17:23:55Z

Chamel69:

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Corentin Hamel, Martin Styner, Clement Vachet
* Dan Marcus, Tim Olsen, John Paulett, Wendy Plesniak, Julien Jomier

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing a Slicer module for population analysis. The module will take as an input a file with all the files needed for the population analysis.
Actually all the files will be download with FetchMI from XNAT.

</div>

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

<h3>Approach, Plan</h3>

Our approach for the project week is to first try out to download not only A MRML scene but any file we need. Then retrieve this files and send them to another module for processing.

</div>

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

<h3>Progress</h3>
We had two meetings this week with people from XNAT and BatchMake which help us define a new approach to perform population analysis. A slicer Qt widget will be create to select some data from XNAT. After that BatchMake will use an xcat file as an input and to dowload the related datas and perform the shape analysis problem.

</div>
</div>

<div style="width: 97%; float: left;">

==References==
<div>
[http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies]

</div>

2010 WinterProject Week XNATUseforPopulationAnalysis

2009-12-15T20:26:43Z

Chamel69: /* Key Investigators */

2010 WinterProject Week XNATUseforPopulationAnalysis

2009-12-15T20:25:32Z

Chamel69: /* Key Investigators */

2010 WinterProject Week XNATUseforPopulationAnalysis

2009-12-15T20:25:14Z

Chamel69: /* Key Investigators */

2010 WinterProject Week XNATUseforPopulationAnalysis

2009-12-15T20:24:55Z

Chamel69: /* Key Investigators */

2010 WinterProject Week XNATUseforPopulationAnalysis

2009-12-15T20:24:38Z

Chamel69: