NAMIC Wiki - User contributions [en]

NAMIC Wiki:Interactive Cut

2013-02-27T18:25:41Z

Egger: /* References */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Jan Egger, Tina Kapur, BWH

Steve Pieper, Isomics

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To implement a graph-cut based interactive segmentation algorithm in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* In this project, we want to realize an interactive graph-based segmentation approach in 3D Slicer that provides real-time feedback of the segmentation result to the user during the segmentation process.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* To be filled out as we go.
</div>
</div>

==References==
#Boykov Y., Kolmogorov V. [http://www.csd.uwo.ca/~yuri/Papers/pami04.pdf An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision]. IEEE Transactions on PAMI, Vol. 26, No. 9, pp. 1124-1137, Sept. 2004.
#Schwarzenberg R. [http://wiki.na-mic.org/Wiki/images/7/7d/RobertSchwarzenberg_BachelorThesis.pdf Semi-Automatic, Graph-Based Vertebra Segmentation in MRI Data]. Bachelor Thesis, Department of Mathematics and Computer Science, University of Marburg, Germany, pp. 1-68, 2012.

=== Publications Describing the Algorithms ===

#Schwarzenberg R., Freisleben B., Kikinis R., Nimsky C., Egger J. [http://link.springer.com/chapter/10.1007%2F978-3-642-36480-8_14 A Cube-Based Approach to Segment Vertebrae in MRI-Acquisitions (in German)]. Proceedings of Bildverarbeitung für die Medizin (BVM), Heidelberg, Germany, Springer, pp. 69-74, 2013.

#Egger J., Freisleben B., Nimsky C., Kapur T. [http://www.nature.com/srep/2012/120524/srep00420/full/srep00420.html Template-Cut: A Pattern-Based Segmentation Paradigm]. Nature - Scientific Reports, Nature Publishing Group (NPG), 2(420), 2012.
#Egger J., Kapur T., Dukatz T., Kolodziej M., Zukić D., Freisleben B., Nimsky C. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031064 Square-Cut: A Segmentation Algorithm on the Basis of a Rectangle Shape]. PLoS One 7(2):e31064, 2012.
#Egger J., Colen R., Freisleben B., Nimsky C. [http://www.spl.harvard.edu/publications/item/view/2169 Manual Refinement System for Graph-based Segmentation Results in the Medical Domain]. J Med Syst., 36(5):2829-39, 2012.
#Egger J., Bauer M.H.A., Kuhnt D., Carl B., Kappus C., Freisleben B., Nimsky C. [http://www.springerlink.com/content/e466543l08k3wm76/ Nugget-Cut: A Segmentation Scheme for Spherically- and Elliptically-Shaped 3D Objects]. DAGM, LNCS 6376:383-392, Springer, 2010.

=== External Libraries/Source Code ===
[http://vision.csd.uwo.ca/code/ Max-flow/min-cut]

File:RobertSchwarzenberg BachelorThesis.pdf

2013-02-27T18:17:06Z

Egger: Bachelor Thesis of Robert Schwarzenberg

Bachelor Thesis of Robert Schwarzenberg

NAMIC Wiki:Interactive Cut

2013-02-26T16:51:10Z

Egger: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Jan Egger, Tina Kapur, BWH

Steve Pieper, Isomics

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To implement a graph-cut based interactive segmentation algorithm in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* In this project, we want to realize an interactive graph-based segmentation approach in 3D Slicer that provides real-time feedback of the segmentation result to the user during the segmentation process.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* To be filled out as we go.
</div>
</div>

==References==
#Boykov Y., Kolmogorov V. [http://www.csd.uwo.ca/~yuri/Papers/pami04.pdf An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision]. IEEE Transactions on PAMI, Vol. 26, No. 9, pp. 1124-1137, Sept. 2004.

=== Publications Describing the Algorithms ===

#Schwarzenberg R., Freisleben B., Kikinis R., Nimsky C., Egger J. [http://link.springer.com/chapter/10.1007%2F978-3-642-36480-8_14 A Cube-Based Approach to Segment Vertebrae in MRI-Acquisitions (in German)]. Proceedings of Bildverarbeitung für die Medizin (BVM), Heidelberg, Germany, Springer, pp. 69-74, 2013.

#Egger J., Freisleben B., Nimsky C., Kapur T. [http://www.nature.com/srep/2012/120524/srep00420/full/srep00420.html Template-Cut: A Pattern-Based Segmentation Paradigm]. Nature - Scientific Reports, Nature Publishing Group (NPG), 2(420), 2012.
#Egger J., Kapur T., Dukatz T., Kolodziej M., Zukić D., Freisleben B., Nimsky C. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031064 Square-Cut: A Segmentation Algorithm on the Basis of a Rectangle Shape]. PLoS One 7(2):e31064, 2012.
#Egger J., Colen R., Freisleben B., Nimsky C. [http://www.spl.harvard.edu/publications/item/view/2169 Manual Refinement System for Graph-based Segmentation Results in the Medical Domain]. J Med Syst., 36(5):2829-39, 2012.
#Egger J., Bauer M.H.A., Kuhnt D., Carl B., Kappus C., Freisleben B., Nimsky C. [http://www.springerlink.com/content/e466543l08k3wm76/ Nugget-Cut: A Segmentation Scheme for Spherically- and Elliptically-Shaped 3D Objects]. DAGM, LNCS 6376:383-392, Springer, 2010.

=== External Libraries/Source Code ===
[http://vision.csd.uwo.ca/code/ Max-flow/min-cut]

NAMIC Wiki:Interactive Cut

2013-02-26T16:47:37Z

Egger: /* References */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Jan Egger, Tina Kapur, BWH

Steve Pieper, Isomics

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To implement a graph-cut based interactive segmentation algorithm in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* This is the approach. Here are the challenges.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* To be filled out as we go.
</div>
</div>

==References==
#Boykov Y., Kolmogorov V. [http://www.csd.uwo.ca/~yuri/Papers/pami04.pdf An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision]. IEEE Transactions on PAMI, Vol. 26, No. 9, pp. 1124-1137, Sept. 2004.

=== Publications Describing the Algorithms ===

#Schwarzenberg R., Freisleben B., Kikinis R., Nimsky C., Egger J. [http://link.springer.com/chapter/10.1007%2F978-3-642-36480-8_14 A Cube-Based Approach to Segment Vertebrae in MRI-Acquisitions (in German)]. Proceedings of Bildverarbeitung für die Medizin (BVM), Heidelberg, Germany, Springer, pp. 69-74, 2013.

#Egger J., Freisleben B., Nimsky C., Kapur T. [http://www.nature.com/srep/2012/120524/srep00420/full/srep00420.html Template-Cut: A Pattern-Based Segmentation Paradigm]. Nature - Scientific Reports, Nature Publishing Group (NPG), 2(420), 2012.
#Egger J., Kapur T., Dukatz T., Kolodziej M., Zukić D., Freisleben B., Nimsky C. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031064 Square-Cut: A Segmentation Algorithm on the Basis of a Rectangle Shape]. PLoS One 7(2):e31064, 2012.
#Egger J., Colen R., Freisleben B., Nimsky C. [http://www.spl.harvard.edu/publications/item/view/2169 Manual Refinement System for Graph-based Segmentation Results in the Medical Domain]. J Med Syst., 36(5):2829-39, 2012.
#Egger J., Bauer M.H.A., Kuhnt D., Carl B., Kappus C., Freisleben B., Nimsky C. [http://www.springerlink.com/content/e466543l08k3wm76/ Nugget-Cut: A Segmentation Scheme for Spherically- and Elliptically-Shaped 3D Objects]. DAGM, LNCS 6376:383-392, Springer, 2010.

=== External Libraries/Source Code ===
[http://vision.csd.uwo.ca/code/ Max-flow/min-cut]

NAMIC Wiki:Interactive Cut

2013-02-26T16:47:15Z

Egger: /* References */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Jan Egger, Tina Kapur, BWH

Steve Pieper, Isomics

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To implement a graph-cut based interactive segmentation algorithm in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* This is the approach. Here are the challenges.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* To be filled out as we go.
</div>
</div>

==References==
#Boykov Y., Kolmogorov V. [http://www.csd.uwo.ca/~yuri/Papers/pami04.pdf An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision]. IEEE Transactions on PAMI, Vol. 26, No. 9, pp. 1124-1137, Sept. 2004.

=== Publications Describing the Algorithms ===

#Schwarzenberg R., Freisleben B., Kikinis R., Nimsky C., Egger J. [http://link.springer.com/chapter/10.1007%2F978-3-642-36480-8_14 A Cube-Based Approach to Segment Vertebrae in MRI-Acquisitions (in German)]. Proceedings of Bildverarbeitung für die Medizin (BVM), Heidelberg, Germany, Springer Press, pp. 69-74, March 2013.

#Egger J., Freisleben B., Nimsky C., Kapur T. [http://www.nature.com/srep/2012/120524/srep00420/full/srep00420.html Template-Cut: A Pattern-Based Segmentation Paradigm]. Nature - Scientific Reports, Nature Publishing Group (NPG), 2(420), 2012.
#Egger J., Kapur T., Dukatz T., Kolodziej M., Zukić D., Freisleben B., Nimsky C. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031064 Square-Cut: A Segmentation Algorithm on the Basis of a Rectangle Shape]. PLoS One 7(2):e31064, 2012.
#Egger J., Colen R., Freisleben B., Nimsky C. [http://www.spl.harvard.edu/publications/item/view/2169 Manual Refinement System for Graph-based Segmentation Results in the Medical Domain]. J Med Syst., 36(5):2829-39, 2012.
#Egger J., Bauer M.H.A., Kuhnt D., Carl B., Kappus C., Freisleben B., Nimsky C. [http://www.springerlink.com/content/e466543l08k3wm76/ Nugget-Cut: A Segmentation Scheme for Spherically- and Elliptically-Shaped 3D Objects]. DAGM, LNCS 6376:383-392, Springer, 2010.

=== External Libraries/Source Code ===
[http://vision.csd.uwo.ca/code/ Max-flow/min-cut]

NAMIC Wiki:Interactive Cut

2013-02-26T16:45:01Z

Egger: /* References */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Jan Egger, Tina Kapur, BWH

Steve Pieper, Isomics

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To implement a graph-cut based interactive segmentation algorithm in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* This is the approach. Here are the challenges.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* To be filled out as we go.
</div>
</div>

==References==
#Boykov Y., Kolmogorov V. [http://www.csd.uwo.ca/~yuri/Papers/pami04.pdf An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision]. IEEE Transactions on PAMI, Vol. 26, No. 9, pp. 1124-1137, Sept. 2004.

=== Publications Describing the Algorithms ===

#Schwarzenberg R., Freisleben B., Kikinis R., Nimsky C., Egger J. [http://link.springer.com/chapter/10.1007%2F978-3-642-36480-8_14 A Cube-Based Approach to Segment Vertebrae in MRI-Acquisitions]. Proceedings of Bildverarbeitung für die Medizin (BVM), Heidelberg, Germany, Springer Press, pp. 69-74, March 2013.

#Egger J., Freisleben B., Nimsky C., Kapur T. [http://www.nature.com/srep/2012/120524/srep00420/full/srep00420.html Template-Cut: A Pattern-Based Segmentation Paradigm]. Nature - Scientific Reports, Nature Publishing Group (NPG), 2(420), 2012.
#Egger J., Kapur T., Dukatz T., Kolodziej M., Zukić D., Freisleben B., Nimsky C. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031064 Square-Cut: A Segmentation Algorithm on the Basis of a Rectangle Shape]. PLoS One 7(2):e31064, 2012.
#Egger J., Colen R., Freisleben B., Nimsky C. [http://www.spl.harvard.edu/publications/item/view/2169 Manual Refinement System for Graph-based Segmentation Results in the Medical Domain]. J Med Syst., 36(5):2829-39, 2012.
#Egger J., Bauer M.H.A., Kuhnt D., Carl B., Kappus C., Freisleben B., Nimsky C. [http://www.springerlink.com/content/e466543l08k3wm76/ Nugget-Cut: A Segmentation Scheme for Spherically- and Elliptically-Shaped 3D Objects]. DAGM, LNCS 6376:383-392, Springer, 2010.

=== External Libraries/Source Code ===
[http://vision.csd.uwo.ca/code/ Max-flow/min-cut]

NAMIC Wiki:Interactive Cut

2013-02-26T16:44:34Z

Egger: /* References */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Jan Egger, Tina Kapur, BWH

Steve Pieper, Isomics

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To implement a graph-cut based interactive segmentation algorithm in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* This is the approach. Here are the challenges.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* To be filled out as we go.
</div>
</div>

==References==
#Boykov Y., Kolmogorov V. [http://www.csd.uwo.ca/~yuri/Papers/pami04.pdf An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision]. IEEE Transactions on PAMI, Vol. 26, No. 9, pp. 1124-1137, Sept. 2004.

=== Publications Describing the Algorithms ===

#Schwarzenberg R., Freisleben B., Kikinis R., Nimsky C., Egger J. [http://link.springer.com/chapter/10.1007%2F978-3-642-36480-8_14 A Cube-Based Approach to Segment Vertebrae in MRI-Acquisitions]. In: Proceedings of Bildverarbeitung für die Medizin (BVM), Heidelberg, Germany, Springer Press, pp. 69-74, to appear, March 2013.

#Egger J., Freisleben B., Nimsky C., Kapur T. [http://www.nature.com/srep/2012/120524/srep00420/full/srep00420.html Template-Cut: A Pattern-Based Segmentation Paradigm]. Nature - Scientific Reports, Nature Publishing Group (NPG), 2(420), 2012.
#Egger J., Kapur T., Dukatz T., Kolodziej M., Zukić D., Freisleben B., Nimsky C. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031064 Square-Cut: A Segmentation Algorithm on the Basis of a Rectangle Shape]. PLoS One 7(2):e31064, 2012.
#Egger J., Colen R., Freisleben B., Nimsky C. [http://www.spl.harvard.edu/publications/item/view/2169 Manual Refinement System for Graph-based Segmentation Results in the Medical Domain]. J Med Syst., 36(5):2829-39, 2012.
#Egger J., Bauer M.H.A., Kuhnt D., Carl B., Kappus C., Freisleben B., Nimsky C. [http://www.springerlink.com/content/e466543l08k3wm76/ Nugget-Cut: A Segmentation Scheme for Spherically- and Elliptically-Shaped 3D Objects]. DAGM, LNCS 6376:383-392, Springer, 2010.

=== External Libraries/Source Code ===
[http://vision.csd.uwo.ca/code/ Max-flow/min-cut]

NAMIC Wiki:Interactive Cut

2013-02-26T16:41:34Z

Egger: /* References */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Jan Egger, Tina Kapur, BWH

Steve Pieper, Isomics

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To implement a graph-cut based interactive segmentation algorithm in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* This is the approach. Here are the challenges.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* To be filled out as we go.
</div>
</div>

==References==
#Boykov Y., Kolmogorov V. [http://www.csd.uwo.ca/~yuri/Papers/pami04.pdf An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision]. IEEE Transactions on PAMI, Vol. 26, No. 9, pp. 1124-1137, Sept. 2004.

=== Publications Describing the Algorithms ===
#Egger J., Freisleben B., Nimsky C., Kapur T. [http://www.nature.com/srep/2012/120524/srep00420/full/srep00420.html Template-Cut: A Pattern-Based Segmentation Paradigm]. Nature - Scientific Reports, Nature Publishing Group (NPG), 2(420), 2012.
#Egger J., Kapur T., Dukatz T., Kolodziej M., Zukić D., Freisleben B., Nimsky C. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031064 Square-Cut: A Segmentation Algorithm on the Basis of a Rectangle Shape]. PLoS One 7(2):e31064, 2012.
#Egger J., Colen R., Freisleben B., Nimsky C. [http://www.spl.harvard.edu/publications/item/view/2169 Manual Refinement System for Graph-based Segmentation Results in the Medical Domain]. J Med Syst., 36(5):2829-39, 2012.
#Egger J., Bauer M.H.A., Kuhnt D., Carl B., Kappus C., Freisleben B., Nimsky C. [http://www.springerlink.com/content/e466543l08k3wm76/ Nugget-Cut: A Segmentation Scheme for Spherically- and Elliptically-Shaped 3D Objects]. DAGM, LNCS 6376:383-392, Springer, 2010.

=== External Libraries/Source Code ===
[http://vision.csd.uwo.ca/code/ Max-flow/min-cut]

NAMIC Wiki:Interactive Cut

2013-02-26T16:40:33Z

Egger: /* References */

NAMIC Wiki:Interactive Cut

2013-02-26T16:38:47Z

Egger: /* References */

NAMIC Wiki:Interactive Cut

2013-02-26T16:31:31Z

Egger: /* External Libraries/Source Code */

2012 Summer Project Week:Bladder Segmentation in Slicer

2012-06-27T18:44:04Z

Egger:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Bladder-segmentation-1.png | Screenshot of 3D bladder.
Image:Bladder-segmentation-2.png| Screenshot of full pelvic region.
Image:Bladder-segmentation-3.png | Screenshot of bladder being segmented with GrowCut algorithm.
</gallery>

==Key Investigators==
*UMass Amherst: Scott Tyler Blevins
*BWH: Scott Tyler Blevins, Nabgha Farhat, Jan Egger, Tobias Penzkofer, Tina Kapur

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

<h3>Objective</h3>
The goal of this project is to investigate efficient (less than 30s) methods for segmentation of bladder from MRI images of the female pelvis in Slicer.

</div>

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

<h3>Approach, Plan</h3>

We will explore different segmentation/editing tools in Slicer to determine which ones can most efficiently segment the bladder from MRI images of the female pelvis. Tools anticipated use include Growcut, Draw, and Crop.

</div>

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

<h3>Progress</h3>

Tools previously mentioned were successfully used to segment out the bladder from MRI images, and 3D images were rendered as a result. Three tutorial modules were created outlining the mechanism of execution, included in this page. Further segmentation efforts will be conducted on different data sets.

[[Media:Draw_Effect_Tool_Tutorial_for_Bladder_Segmentation.doc|Draw Tutorial]]
[[Media:Crop_Tool_and_Grow_Cut_Segmentation_Tool_Tutorial_Using_Bladder_Images.doc|Crop and GrowCut Tutorial]]
[[Media:Combined_Cropping_Growcut_and_Draw_Tool_Tutorial_for_Bladder_Imaging.doc|Combined GrowCut, Crop, and Draw Tutorial]]

</div>
</div>

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

==Delivery Mechanism==

N/A

==References==

</div>

File:Bladder-segmentation-3.png

2012-06-27T18:41:50Z

Egger:

File:Bladder-segmentation-2.png

2012-06-27T18:41:37Z

Egger:

File:Bladder-segmentation-1.png

2012-06-27T18:41:16Z

Egger:

2012 Winter Project Week

2012-01-19T21:28:19Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== [[AHM_2012#Agenda|'''AGENDA''']] and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:GeometricMetamorphosisTBI|Geometric Metamorphosis for TBI]] (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
* [[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger, Isaiah Norton, Jayashree)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen, Junichi Tokuda)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Isaiah Norton, Mehdi Moradi, Tamas Ungi)
*[[2012_Winter_Project_Week:LaserAblationAndGuidance|Slicer-BrainLab integration for laser ablation]] (Erol Yeniaras, Isaiah Norton, Pratik Patel)
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brachytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Matthew Toews, Stephen Aylward)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer for Neurosurgery]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]
* [[2012_Winter_Project_Week:CTLiverRegistration|Register liver CT images for tumor progress monitoring]] (Karl Diedrich, Nobuhiko Hata, Atsushi Yamada)
* [[2012_Winter_Project_Week:Fast Multi-modal Registration|Fast Registration with User-guidance for AMIGO]] (Dave Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:UKFTractography|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===NA-MIC Kit Internals===
*[[2012_Project_Week:AfibDataOnMidas| Afib Data on MIDAS]] (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
*[[2012_Project_Week:RemoveSlicerLegacyCode|Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)]]
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra, Dave Welch)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)
*[[2012_Winter_Project_Week:ScriptView|Consistent, scripted setup of Slicer view for multiple subjects]] (Albert, Steve)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week

2012-01-13T15:11:14Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== [[AHM_2012#Agenda|'''AGENDA''']] and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:GeometricMetamorphosisTBI|Geometric Metamorphosis for TBI]] (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
* [[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger, Isaiah Norton, Jayashree)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen, Junichi Tokuda)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Isaiah Norton, Mehdi Moradi, Tamas Ungi)
*[[2012_Winter_Project_Week:LaserAblationAndGuidance|Slicer-BrainLab integration for laser ablation]] (Erol Yeniaras, Isaiah Norton, Pratik Patel)
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer for Neurosurgery]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]
* [[2012_Winter_Project_Week:CTLiverRegistration|Register liver CT images for tumor progress monitoring]] (Karl Diedrich, Nobuhiko Hata, Atsushi Yamada)
* [[2012_Winter_Project_Week:Fast Multi-modal Registration|Fast Registration with User-guidance for AMIGO]] (Dave Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:UKFTractography|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plesniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
*[[2012_Project_Week:RemoveSlicerLegacyCode|Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)]]
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra, Dave Welch)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:hybridMRS

2012-01-13T04:49:58Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
</gallery>

Project Title: '''Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer'''

==Key Investigators==
* SPL: Jan Egger, Isaiah Norton, Tina Kapur, Alexandra Golby
* UKGM: Daniel Hořínek, Jens Sommer, Christopher Nimsky
* ETHZ: Bjoern Menze
* IKEM: Antonín Škoch

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

<h3>Objective</h3>

Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO. A hybrid MR-Spectroscopic dataset can for example be used for biopsy targeting in brain tumors. Besides, the metabolic concentrations and ratios can help to diagnose lesions.

</div>

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

<h3>Approach, Plan</h3>

Try to process MRS data with the MRSI module from Bjoern Menze developed at a previous project week. The module interfaces SIVIC, which is an open-source standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data.

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

==Bibliography==
[http://www.ncbi.nlm.nih.gov/pubmed/16424238 Preoperative Grading of Gliomas by Using Metabolite Quantification with High-Spatial-Resolution Proton MR Spectroscopic Imaging.] Radiology 2006 Mar;238(3):958-69.

[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.

==Resources==
[http://sourceforge.net/apps/trac/sivic/ Sivic]
[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/

[http://www.sites.google.com/site/jsiprotool/ jSIPRO - MR Spectroscopic Imaging Processing Tool]

</div>

2012 Winter Project Week:hybridMRS

2012-01-13T04:49:05Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
</gallery>

Project Title: '''Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer'''

==Key Investigators==
* SPL: Jan Egger, Isaiah Norton, Tina Kapur, Alexandra Golby
* UKGM: Daniel Hořínek, Jens Sommer, Christopher Nimsky
* ETHZ: Bjoern Menze
* IKEM: Antonín Škoch

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

<h3>Objective</h3>

Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO. A hybrid MR-Spectroscopic dataset can for example be used for biopsy targeting in brain tumors.

</div>

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

<h3>Approach, Plan</h3>

Try to process MRS data with the MRSI module from Bjoern Menze developed at a previous project week. The module interfaces SIVIC, which is an open-source standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data.

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

==Bibliography==
[http://www.ncbi.nlm.nih.gov/pubmed/16424238 Preoperative Grading of Gliomas by Using Metabolite Quantification with High-Spatial-Resolution Proton MR Spectroscopic Imaging.] Radiology 2006 Mar;238(3):958-69.

[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.

==Resources==
[http://sourceforge.net/apps/trac/sivic/ Sivic]
[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/

[http://www.sites.google.com/site/jsiprotool/ jSIPRO - MR Spectroscopic Imaging Processing Tool]

</div>

2012 Winter Project Week:iGyne

2012-01-13T04:30:26Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the pre-developed iGyne Prototype
Image:IGyne-ScreenShot-Slicer4.png|Screenshot of the actual iGyne Module under Slicer4

</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur
* LROC: Antonio Damato, Kanokpis Townamchai, Akila Viswanathan

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

<h3>Objective</h3>

The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
</div>

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

<h3>Approach, Plan</h3>

A software prototype supporting Gynecologic Radiation Treatment has already been pre-developed. The pre-developed software prototype has been brought to AMIGO cases and the workflow of the prototype has been discussed with the treating physician.

</div>

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

<h3>Progress</h3>

Currently, a module for Slicer is under development. The module already allows the visualization of a gynecological template for brachytherapy in a preoperative patient dataset. Furthermore, interstitial needles can already be visualized for treatment planning.

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

2012 Winter Project Week:iGyne

2012-01-13T04:24:33Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the pre-developed iGyne Prototype
Image:IGyne-ScreenShot-Slicer4.png|Screenshot of the actual iGyne Module under Slicer4

</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur
* LROC: Antonio Damato, Kanokpis Townamchai, Akila Viswanathan

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

<h3>Objective</h3>

The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
</div>

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

<h3>Approach, Plan</h3>

A software prototype supporting Gynecologic Radiation Treatment has already been pre-developed. The pre-developed software prototype has been brought to AMIGO cases and the workflow of the prototype has been discussed with the treating physician.

</div>

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

<h3>Progress</h3>

Currently, a module for Slicer is under development. The module allows the visualization of a gynecological template for brachytherapy in a preoperative patient dataset. Furthermore, interstitial needles can be visualized for treatment planning.

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

2012 Winter Project Week

2012-01-07T23:43:07Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
*[[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:hybridMRS

2012-01-07T23:42:24Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
</gallery>

Project Title: '''Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer'''

==Key Investigators==
* SPL: Jan Egger, Isaiah Norton, Tina Kapur, Alexandra Golby
* UKGM: Daniel Hořínek, Jens Sommer, Christopher Nimsky
* ETHZ: Bjoern Menze
* IKEM: Antonín Škoch

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

<h3>Objective</h3>

Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

==Bibliography==
[http://www.ncbi.nlm.nih.gov/pubmed/16424238 Preoperative Grading of Gliomas by Using Metabolite Quantification with High-Spatial-Resolution Proton MR Spectroscopic Imaging.] Radiology 2006 Mar;238(3):958-69.

[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.

==Resources==
[http://sourceforge.net/apps/trac/sivic/ Sivic]
[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/

[http://www.sites.google.com/site/jsiprotool/ jSIPRO - MR Spectroscopic Imaging Processing Tool]

</div>

2012 Winter Project Week

2012-01-06T16:55:45Z

Egger: /* Head and Neck Cancer */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
*[[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:GBMseg

2012-01-06T16:48:10Z

Egger:

==Key Investigators==
* WUSM: Dan Marcus, Misha Milchenko
* Brigham and Women's: Andrey Fedorov, Jan Egger

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

<h3>Objective</h3>
We are looking to segment and visualize GBM's from various MR sequences in Slicer, and create an integrated display for clinisian review, both radiologist and non-radiologist.

</div>

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

<h3>Approach, Plan</h3>

The approach is to obtain accurate registration of a number of MR sequences of each tumor case, and analyze correlation with pathology data.

</div>

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

<h3>Progress</h3>
</div>
</div>

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

==Delivery Mechanism==

==References==

</div>

2012 Winter Project Week

2012-01-04T15:33:02Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:hybridMRS

2012-01-04T15:32:24Z

Egger:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
</gallery>

Project Title: '''Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer'''

==Key Investigators==
* SPL: Jan Egger, Isaiah Norton, Tina Kapur
* UKGM: Daniel Hořínek, Jens Sommer, Christopher Nimsky
* ETHZ: Bjoern Menze
* IKEM: Antonín Škoch

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

<h3>Objective</h3>

Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

==Bibliography==
[http://www.ncbi.nlm.nih.gov/pubmed/16424238 Preoperative Grading of Gliomas by Using Metabolite Quantification with High-Spatial-Resolution Proton MR Spectroscopic Imaging.] Radiology 2006 Mar;238(3):958-69.

[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.

==Resources==
[http://sourceforge.net/apps/trac/sivic/ Sivic]
[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/

[http://www.sites.google.com/site/jsiprotool/ jSIPRO - MR Spectroscopic Imaging Processing Tool]

</div>

2012 Winter Project Week

2011-12-30T15:22:59Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Give Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:iGyne

2011-12-30T15:22:36Z

Egger:

2012 Winter Project Week:iGyne

2011-12-30T14:13:11Z

Egger:

2012 Winter Project Week:iGyne

2011-12-29T19:20:38Z

Egger:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the iGyne Prototype
Image:IGyne-ScreenShot-Slicer4.png|Screenshot of the iGyne Prototype under Slicer4

</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur
* LROC: Antonio Damato, Akila Viswanathan

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

<h3>Objective</h3>

Development of an iGyne module under 3DSlicer.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

2012 Winter Project Week:iGyne

2011-12-29T19:16:41Z

Egger:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the iGyne Prototype
Image:IGyne-ScreenShot-Slicer4.png|Screenshot of the iGyne Prototype for Slicer4

</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur
* LROC: Antonio Damato, Akila Viswanathan

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

<h3>Objective</h3>

Development of an iGyne module under 3DSlicer.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

File:IGyne-ScreenShot-Slicer4.png

2011-12-29T19:14:48Z

Egger:

2012 Winter Project Week:hybridMRS

2011-12-29T16:20:38Z

Egger: /* Resources */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
</gallery>

Project Title: '''Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer'''

==Key Investigators==
* SPL: Jan Egger, Isaiah Norton, Tina Kapur
* UKGM: Daniel Hořínek, Christopher Nimsky
* ETHZ: Bjoern Menze
* IKEM: Antonín Škoch

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

<h3>Objective</h3>

Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

==Bibliography==
[http://www.ncbi.nlm.nih.gov/pubmed/16424238 Preoperative Grading of Gliomas by Using Metabolite Quantification with High-Spatial-Resolution Proton MR Spectroscopic Imaging.] Radiology 2006 Mar;238(3):958-69.

[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.

==Resources==
[http://sourceforge.net/apps/trac/sivic/ Sivic]
[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/

[http://www.sites.google.com/site/jsiprotool/ jSIPRO - MR Spectroscopic Imaging Processing Tool]

</div>

2012 Winter Project Week:hybridMRS

2011-12-29T16:16:49Z

Egger: /* Bibliography */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
</gallery>

Project Title: '''Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer'''

==Key Investigators==
* SPL: Jan Egger, Isaiah Norton, Tina Kapur
* UKGM: Daniel Hořínek, Christopher Nimsky
* ETHZ: Bjoern Menze
* IKEM: Antonín Škoch

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

<h3>Objective</h3>

Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

==Bibliography==
[http://www.ncbi.nlm.nih.gov/pubmed/16424238 Preoperative Grading of Gliomas by Using Metabolite Quantification with High-Spatial-Resolution Proton MR Spectroscopic Imaging.] Radiology 2006 Mar;238(3):958-69.

[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.

==Resources==
[http://sourceforge.net/apps/trac/sivic/ Sivic]
[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/
</div>

2012 Winter Project Week

2011-12-29T14:40:21Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Give Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:hybridMRS

2011-12-29T14:39:53Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
</gallery>

Project Title: '''Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer'''

==Key Investigators==
* SPL: Jan Egger, Isaiah Norton, Tina Kapur
* UKGM: Daniel Hořínek, Christopher Nimsky
* ETHZ: Bjoern Menze
* IKEM: Antonín Škoch

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

<h3>Objective</h3>

Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

==Bibliography==
[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.

==Resources==
[http://sourceforge.net/apps/trac/sivic/ Sivic]
[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/
</div>

2012 Winter Project Week

2011-12-29T14:38:38Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Horinek, Antonín Škoch, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Give Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:hybridMRS

2011-12-29T14:38:08Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
</gallery>

Project Title: '''Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer'''

==Key Investigators==
* SPL: Jan Egger, Isaiah Norton, Tina Kapur
* UKGM: Daniel Horinek, Christopher Nimsky
* ETHZ: Bjoern Menze
* IKEM: Antonín Škoch

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

<h3>Objective</h3>

Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

==Bibliography==
[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.

==Resources==
[http://sourceforge.net/apps/trac/sivic/ Sivic]
[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/
</div>

2012 Winter Project Week:hybridMRS

2011-12-22T19:58:05Z

Egger: /* Key Investigators */

2012 Winter Project Week

2011-12-22T19:57:06Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Horinek, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Give Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, J2, JC)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:hybridMRS

2011-12-22T19:56:17Z

Egger: /* Key Investigators */

2012 Winter Project Week

2011-12-22T17:45:51Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Daniel Horinek, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Give Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, J2, JC)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:hybridMRS

2011-12-22T17:45:18Z

Egger:

2012 Winter Project Week:iGyne

2011-12-22T17:22:40Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the iGyne Prototype
</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur
* LROC: Antonio Damato, Akila Viswanathan

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

<h3>Objective</h3>

Development of an iGyne module under 3DSlicer.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

2012 Winter Project Week

2011-12-21T20:59:09Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Give Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, J2, JC)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:iGyne

2011-12-21T20:58:44Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the iGyne Prototype
</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Tina Kapur, Akila Viswanathan

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

<h3>Objective</h3>

Development of an iGyne module under 3DSlicer.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

2012 Winter Project Week

2011-12-21T18:31:19Z

Egger: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Give Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, J2, JC)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week:iGyne

2011-12-21T18:30:43Z

Egger: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the iGyne Prototype
</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur, Akila Viswanathan

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

<h3>Objective</h3>

Development of an iGyne module under 3DSlicer.

</div>

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

<h3>Approach, Plan</h3>

-

</div>

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

<h3>Progress</h3>

-

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

File:MRS2.png

2011-12-21T16:23:21Z

Egger: uploaded a new version of "File:MRS2.png"