NAMIC Wiki - User contributions [en]

File:MICCAI2010 NAMIC Tutorial HAMMER ShenDG.pdf

2010-09-08T02:48:24Z

Grwu: uploaded a new version of "File:MICCAI2010 NAMIC Tutorial HAMMER ShenDG.pdf"

File:MICCAI2010 NAMIC Tutorial HAMMER ShenDG.pdf

2010-09-08T02:37:59Z

Grwu: uploaded a new version of "File:MICCAI2010 NAMIC Tutorial HAMMER ShenDG.pdf"

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T19:11:24Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map
Image: namic.png|The output deformation filed by HAMMER
Image: b1.png|Hierarchical Registration
Image: b3.png|Processing pipeline in Slicer3
Image: b2.png|Warping result by HAMMER
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* Project week (Boston, 2010): We have 1) extended HAMMER registration algorithm to work on intensity image, bypassing the pre-segment of MR images; 2) replacing the gaussian propagation with the thin-plate interpolation to achieve more accurate and efficient registration; 3) implement the soft-assignment strategy, instead of the one-to-one correspondence, in detecting correspondence during registration.

* Project week (Utah, 2010): We have finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Project week 2009 in Utah: we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T19:04:42Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map
Image: namic.png|The output deformation filed by HAMMER
Image: b1.png|Hierarchical Registration
Image: b3.png|Processing pipeline in Slicer3
Image: b2.png|Warping result by HAMMER
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T19:02:41Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map
Image: namic.png|The output deformation filed by HAMMER
Image: b1.png|Hierarchical Registration
Image: b3.png|Processing pipeline in Slicer3
Image: b2.png|Warping result by HAMMER
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

<h3>HAMMER users (will update as the list grows):</h3>

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T19:01:44Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map
Image: namic.png|The output deformation filed by HAMMER
Image: b1.png|Hierarchical Registration
Image: hammer.png|HAMMER in Slicer3
Image: b2.png|HAMMER in Slicer3
Image: b3.png|HAMMER in Slicer3
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

<h3>HAMMER users (will update as the list grows):</h3>

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

File:B3.png

2010-06-16T19:00:28Z

Grwu:

File:B2.png

2010-06-16T19:00:14Z

Grwu:

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T18:57:40Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map
Image: namic.png|The output deformation filed by HAMMER
Image: b1.png|Hierarchical Registration
Image: hammer.png|HAMMER in Slicer3
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

<h3>HAMMER users (will update as the list grows):</h3>

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T18:57:07Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
Image: b1.png|Hierarchical Registration
Image: hammer.png|HAMMER in Slicer3
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

<h3>HAMMER users (will update as the list grows):</h3>

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

File:B1.png

2010-06-16T18:56:19Z

Grwu:

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T18:54:02Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
[[File:b1.bmp]]
Image: b1.bmp|Hierarchical Registration
Image: hammer.png|HAMMER in Slicer3
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

<h3>HAMMER users (will update as the list grows):</h3>

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T18:53:23Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
Image: b1.bmp|Hierarchical Registration
Image: hammer.png|HAMMER in Slicer3
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

<h3>HAMMER users (will update as the list grows):</h3>

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T18:52:39Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
Image: hammer.png|HAMMER in Slicer3
Image: b1.bmp|Hierarchical Registration
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

<h3>HAMMER users (will update as the list grows):</h3>

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Summer Project Week HAMMER: Deformable Registration

2010-06-16T18:41:20Z

Grwu: Created page with '__NOTOC__ <gallery> Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors. Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) f…'

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
Image: hammer.png|HAMMER in Slicer3
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
* During this past week (2010), we finalized HAMMER "alpha" release on NITRC and gave a tutorial. In the next couple of weeks, we will continue to polish the tutorial and code, provide support to and collect feedback from early HAMMER adapters.

* Since winter project week 2009 in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

<div style="margin: 20px;">
<div style="width: 90%; float: left; padding-right: 3%;">

<h3>HAMMER users (will update as the list grows):</h3>

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Summer Project Week

2010-05-12T01:00:39Z

Grwu: /* Registration */

__NOTOC__

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

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

==Background==

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

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

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

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

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

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

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

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

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== TENTATIVE Agenda==

'''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.
'''
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

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

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

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

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

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, ?)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Greg Sharp, Nadya Shusharina)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)

=== IGT ===
* Liver Ablation (Ziv Yaniv, Haiying Liu)

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

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)

=== Informatics ===

=== Diffusion ===

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, Nicole)
*Superbuild (Dave Partika)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

2010 Summer Project Week

2010-05-12T01:00:17Z

Grwu: /* Registration */

__NOTOC__

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

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

==Background==

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

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

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

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

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

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

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

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

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== TENTATIVE Agenda==

'''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.
'''
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

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

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

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

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

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, ?)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Greg Sharp, Nadya Shusharina)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, and Dinggang Shen)

=== IGT ===
* Liver Ablation (Ziv Yaniv, Haiying Liu)

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

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)

=== Informatics ===

=== Diffusion ===

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, Nicole)
*Superbuild (Dave Partika)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

2010 Summer Project Week

2010-05-12T00:59:49Z

Grwu: /* Registration */

__NOTOC__

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

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

==Background==

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

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

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

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

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

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

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

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

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== TENTATIVE Agenda==

'''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.
'''
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

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

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

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

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

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, ?)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Greg Sharp, Nadya Shusharina)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller and Dinggang Shen)

=== IGT ===
* Liver Ablation (Ziv Yaniv, Haiying Liu)

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

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)

=== Informatics ===

=== Diffusion ===

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, Nicole)
*Superbuild (Dave Partika)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

2010 Summer Project Week

2010-05-12T00:57:05Z

Grwu: /* Registration */

__NOTOC__

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

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

==Background==

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

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

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

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

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

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

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

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

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== TENTATIVE Agenda==

'''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.
'''
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

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

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

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

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

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, ?)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Greg Sharp, Nadya Shusharina)
*[[2010_Summer_Project_Week_HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration|HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller and Dinggang Shen)

=== IGT ===
* Liver Ablation (Ziv Yaniv, Haiying Liu)

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

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)

=== Informatics ===

=== Diffusion ===

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, Nicole)
*Superbuild (Dave Partika)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

File:HAMMER Tutorial V3.pdf

2010-01-07T15:46:29Z

Grwu: uploaded a new version of "File:HAMMER Tutorial V3.pdf"

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-06T14:06:19Z

Grwu: /* Downloads */

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-06T14:05:20Z

Grwu:

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-06T14:04:54Z

Grwu:

File:TutorialData HAMMER.zip

2010-01-06T14:03:43Z

Grwu:

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-06T13:59:57Z

Grwu:

File:HAMMER Tutorial V3.pdf

2010-01-06T13:57:54Z

Grwu:

AHM2010:Tutorial Contest

2010-01-06T06:40:43Z

Grwu: /* Tutorial List */

=Background=

[http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. For examples for such existing tutorials as well as tutorials of the past contests are posted on the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].

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

There will be two categories:
#'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least:
#*materials about the scientific and application background and motivation,
#*step-by-step guides, and
#*sample data
#*Example: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]
#'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:
#*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment
#*step-by-step guides, and
#*at least two different sample data sets from two different institutions
#*Example: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]

=Template=
A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]
*Note: The examples above predate the template.

=Rules=
*Tutorial must be based on a snapshot or release of Slicer 3
*Tutorial must follow the guidelines specified above
*If applicable, provide clear directions for downloading and installing additional modules
*The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).

=Dates and Submission Dead-line=

*Presentation: all tutorials will be presented by the authors on '''Wednesday January 6 from 8 am to 9 am''' during the Project Week. Each tutorial presentation should be 10 minutes long.
* <span style="background-color: yellow"> If you wish to participate in the contest, please create a wiki page for your tutorial, upload your slides and tutorial dataset and add a link to your tutorial page in the section below. Please name your tutorial file as 'TutorialName_Winter2010AHM.pdf' and tutorial data as 'TutorialName_Data_Winter2010AHM.pdf'</span>
'''Submission dead-line: Monday January 4, 2010'''

=Tutorial List=
#[[AHM 2010 Tutorial Contest - Hammer Registration | Hammer Registration ]] (Guorong Wu)
#[[AHM 2010 Tutorial Contest - CoronaryArteriesCenterlinesVMTK | Centerline Extraction of Coronary Arteries using VMTK]] (Daniel Haehn)
#[[AHM 2010 Tutorial Contest - Port of Slicer to Qt| Port of Slicer to Qt]] (Julien Finet)

AHM2010:Tutorial Contest

2010-01-05T16:18:15Z

Grwu: /* Tutorial List */

=Background=

[http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. For examples for such existing tutorials as well as tutorials of the past contests are posted on the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].

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

There will be two categories:
#'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least:
#*materials about the scientific and application background and motivation,
#*step-by-step guides, and
#*sample data
#*Example: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]
#'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:
#*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment
#*step-by-step guides, and
#*at least two different sample data sets from two different institutions
#*Example: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]

=Template=
A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]
*Note: The examples above predate the template.

=Rules=
*Tutorial must be based on a snapshot or release of Slicer 3
*Tutorial must follow the guidelines specified above
*If applicable, provide clear directions for downloading and installing additional modules
*The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).

=Dates and Submission Dead-line=

*Presentation: all tutorials will be presented by the authors on '''Wednesday January 6 from 8 am to 9 am''' during the Project Week. Each tutorial presentation should be 10 minutes long.
* <span style="background-color: yellow"> If you wish to participate in the contest, please create a wiki page for your tutorial, upload your slides and tutorial dataset and add a link to your tutorial page in the section below. Please name your tutorial file as 'TutorialName_Winter2010AHM.pdf' and tutorial data as 'TutorialName_Data_Winter2010AHM.pdf'</span>
'''Submission dead-line: Monday January 4, 2010'''

=Tutorial List=
#[[AHM 2010 Tutorial Contest - Hammer Registration | Hammer Registration (Dinggang)]] (Guorong Wu)
#[[AHM 2010 Tutorial Contest - Skull Stripping | Skull Stripping ]](XTao)
#[[AHM 2010 Tutorial Contest - CoronaryArteriesCenterlinesVMTK | Centerline Extraction of Coronary Arteries using VMTK]] (Daniel Haehn)

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:54:48Z

Grwu: /* Downloads */

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:54:05Z

Grwu:

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:52:02Z

Grwu:

File:Tutorial HAMMER Winter2010AHM.pdf

2010-01-05T05:50:12Z

Grwu: uploaded a new version of "File:Tutorial HAMMER Winter2010AHM.pdf"

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:48:17Z

Grwu: /* Downloads */

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:46:06Z

Grwu:

File:Tutorial HAMMER Winter2010AHM.pdf

2010-01-05T05:41:57Z

Grwu:

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:40:22Z

Grwu:

2010 Winter Project Week HAMMER

2010-01-05T05:39:33Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
Image: hammer.png|HAMMER in Slicer3
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

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

<h3>Users List</h3>
We have released our registration method to the Na-mic society. Below is the list of users:

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

File:Hammer.png

2010-01-05T05:38:46Z

Grwu:

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:28:15Z

Grwu:

<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

=== Objective ===
Present our namic project on HAMMER registration algorithm and introduce how to use HAMMER in Slicer3.

=== Downloads ===
# [http://www.na-mic.org/Wiki/images/4/40/TutorialVMTKCoronariesCenterlinesMRI_Winter2010AHM.pdf Tutorial Slides]
# [http://www.na-mic.org/Wiki/images/a/aa/TutorialVMTKCoronariesCenterlinesMRI_Data_Winter2010AHM.zip Tutorial Data]

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:26:48Z

Grwu:

== Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools ==
<gallery>
File:VMTKCenterlines Tutorial first slide.png|
Image:Vmtkcloseupvoronoicenterlinewithreference.png|Lumen Segmentation, Voronoi diagram and centerline of a coronary artery.
Image:Vmtkafterevolutionanim.gif|An over-layed label map showing the segmentation in 2D.
</gallery>

=== Objective ===
Present our namic project on HAMMER registration algorithm and introduce how to use HAMMER in Slicer3.

=== Downloads ===
# [http://www.na-mic.org/Wiki/images/4/40/TutorialVMTKCoronariesCenterlinesMRI_Winter2010AHM.pdf Tutorial Slides]
# [http://www.na-mic.org/Wiki/images/a/aa/TutorialVMTKCoronariesCenterlinesMRI_Data_Winter2010AHM.zip Tutorial Data]

AHM 2010 Tutorial Contest - Hammer Registration

2010-01-05T05:25:43Z

Grwu: Created page with '== Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools == <gallery> File:VMTKCenterlines Tutorial first slide.png| Image:Vmtkcloseupvoronoicenterlinewi…'

== Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools ==
<gallery>
File:VMTKCenterlines Tutorial first slide.png|
Image:Vmtkcloseupvoronoicenterlinewithreference.png|Lumen Segmentation, Voronoi diagram and centerline of a coronary artery.
Image:Vmtkafterevolutionanim.gif|An over-layed label map showing the segmentation in 2D.
</gallery>

=== Objective ===
Guiding you step by step through the process of centerline extraction of Coronary Arteries in a cardiac blood-pool MRI using VMTK based Tools.

=== Downloads ===
# [http://www.na-mic.org/Wiki/images/4/40/TutorialVMTKCoronariesCenterlinesMRI_Winter2010AHM.pdf Tutorial Slides]
# [http://www.na-mic.org/Wiki/images/a/aa/TutorialVMTKCoronariesCenterlinesMRI_Data_Winter2010AHM.zip Tutorial Data]

2010 Winter Project Week HAMMER

2010-01-04T05:42:33Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

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

<h3>Users List</h3>
We have released our registration method to the Na-mic society. Below is the list of users:

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2010 Winter Project Week WMLS

2010-01-04T05:41:00Z

Grwu:

__NOTOC__
<gallery>
Image:itk_wmls_pipeline.png| Pipeline of WML segmentation
Image:UNCWMLSegmentation.png|One training dataset (T1, T2, PD, FLAIR images and wml segmentation)
Image:itk_wmls.png| One testing dataset and segmentation result
</gallery>

==Key Investigators==
* UNC: Minjeong Kim, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developing and testing the white matter lesion segmentation algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the white matter lesion segmentation algorithm. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since summer project week in Boston, we have developed/implemented a WML segmentation algorithm using ITK classes. Also, we have integrated into the Slicer3. We have made the tutorial for this project meeting to present how to use our learning-based white matter lesion segmenation algorithm in Slicer 3. Subtasks implemented include: (1) a skull stripping algorithm working on T1 weighted images; (2) a fuzzy clustering algorithm for tissue segmentation; (3) a parametric model for gain field correction. All of these subtasks are implemented by using ITK. The training step uses AdaBoost and the segmenation step uses a support vector machine.

</div>
</div>

==References==
* Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition, Academic Radiology, 15(3):300-313, March 2008.
[http://www.academicradiology.org/article/S1076-6332(07)00583-1/abstract]

2010 Winter Project Week WMLS

2010-01-04T05:39:05Z

Grwu: Created page with '__NOTOC__ <gallery> Image:itk_wmls_pipeline.png| Pipeline of WML segmentation Image:UNCWMLSegmentation.png|One training dataset (T1, T2, PD, FLAIR images and wml segmentation) Im…'

__NOTOC__
<gallery>
Image:itk_wmls_pipeline.png| Pipeline of WML segmentation
Image:UNCWMLSegmentation.png|One training dataset (T1, T2, PD, FLAIR images and wml segmentation)
Image:itk_wmls.png| One testing dataset and segmentation result
</gallery>

==Key Investigators==
* UNC: Minjeong Kim, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developing and testing the white matter lesion segmentation algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the white matter lesion segmentation algorithm. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented a WML segmentation algorithm using ITK classes. Subtasks implemented include: (1) a skull stripping algorithm working on T1 weighted images; (2) a fuzzy clustering algorithm for tissue segmentation; (3) a parametric model for gain field correction. All of these subtasks are implemented by using ITK. The training step uses AdaBoost and the segmenation step uses a support vector machine.

</div>
</div>

==References==
* Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition, Academic Radiology, 15(3):300-313, March 2008.
[http://www.academicradiology.org/article/S1076-6332(07)00583-1/abstract]

2010 Winter Project Week

2010-01-04T05:38:32Z

Grwu: /* Segmentation */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__
[[Image:PW-SLC2010.png|300px]]

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange 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]].

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates_Venue_Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)
#[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa, Polina Golland, Ehud Schmidt, Ron Kikinis)
#[[2010_Winter_Project_Week_Musco_Skeletal_Segmentation | Rapid Segmentation of Knee Structures for Simulation]] (Harish Doddi, Saikat Pal, Luis Ibanez, Scott Delp)
#[[2010_Winter_Project_Week_WMLS | White Matter Lesion segmentation]] (Minjeong Kim UNC)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[2010_Winter_Project_Week_Deformation_Field_Visualization|Deformation Field and Tensor Visualization]] (Garrett Larson, Martin Styner)
#[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski, Dominik Meier, Ron Kikinis)
# [[ 2010_Winter_Project_Week_testbed|Testbed for Evaluation, Comparison, and Parameter Exploration for 3D Registration]] (James Fishbaugh, Guido Gerig)
# [[ 2010_Winter_Project_Week_HAMMER|HAMMER Registration Algorithm in Slicer 3]] (Guorong Wu, Xiaodong Tao, Jim Miller, and Dinggang Shen)

=== IGT ===
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters for Tumor Resection]] (Petter Risholm, Sandy Wells)
#[[2010_Winter_Project_Week_MRI_Reconstruction_by_Registration | MRI Reconstruction by Registration for Focused Ultrasound Therapy]] (Ben Schwartz, Sandy Wells)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)
#[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation for Neurosurgical Planning]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI|Fast Imaging Library, and Siemens EPI for IGT]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin|DicomRT plugin for Slicer]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

=== Analysis ===
#[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
#[[2010_WinterProject_Week_MRSIModule|MRSI Module]] (Bjoern Menze, Polina Golland)
#[[2010_WinterProject_Week_CorticalThicknessAnalysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_WinterProject_Week_XNATUseforPopulationAnalysis|XNAT Use for Population Analysis]] (Corentin Hamel, Martin Styner, Clement Vachet)

=== Informatics ===
#[[2010_Winter_Project_Week_XND|XNAT Desktop User Interface]] (Dan M, Wendy P, Ron K)
#[[2010_Winter_Project_Week_Slicer_XNAT|Slicer 3 XNAT Performance Tuning]] (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
#[[2010_Winter_Project_Week_catalyst|Harvard CTSC XNAT]] (Yong Gao, Dan M, Tim Olson, John Paulett)
#[[2010_Winter_Project_Week_xnatfs|xnatfs Integration into XNAT core]] (Dan Blezek, John Paulett, Tim Olsen)
#[[2010_Winter_Project_Week_OAWMB|Open Access Whole body CT/MR data set]] (Dan Marcus, Steve Pieper)
#[[2010_Winter_Project_Week_mComment | Annotation of Medical Images]] (Kilian Pohl, Yong Zhang, Nicole Aucion, Wendy Plesniak, Steve Pieper)

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
#[[2010_Winter_Project_Week_TractographyPickingEditing|Tractography Picking and Bundle Editing]] (Jim Miller, Mahnaz Maddah, Nicole Aucoin, Wendy Plesniak, James Malcolm, Alex Yarmarkovich)
#[[ 2010_Winter_Project_Week_DTI_Fiber_Tract_Statistics|DTI Fiber-Tract Statistics]] (Anuja Sharma, Guido Gerig)

=== NA-MIC Kit Internals ===
#[[2010_Winter_Project_Week_Testing_for_Extensions|Testing for Extensions]] (Steve, Andriy Fedorov, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen, Jim Miller)
#[[2010_Winter_Project_Week_VTK_3D_Widgets_in_Slicer3|VTK 3D Widgets in Slicer3]] (Nicole Aucoin, Karthik, Will)
#[[2010_Winter_Project_Week_Slicer3_Colors_Module|Updates to Slicer3 Colors Module]] (Nicole Aucoin)
#CMAKE Build process (Dave Partyka, Katie Hayes)
#[[2010_Winter_Project_Week_XNAT_Packaging_For_Slicer | Integration of XNAT Packaging for Slicer Internals]] (Dan, Tim Olsen, Steve Pieper, Dave Partyka, Wendy, Randy)
#[[2010_Winter_Project_Week_Orthogonal_Planes_Issues|Orthogonal planes in reformat widget issues in Slicer3.5]] (Michal Depa, Steve Pieper)
#[[2010_Winter_Project_Week_Slicer_Dashboard|Slicer Dashboard]] (Luis, Steve, Bill & All)

(Other possibilities: Plotting, Layouts)

=== NA-MIC Outreach ===
#[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

=== Execution Model ===
# [[2010_Winter_Project_Week_Qt-ing the Command Line Module | Qt-ing the Command Line Module]] (Jim Miller, Jean-Christophe Fillion-Robin, Julien Finet)
# [[2010_Winter_Project_Week_Command Line Module Simple Return Types | Simple Return Types]] (Jim Miller)

=== 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 15th, 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 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[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 17, 2009: 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. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2010 Winter Project Week HAMMER

2010-01-04T05:36:06Z

Grwu:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

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

<h3>Users List</h3>
We have released our registration method to the Na-mic society. Below is the list of users:

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2009 Summer Project Week HAMMER Registration

2010-01-04T05:35:16Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER.
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since summer project week in Boston, we have integrated HAMMER into Slicer as a moduler. Each component has been tested. We have made the tutorial to present how to use HAMMER in Slicer3. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

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

<h3>Users List</h3>
We have released our registration method to the Na-mic society. Below is the list of users:

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2009 Summer Project Week HAMMER Registration

2010-01-04T05:31:33Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER.
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

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

<h3>Users List</h3>
We have released our registration method to the Na-mic society. Below is the list of users:

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2009 Summer Project Week HAMMER Registration

2010-01-04T05:30:21Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER.
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

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

<h3>Progress in this na-mic meeting</h3>
We have finished following work in this na-mic project meeting:

1. Implemented the framework of multi-resolution.

2. Integrated affine registration as the pre-processing step before HAMMER algorithm.

3. Build up the interface for algorithm.

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

<h3>Future plan</h3>
We will continue developping and testing our project after Na-mic meeting. Below is the TO-DO list:

1. Automatically performing skull striping;

2. Integrating HAMMER algorithm as the the module in Slicer

3. Do extensive test on the algorithm and release to the Na-mic community.

</div>
<h3>Users List</h3>
We have released our registration method to the Na-mic society. Below is the list of users:

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2009 Summer Project Week HAMMER Registration

2010-01-04T05:29:58Z

Grwu:

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER.
[[File:hammer.png]|User]
Image: hammer.png|User interface in Slicer
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

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

<h3>Progress in this na-mic meeting</h3>
We have finished following work in this na-mic project meeting:

1. Implemented the framework of multi-resolution.

2. Integrated affine registration as the pre-processing step before HAMMER algorithm.

3. Build up the interface for algorithm.

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

<h3>Future plan</h3>
We will continue developping and testing our project after Na-mic meeting. Below is the TO-DO list:

1. Automatically performing skull striping;

2. Integrating HAMMER algorithm as the the module in Slicer

3. Do extensive test on the algorithm and release to the Na-mic community.

</div>
<h3>Users List</h3>
We have released our registration method to the Na-mic society. Below is the list of users:

1. Minjie Wu, Geriatric Psychiatry Neuroimaging Lab, University of Pittsburgh
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.