https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=MelanieGrebeNAMIC Wiki - User contributions [en]2026-04-08T04:57:06ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=File:SlicerImage_lut_1.jpg&diff=39646File:SlicerImage lut 1.jpg2009-06-25T13:55:55Z<p>MelanieGrebe: </p>
<hr />
<div>Volume Rendering in Slicer using XIP</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39645Plug-In 3D Viewer based on XIP2009-06-25T13:55:24Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:Xipexample.jpg|[http://openxip.org/ XIP: eXtensible Imaging Platform]<br />
Image:SlicerImage_lut_1.jpg|Volume Rendering in Slicer using XIP<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39644Plug-In 3D Viewer based on XIP2009-06-25T13:53:30Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:Xipexample.jpg|XIP: eXtensible Imaging Platform<br />
Image:SlicerImage_lut_1.jpg|Volume Rendering in Slicer using XIP Open Inventor<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39643Plug-In 3D Viewer based on XIP2009-06-25T13:51:56Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:Xipexample.jpg|[[XIP: eXtensible Imaging Platform]]<br />
Image:SlicerImage_lut_1.jpg|[[Volume Rendering in Slicer using XIP Open Inventor|Volume Rendering in Slicer using XIP Open Inventor]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39642Plug-In 3D Viewer based on XIP2009-06-25T13:49:32Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:Xipexample.jpg|[[XIP eXtensible Imaging Platform|XIP: eXtensible Imaging Platform]]<br />
Image:SlicerImage_lut_1.jpg|[[Volume Rendering in Slicer using XIP Open Inventor|Volume Rendering in Slicer using XIP Open Inventor]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39640Plug-In 3D Viewer based on XIP2009-06-25T13:48:27Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:Xipexample.jpg|[[XIP eXtensible Imaging Platform|eXtensible Imaging Platform]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39639Plug-In 3D Viewer based on XIP2009-06-25T13:47:45Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:xipexample.jpg|[[XIP eXtensible Imaging Platform|eXtensible Imaging Platform]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=File:Xipexample.jpg&diff=39638File:Xipexample.jpg2009-06-25T13:45:56Z<p>MelanieGrebe: XIP - eXtensible Imaging Platform</p>
<hr />
<div>XIP - eXtensible Imaging Platform</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=File:SlicerImage_lut_1.jpg&diff=39637File:SlicerImage lut 1.jpg2009-06-25T13:45:09Z<p>MelanieGrebe: Volume Rendering in Slicer using XIP Open Inventor</p>
<hr />
<div>Volume Rendering in Slicer using XIP Open Inventor</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39636Plug-In 3D Viewer based on XIP2009-06-25T13:41:14Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39635Plug-In 3D Viewer based on XIP2009-06-25T13:41:02Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:SlicerImage_lut_1.jpg|[[]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=39634Plug-In 3D Viewer based on XIP2009-06-25T13:26:56Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
* Steve Pieper<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We implemented a prototype that directly embedded the XIP in the existing Volume Rendering Module of the 3D Slicer where we take the output volume and other parameters from Slicer/VTK and use them to build and render an XIP scenegraph using XIP's volume rendering nodes. <br />
<br />
Future work:<br />
During the week we talked to Ron, Steve, Jim and many others to explore other ways of integrating the XIP and 3D Slicer. Among them are: (1) Uses the socket connection / Slicer Daemon to establish a host/plug-in architecture where we can leverage the strength of both the XIP/slicer world. One example is that XIP serves as a Dicom explorer host and slicer as a post-processing plugin. (2) Uses XIP to help the users to further process / perform visual programming of for example the slicer command line module results.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=User:MelanieGrebe&diff=38338User:MelanieGrebe2009-06-08T17:27:19Z<p>MelanieGrebe: </p>
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<div><div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
Melanie Grebe<br /> <br />
Siemens Corporate Research<br />
</div> <br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=User:MelanieGrebe&diff=38337User:MelanieGrebe2009-06-08T17:26:18Z<p>MelanieGrebe: Replaced content with 'Melanie Grebe
Siemens Corporate Research'</p>
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<div>Melanie Grebe<br />
Siemens Corporate Research</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=38336Plug-In 3D Viewer based on XIP2009-06-08T17:18:38Z<p>MelanieGrebe: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach and Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
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<div style="width: 40%; float: left;"><br />
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<h3>Our Progress</h3><br />
We will bring a rough prototype and resolve pending issues during Project Week.<br />
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</div><br />
</div><br />
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<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=38335Plug-In 3D Viewer based on XIP2009-06-08T17:18:10Z<p>MelanieGrebe: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Siemens Corporate Research: Lining Yang, Melanie Grebe<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
Our objective is to create a new 3D Slicer Plug-in based on NCI's eXtensible Imaging Platform (XIP), which can then be used as a starting point for future projects involving NA-MIC and caBIG.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach, Plan</h3><br />
<br />
We will implement a Host/Plug-in interface API that leverages the use of XIP modules (based on Open Inventor), and as a first example we will implement a simple 3D Viewer that can load and display DICOM data and visualize/navigate it using 3 synchronized MPR windows and a 3D volume rendering window, with the ability to render fused MR brain data.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
We will bring a rough prototype and resolve pending issues during Project Week.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 2009 Winter project week]<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=PlugIn3DViewerBasedOnXIP&diff=38334PlugIn3DViewerBasedOnXIP2009-06-08T17:10:13Z<p>MelanieGrebe: Blanked the page</p>
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<div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-In_3D_Viewer_based_on_XIP&diff=38330Plug-In 3D Viewer based on XIP2009-06-08T16:26:37Z<p>MelanieGrebe: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus ...'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig<br />
* Utah: Tom Fletcher, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.<br />
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<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
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<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
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<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=383292009 Summer Project Week2009-06-08T16:26:09Z<p>MelanieGrebe: /* NA-MIC Engineering Projects */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW2009-v3.png|300px]]<br />
<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
<br />
<br />
==Introduction to the FIRST JOINT PROJECT WEEK==<br />
<br />
We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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. <br />
<br />
Active preparation will begin on''' Thursday, April 16th 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. <br />
<br />
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.<br />
<br />
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. <br />
<br />
A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br />
<br />
== Agenda==<br />
* Monday <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 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]) <br />
** 3:30-5:30pm Start project work<br />
* Tuesday <br />
** 8:30am breakfast<br />
**9:30-10am: NA-MIC Kit Overview (Jim Miller)<br />
** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br />
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br />
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br />
** noon lunch<br />
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)<br />
** 5:30pm adjourn for day<br />
* Wednesday <br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br />
** 5:30pm adjourn for day<br />
* Thursday<br />
** 8:30am breakfast<br />
** 9-11pm Tutorial Contest Presentations<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)<br />
** 5:30pm adjourn for day<br />
* Friday <br />
** 8:30am breakfast<br />
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br />
<br />
== Projects ==<br />
<br />
The list of projects for this week will go here.<br />
=== Collaboration Projects ===<br />
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]<br />
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)<br />
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)]]<br />
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)<br />
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)<br />
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)<br />
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?<br />
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)<br />
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)<br />
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]<br />
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)<br />
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)<br />
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)<br />
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)<br />
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)<br />
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)<br />
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)<br />
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)<br />
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)<br />
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)<br />
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)<br />
<br />
===IGT Projects:===<br />
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)<br />
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)<br />
#integration of stereo video into Slicer (Mehdi)<br />
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br />
#neuroendoscope workflow presentation (sebastien barre)<br />
#breakout session on Dynamic Patient Models (James Balter)<br />
<br />
===NA-MIC Engineering Projects===<br />
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)<br />
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)<br />
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)<br />
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)<br />
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)<br />
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)<br />
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)<br />
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)<br />
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)<br />
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)<br />
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)<br />
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)<br />
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)<br />
<br />
===CUDA Projects===<br />
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)<br />
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# Join the kickoff TCON on April 16, 3pm ET.<br />
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br />
# By 3pm ET on June 11, 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.<br />
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## 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)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## 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)<br />
# 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...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
==Attendee List==<br />
If you plan to attend, please add your name here.<br />
<br />
#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)<br />
#Ferenc Jolesz, BWH (NCIGT, NAC)<br />
#Clare Tempany, BWH (NCIGT)<br />
#Tina Kapur, BWH (NA-MIC, NCIGT)<br />
#Steve Pieper, Isomics Inc<br />
#Jim Miller, GE Research<br />
#Xiaodong Tao, GE Research<br />
#Randy Gollub, MGH<br />
#Nicole Aucoin, BWH (NA-MIC)<br />
#Dan Marcus, WUSTL<br />
#Junichi Tokuda, BWH (NCIGT)<br />
#Alex Gouaillard, Harvard Systems Biology<br />
#Arnaud Gelas, Harvard Systems Biology <br />
#Kishore Mosanliganti, Harvard Systems Biology<br />
#Lydie Souhait, Harvard Systems Biology<br />
#Luis Ibanez, Kitware Inc<br />
#Vincent Magnotta, UIowa<br />
#Hans Johnson, UIowa<br />
#Xenios Papademetris, Yale<br />
#Gregory S. Fischer, WPI (Mon, Tue, Wed)<br />
#Daniel Blezek, Mayo (Tue-Fri)<br />
#Danielle Pace, Robarts Research Institute / UWO<br />
#Clement Vachet, UNC-Chapel Hill<br />
#Dave Welch, UIowa<br />
#Demian Wassermann, Odyssée lab, INRIA, France<br />
#Manasi Ramachandran, UIowa<br />
#Greg Sharp, MGH<br />
#Rui Li, MGH<br />
#Mehdi Esteghamatian, Robarts Research Institute / UWO<br />
#Misha Milchenko, WUSTL<br />
#Kevin Archie, WUSTL<br />
#Tim Olsen, WUSTL<br />
#Wendy Plesniak BWH (NAC)<br />
#Haiying Liu BWH (NCIGT)<br />
#Curtis Lisle, KnowledgeVis / Isomics<br />
#Diego Cantor, Robarts Research Institute / UWO<br />
#Daniel Haehn, BWH<br />
#Nicolas Rannou, BWH<br />
#Sylvain Jaume, MIT<br />
#Alex Yarmarkovich, Isomics<br />
#Marco Ruiz, UCSD<br />
#Andriy Fedorov, BWH (NA-MIC)<br />
#Harish Doddi, Stanford University<br />
#Saikat Pal, Stanford University<br />
#Scott Hoge, BWH (NCIGT)<br />
#Vandana Mohan, Georgia Tech<br />
#Ivan Kolosev, Georgia Tech<br />
#Behnood Gholami, Georgia Tech<br />
#James Balter, U Michigan<br />
#Dan McShan, U Michigan<br />
#Zhou Shen, U Michigan<br />
#Maria Francesca Spadea, Italy<br />
#Lining Yang, Siemens Corporate Research<br />
#Beatriz Paniagua, UNC-Chapel Hill<br />
#Bennett Landman, Johns Hopkins University <br />
#Snehashis Roy, Johns Hopkins University<br />
#Marta Peroni, Politecnico di Milano<br />
#Sebastien Barre, Kitware, Inc.<br />
#Samuel Gerber, SCI University of Utah<br />
#Ran Tao, SCI University of Utah<br />
#Marcel Prastawa, SCI University of Utah<br />
#Katie Hayes, BWH (NA-MIC)<br />
#Sonia Pujol, BWH (NA-MIC)<br />
#Andras Lasso, Queen's University<br />
#Yong Gao, MGH<br />
#Minjeong Kim, UNC-Chapel Hill<br />
#Guorong Wu, UNC-Chapel Hill<br />
#Jeffrey Yager, UIowa<br />
#Yanling Liu, SAIC/NCI-Frederick<br />
#Ziv Yaniv, Georgetown<br />
#Bjoern Menze, MIT<br />
#Vidya Rajagopalan, Virginia Tech<br />
#Sandy Wells, BWH (NAC, NCIGT)<br />
#Lilla Zollei, MGH (NAC)<br />
#Lauren O'Donnell, BWH<br />
#Florin Talos, BWH (NAC)<br />
#Nobuhiko Hata, BWH (NCIGT)<br />
#Alark Joshi, Yale<br />
#Yogesh Rathi, BWH<br />
#Jimi Malcolm, BWH<br />
#Dustin Scheinost, Yale<br />
#Dominique Belhachemi, Yale<br />
#Sam Song, JHU<br />
#Nathan Cho, JHU<br />
#Julien de Siebenthal, BWH<br />
#Peter Savadjiev, BWH<br />
#Carl-Fredrik Westin, BWH<br />
#John Melonakos, AccelerEyes (Wed & Thu morning)<br />
#Yi Gao, Georgia Tech<br />
#Sylvain Bouix, BWH<br />
#Zhexing Liu, UNC-CH<br />
#Eric Melonakos, BWH<br />
#Lei Qin, BWH<br />
#Giovanna Danagoulian, BWH<br />
#Andrew Rausch, BWH (1st day only)<br />
#Haytham Elhawary, BWH<br />
#Jayender Jagadeesan, BWH<br />
#Marek Kubicki, BWH<br />
#Doug Terry, BWH<br />
#Nathan Hageman, LONI (UCLA)<br />
#Dana Peters, Beth Israel Deaconess<br />
#Sun Woo Lee, BWH<br />
# Melanie Grebe, Siemens Corporate Research<br />
# Megumi Nakao, BWH/NAIST<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br />
*'''Registration Method''' Add your name to the Attendee List section of this page<br />
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br />
*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.<br />
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br />
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=383282009 Summer Project Week2009-06-08T16:24:56Z<p>MelanieGrebe: /* NA-MIC Engineering Projects */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW2009-v3.png|300px]]<br />
<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
<br />
<br />
==Introduction to the FIRST JOINT PROJECT WEEK==<br />
<br />
We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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. <br />
<br />
Active preparation will begin on''' Thursday, April 16th 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. <br />
<br />
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.<br />
<br />
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. <br />
<br />
A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br />
<br />
== Agenda==<br />
* Monday <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 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]) <br />
** 3:30-5:30pm Start project work<br />
* Tuesday <br />
** 8:30am breakfast<br />
**9:30-10am: NA-MIC Kit Overview (Jim Miller)<br />
** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br />
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br />
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br />
** noon lunch<br />
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)<br />
** 5:30pm adjourn for day<br />
* Wednesday <br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br />
** 5:30pm adjourn for day<br />
* Thursday<br />
** 8:30am breakfast<br />
** 9-11pm Tutorial Contest Presentations<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)<br />
** 5:30pm adjourn for day<br />
* Friday <br />
** 8:30am breakfast<br />
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br />
<br />
== Projects ==<br />
<br />
The list of projects for this week will go here.<br />
=== Collaboration Projects ===<br />
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]<br />
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)<br />
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)]]<br />
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)<br />
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)<br />
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)<br />
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?<br />
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)<br />
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)<br />
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]<br />
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)<br />
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)<br />
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)<br />
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)<br />
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)<br />
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)<br />
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)<br />
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)<br />
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)<br />
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)<br />
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)<br />
<br />
===IGT Projects:===<br />
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)<br />
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)<br />
#integration of stereo video into Slicer (Mehdi)<br />
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br />
#neuroendoscope workflow presentation (sebastien barre)<br />
#breakout session on Dynamic Patient Models (James Balter)<br />
<br />
===NA-MIC Engineering Projects===<br />
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)<br />
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)<br />
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)<br />
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)<br />
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)<br />
# [[PlugIn3DViewerBasedOnXIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)<br />
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)<br />
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)<br />
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)<br />
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)<br />
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)<br />
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)<br />
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)<br />
<br />
===CUDA Projects===<br />
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)<br />
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# Join the kickoff TCON on April 16, 3pm ET.<br />
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br />
# By 3pm ET on June 11, 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.<br />
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## 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)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## 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)<br />
# 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...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
==Attendee List==<br />
If you plan to attend, please add your name here.<br />
<br />
#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)<br />
#Ferenc Jolesz, BWH (NCIGT, NAC)<br />
#Clare Tempany, BWH (NCIGT)<br />
#Tina Kapur, BWH (NA-MIC, NCIGT)<br />
#Steve Pieper, Isomics Inc<br />
#Jim Miller, GE Research<br />
#Xiaodong Tao, GE Research<br />
#Randy Gollub, MGH<br />
#Nicole Aucoin, BWH (NA-MIC)<br />
#Dan Marcus, WUSTL<br />
#Junichi Tokuda, BWH (NCIGT)<br />
#Alex Gouaillard, Harvard Systems Biology<br />
#Arnaud Gelas, Harvard Systems Biology <br />
#Kishore Mosanliganti, Harvard Systems Biology<br />
#Lydie Souhait, Harvard Systems Biology<br />
#Luis Ibanez, Kitware Inc<br />
#Vincent Magnotta, UIowa<br />
#Hans Johnson, UIowa<br />
#Xenios Papademetris, Yale<br />
#Gregory S. Fischer, WPI (Mon, Tue, Wed)<br />
#Daniel Blezek, Mayo (Tue-Fri)<br />
#Danielle Pace, Robarts Research Institute / UWO<br />
#Clement Vachet, UNC-Chapel Hill<br />
#Dave Welch, UIowa<br />
#Demian Wassermann, Odyssée lab, INRIA, France<br />
#Manasi Ramachandran, UIowa<br />
#Greg Sharp, MGH<br />
#Rui Li, MGH<br />
#Mehdi Esteghamatian, Robarts Research Institute / UWO<br />
#Misha Milchenko, WUSTL<br />
#Kevin Archie, WUSTL<br />
#Tim Olsen, WUSTL<br />
#Wendy Plesniak BWH (NAC)<br />
#Haiying Liu BWH (NCIGT)<br />
#Curtis Lisle, KnowledgeVis / Isomics<br />
#Diego Cantor, Robarts Research Institute / UWO<br />
#Daniel Haehn, BWH<br />
#Nicolas Rannou, BWH<br />
#Sylvain Jaume, MIT<br />
#Alex Yarmarkovich, Isomics<br />
#Marco Ruiz, UCSD<br />
#Andriy Fedorov, BWH (NA-MIC)<br />
#Harish Doddi, Stanford University<br />
#Saikat Pal, Stanford University<br />
#Scott Hoge, BWH (NCIGT)<br />
#Vandana Mohan, Georgia Tech<br />
#Ivan Kolosev, Georgia Tech<br />
#Behnood Gholami, Georgia Tech<br />
#James Balter, U Michigan<br />
#Dan McShan, U Michigan<br />
#Zhou Shen, U Michigan<br />
#Maria Francesca Spadea, Italy<br />
#Lining Yang, Siemens Corporate Research<br />
#Beatriz Paniagua, UNC-Chapel Hill<br />
#Bennett Landman, Johns Hopkins University <br />
#Snehashis Roy, Johns Hopkins University<br />
#Marta Peroni, Politecnico di Milano<br />
#Sebastien Barre, Kitware, Inc.<br />
#Samuel Gerber, SCI University of Utah<br />
#Ran Tao, SCI University of Utah<br />
#Marcel Prastawa, SCI University of Utah<br />
#Katie Hayes, BWH (NA-MIC)<br />
#Sonia Pujol, BWH (NA-MIC)<br />
#Andras Lasso, Queen's University<br />
#Yong Gao, MGH<br />
#Minjeong Kim, UNC-Chapel Hill<br />
#Guorong Wu, UNC-Chapel Hill<br />
#Jeffrey Yager, UIowa<br />
#Yanling Liu, SAIC/NCI-Frederick<br />
#Ziv Yaniv, Georgetown<br />
#Bjoern Menze, MIT<br />
#Vidya Rajagopalan, Virginia Tech<br />
#Sandy Wells, BWH (NAC, NCIGT)<br />
#Lilla Zollei, MGH (NAC)<br />
#Lauren O'Donnell, BWH<br />
#Florin Talos, BWH (NAC)<br />
#Nobuhiko Hata, BWH (NCIGT)<br />
#Alark Joshi, Yale<br />
#Yogesh Rathi, BWH<br />
#Jimi Malcolm, BWH<br />
#Dustin Scheinost, Yale<br />
#Dominique Belhachemi, Yale<br />
#Sam Song, JHU<br />
#Nathan Cho, JHU<br />
#Julien de Siebenthal, BWH<br />
#Peter Savadjiev, BWH<br />
#Carl-Fredrik Westin, BWH<br />
#John Melonakos, AccelerEyes (Wed & Thu morning)<br />
#Yi Gao, Georgia Tech<br />
#Sylvain Bouix, BWH<br />
#Zhexing Liu, UNC-CH<br />
#Eric Melonakos, BWH<br />
#Lei Qin, BWH<br />
#Giovanna Danagoulian, BWH<br />
#Andrew Rausch, BWH (1st day only)<br />
#Haytham Elhawary, BWH<br />
#Jayender Jagadeesan, BWH<br />
#Marek Kubicki, BWH<br />
#Doug Terry, BWH<br />
#Nathan Hageman, LONI (UCLA)<br />
#Dana Peters, Beth Israel Deaconess<br />
#Sun Woo Lee, BWH<br />
# Melanie Grebe, Siemens Corporate Research<br />
# Megumi Nakao, BWH/NAIST<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br />
*'''Registration Method''' Add your name to the Attendee List section of this page<br />
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br />
*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.<br />
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br />
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=User:MelanieGrebe&diff=38324User:MelanieGrebe2009-06-08T16:19:31Z<p>MelanieGrebe: moved Plug-in 3D Viewer based on XIP to User:MelanieGrebe over redirect</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig<br />
* Utah: Tom Fletcher, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.<br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Plug-in_3D_Viewer_based_on_XIP&diff=38325Plug-in 3D Viewer based on XIP2009-06-08T16:19:31Z<p>MelanieGrebe: moved Plug-in 3D Viewer based on XIP to User:MelanieGrebe over redirect</p>
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<div>#REDIRECT [[User:MelanieGrebe]]</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=User_talk:MelanieGrebe&diff=38326User talk:MelanieGrebe2009-06-08T16:19:31Z<p>MelanieGrebe: moved Talk:Plug-in 3D Viewer based on XIP to User talk:MelanieGrebe over redirect</p>
<hr />
<div>'''Welcome to ''NAMIC''!'''<br />
We hope you will contribute much and well. <br />
You will probably want to read the [[Help:Contents|help pages]].<br />
Again, welcome and have fun! [[User:Zack|Zack]] 15:55, 8 June 2009 (UTC)</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=Talk:Plug-in_3D_Viewer_based_on_XIP&diff=38327Talk:Plug-in 3D Viewer based on XIP2009-06-08T16:19:31Z<p>MelanieGrebe: moved Talk:Plug-in 3D Viewer based on XIP to User talk:MelanieGrebe over redirect</p>
<hr />
<div>#REDIRECT [[User talk:MelanieGrebe]]</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=PlugIn3DViewerBasedOnXIP&diff=38323PlugIn3DViewerBasedOnXIP2009-06-08T16:18:11Z<p>MelanieGrebe: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus ...'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig<br />
* Utah: Tom Fletcher, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.<br />
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<br />
<br />
<br />
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<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
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<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=383222009 Summer Project Week2009-06-08T16:16:49Z<p>MelanieGrebe: </p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
<br />
[[Image:PW2009-v3.png|300px]]<br />
<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
<br />
<br />
==Introduction to the FIRST JOINT PROJECT WEEK==<br />
<br />
We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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. <br />
<br />
Active preparation will begin on''' Thursday, April 16th 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. <br />
<br />
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.<br />
<br />
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. <br />
<br />
A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br />
<br />
== Agenda==<br />
* Monday <br />
** noon-1pm lunch <br />
**1pm: Welcome (Ron Kikinis)<br />
** 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]) <br />
** 3:30-5:30pm Start project work<br />
* Tuesday <br />
** 8:30am breakfast<br />
**9:30-10am: NA-MIC Kit Overview (Jim Miller)<br />
** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br />
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br />
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br />
** noon lunch<br />
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)<br />
** 5:30pm adjourn for day<br />
* Wednesday <br />
** 8:30am breakfast<br />
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br />
** 5:30pm adjourn for day<br />
* Thursday<br />
** 8:30am breakfast<br />
** 9-11pm Tutorial Contest Presentations<br />
** noon lunch<br />
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)<br />
** 5:30pm adjourn for day<br />
* Friday <br />
** 8:30am breakfast<br />
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br />
*** Noon: Lunch boxes and adjourn by 1:30pm.<br />
***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br />
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br />
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br />
<br />
== Projects ==<br />
<br />
The list of projects for this week will go here.<br />
=== Collaboration Projects ===<br />
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]<br />
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)<br />
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)]]<br />
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)<br />
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)<br />
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)<br />
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?<br />
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)<br />
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)<br />
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]<br />
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]<br />
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)<br />
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)<br />
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)<br />
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)<br />
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)<br />
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)<br />
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)<br />
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)<br />
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)<br />
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)<br />
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)<br />
<br />
===IGT Projects:===<br />
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)<br />
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)<br />
#integration of stereo video into Slicer (Mehdi)<br />
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br />
#neuroendoscope workflow presentation (sebastien barre)<br />
#breakout session on Dynamic Patient Models (James Balter)<br />
<br />
===NA-MIC Engineering Projects===<br />
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)<br />
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)<br />
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)<br />
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)<br />
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)<br />
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)<br />
# [[PlugIn3DViewerBasedOnXIP | Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)<br />
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)<br />
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)<br />
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)<br />
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)<br />
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)<br />
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)<br />
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)<br />
<br />
===CUDA Projects===<br />
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)<br />
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# Join the kickoff TCON on April 16, 3pm ET.<br />
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br />
# By 3pm ET on June 11, 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.<br />
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## 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)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## 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)<br />
# 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...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
==Attendee List==<br />
If you plan to attend, please add your name here.<br />
<br />
#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)<br />
#Ferenc Jolesz, BWH (NCIGT, NAC)<br />
#Clare Tempany, BWH (NCIGT)<br />
#Tina Kapur, BWH (NA-MIC, NCIGT)<br />
#Steve Pieper, Isomics Inc<br />
#Jim Miller, GE Research<br />
#Xiaodong Tao, GE Research<br />
#Randy Gollub, MGH<br />
#Nicole Aucoin, BWH (NA-MIC)<br />
#Dan Marcus, WUSTL<br />
#Junichi Tokuda, BWH (NCIGT)<br />
#Alex Gouaillard, Harvard Systems Biology<br />
#Arnaud Gelas, Harvard Systems Biology <br />
#Kishore Mosanliganti, Harvard Systems Biology<br />
#Lydie Souhait, Harvard Systems Biology<br />
#Luis Ibanez, Kitware Inc<br />
#Vincent Magnotta, UIowa<br />
#Hans Johnson, UIowa<br />
#Xenios Papademetris, Yale<br />
#Gregory S. Fischer, WPI (Mon, Tue, Wed)<br />
#Daniel Blezek, Mayo (Tue-Fri)<br />
#Danielle Pace, Robarts Research Institute / UWO<br />
#Clement Vachet, UNC-Chapel Hill<br />
#Dave Welch, UIowa<br />
#Demian Wassermann, Odyssée lab, INRIA, France<br />
#Manasi Ramachandran, UIowa<br />
#Greg Sharp, MGH<br />
#Rui Li, MGH<br />
#Mehdi Esteghamatian, Robarts Research Institute / UWO<br />
#Misha Milchenko, WUSTL<br />
#Kevin Archie, WUSTL<br />
#Tim Olsen, WUSTL<br />
#Wendy Plesniak BWH (NAC)<br />
#Haiying Liu BWH (NCIGT)<br />
#Curtis Lisle, KnowledgeVis / Isomics<br />
#Diego Cantor, Robarts Research Institute / UWO<br />
#Daniel Haehn, BWH<br />
#Nicolas Rannou, BWH<br />
#Sylvain Jaume, MIT<br />
#Alex Yarmarkovich, Isomics<br />
#Marco Ruiz, UCSD<br />
#Andriy Fedorov, BWH (NA-MIC)<br />
#Harish Doddi, Stanford University<br />
#Saikat Pal, Stanford University<br />
#Scott Hoge, BWH (NCIGT)<br />
#Vandana Mohan, Georgia Tech<br />
#Ivan Kolosev, Georgia Tech<br />
#Behnood Gholami, Georgia Tech<br />
#James Balter, U Michigan<br />
#Dan McShan, U Michigan<br />
#Zhou Shen, U Michigan<br />
#Maria Francesca Spadea, Italy<br />
#Lining Yang, Siemens Corporate Research<br />
#Beatriz Paniagua, UNC-Chapel Hill<br />
#Bennett Landman, Johns Hopkins University <br />
#Snehashis Roy, Johns Hopkins University<br />
#Marta Peroni, Politecnico di Milano<br />
#Sebastien Barre, Kitware, Inc.<br />
#Samuel Gerber, SCI University of Utah<br />
#Ran Tao, SCI University of Utah<br />
#Marcel Prastawa, SCI University of Utah<br />
#Katie Hayes, BWH (NA-MIC)<br />
#Sonia Pujol, BWH (NA-MIC)<br />
#Andras Lasso, Queen's University<br />
#Yong Gao, MGH<br />
#Minjeong Kim, UNC-Chapel Hill<br />
#Guorong Wu, UNC-Chapel Hill<br />
#Jeffrey Yager, UIowa<br />
#Yanling Liu, SAIC/NCI-Frederick<br />
#Ziv Yaniv, Georgetown<br />
#Bjoern Menze, MIT<br />
#Vidya Rajagopalan, Virginia Tech<br />
#Sandy Wells, BWH (NAC, NCIGT)<br />
#Lilla Zollei, MGH (NAC)<br />
#Lauren O'Donnell, BWH<br />
#Florin Talos, BWH (NAC)<br />
#Nobuhiko Hata, BWH (NCIGT)<br />
#Alark Joshi, Yale<br />
#Yogesh Rathi, BWH<br />
#Jimi Malcolm, BWH<br />
#Dustin Scheinost, Yale<br />
#Dominique Belhachemi, Yale<br />
#Sam Song, JHU<br />
#Nathan Cho, JHU<br />
#Julien de Siebenthal, BWH<br />
#Peter Savadjiev, BWH<br />
#Carl-Fredrik Westin, BWH<br />
#John Melonakos, AccelerEyes (Wed & Thu morning)<br />
#Yi Gao, Georgia Tech<br />
#Sylvain Bouix, BWH<br />
#Zhexing Liu, UNC-CH<br />
#Eric Melonakos, BWH<br />
#Lei Qin, BWH<br />
#Giovanna Danagoulian, BWH<br />
#Andrew Rausch, BWH (1st day only)<br />
#Haytham Elhawary, BWH<br />
#Jayender Jagadeesan, BWH<br />
#Marek Kubicki, BWH<br />
#Doug Terry, BWH<br />
#Nathan Hageman, LONI (UCLA)<br />
#Dana Peters, Beth Israel Deaconess<br />
#Sun Woo Lee, BWH<br />
# Melanie Grebe, Siemens Corporate Research<br />
# Megumi Nakao, BWH/NAIST<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 22-26, 2009<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br />
*'''Registration Method''' Add your name to the Attendee List section of this page<br />
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br />
*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.<br />
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br />
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=User:MelanieGrebe&diff=38318User:MelanieGrebe2009-06-08T16:10:32Z<p>MelanieGrebe: moved User:MelanieGrebe to Plug-in 3D Viewer based on XIP</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig<br />
* Utah: Tom Fletcher, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.<br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=User_talk:MelanieGrebe&diff=38320User talk:MelanieGrebe2009-06-08T16:10:32Z<p>MelanieGrebe: moved User talk:MelanieGrebe to Talk:Plug-in 3D Viewer based on XIP</p>
<hr />
<div>'''Welcome to ''NAMIC''!'''<br />
We hope you will contribute much and well. <br />
You will probably want to read the [[Help:Contents|help pages]].<br />
Again, welcome and have fun! [[User:Zack|Zack]] 15:55, 8 June 2009 (UTC)</div>MelanieGrebehttps://www.na-mic.org/w/index.php?title=User:MelanieGrebe&diff=38317User:MelanieGrebe2009-06-08T16:07:47Z<p>MelanieGrebe: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus ...'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig<br />
* Utah: Tom Fletcher, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Objective</h3><br />
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.<br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Our Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Our Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 970%; float: left;"><br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>MelanieGrebe