NAMIC Wiki - User contributions [en]

2011 Winter Project Week:SurgicalToolsTracking

2010-12-18T20:01:07Z

Fli:

2011 Winter Project Week:SurgicalToolsTracking

2010-12-18T19:59:44Z

Fli:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:MitralValveAnnulusLinte.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:RobartsIntraCardiacSetup1.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Key Investigators==
* Robarts Research Institute: Martin Rajchl, Feng Li

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

<h3>Objective</h3>
We are trying to port a mixed reality environment for intra-cardiac interventions from the Atamai Viewer platform to Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to implement step by step Atamai Viewer modules into Slicer and/or use existing functionalities from Slicer (i.e. navigation).

</div>

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

<h3>Progress</h3>
We got navigation using OpenIGTLink 1.1 and IGSTK Sandbox to run with the NDI Aurora EM tracking system on Win32. We developed models for all necessary surgical tools for mitral valve implant and atrial septal defect repair.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#Slicer Module

==References==
*Linte C.A., Virtual and Augmented Reality Techniques for minimally Invasive Cardiac Interventions: Concept, Design, Evaluation, and Pre-clinical Implementation, Doctoral Dissertation, Robarts Research Institute, 2010

</div>

Project Week/Template

2010-12-18T19:58:47Z

Fli: Undo revision 62532 by Fli (Talk)

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

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

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

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

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

Project Week/Template

2010-12-18T19:58:33Z

Fli: Undo revision 62534 by Fli (Talk)

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:RobartsIntraCardiacSetup1.jpg|Experimental Setup for IGI in intra-cardiac surgery.
</gallery>

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

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

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

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

Project Week/Template

2010-12-18T19:57:11Z

Fli:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:MitralValveAnnulusLinte.jpg|Model of the mitral valve annulus from pre-operative MRI.
Image:RobartsIntraCardiacSetup1.jpg|Experimental Setup for IGI in intra-cardiac surgery.
</gallery>

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

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

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

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

File:MitralValveAnnulusLinte.jpg

2010-12-18T19:55:58Z

Fli:

Project Week/Template

2010-12-18T19:51:10Z

Fli:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:RobartsIntraCardiacSetup1.jpg|Experimental Setup for IGI in intra-cardiac surgery.
</gallery>

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

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

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

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

File:RobartsIntraCardiacSetup1.jpg

2010-12-18T19:49:37Z

Fli:

2011 Winter Project Week:SurgicalToolsTracking

2010-12-18T19:09:56Z

Fli:

2011 Winter Project Week:SurgicalToolsTracking

2010-12-18T18:51:29Z

Fli:

2011 Winter Project Week:SurgicalToolsTracking

2010-12-18T18:50:35Z

Fli: Created page with ' Projects List Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain. Regression of FA data; solid line represents the mean and dott…'

Projects List

Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.

Regression of FA data; solid line represents the mean and dotted lines the standard deviation.

[edit]Instructions for Use of this Template

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

UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
Utah: Tom Fletcher, Ross Whitaker
Objective
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

Approach, Plan
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

Progress
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the DTI Software Infrastructure project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

[edit]Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

ITK Module
Slicer Module
Built-in
Extension -- commandline
Extension -- loadable
Other (Please specify)
[edit]References

Fletcher P, Tao R, Jeong W, Whitaker R. A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI. Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis. Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis. Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

2011 Winter Project Week

2010-12-18T18:48:47Z

Fli: /* IGT */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2011]], [[Events]]

__NOTOC__
[[image:PW-SLC2011.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2011#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2011#Agenda|click here for the agenda for AHM 2011 and Project Week]].

==Background==

From January 10-14, 2011, the twelfth 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 engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

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

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

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

==Projects==

=== Segmentation ===
* [[2011_Winter_Project_Week:Extension of ABC to detect pathology categories|Extension of ABC (Atlas-Based Classification) to detect pathology categories, with tests on TBI images]] (Bo Wang, Jack Van Horn, Marcel Prastawa, Guido Gerig).
* [[2011_Winter_Project_Week:Atrial_Fibrillation|Segmentation of the left atrial wall for atrial fibrillation ablation therapy]] (Behnood Gholami, Yi Gao, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*TubeTK for vascular image segmentation and analysis (Stephen Aylward, Danielle Pace, Steve Pieper)
* [[2011_Winter_Project_Week:StenosisDetector|A stenosis detector in Slicer4 using VMTK ]](Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)
* [[2011_Winter_Project_Week:MeshCurvolver|Surface Region Segmentation for Surgical Planning and Mapping ]] (Peter Karasev, Karol Chudy, Allen Tannenbaum)
* [[2011_Winter_Project_Week:SPECTRE_Integration|Integration of SPECTRE into Slicer]] (Nicole Aucoin, Min Chen)
* [[2011_Winter_Project_Week:Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ehud Schmidt, Polina Golland)

=== Registration ===
*[[2011_Winter_Project_Week:RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier,Ron Kikinis)
*[[2011_Winter_Project_Week:RegistrationAnisotropy|Voxel Anisotropy and Bias Field Effects on Slicer Image Registration]] (Dominik Meier, Andriy Fedorov) (tentative)
* [[2011_Winter_Project_Week:Efficient co-registration of multiple MR modalities using the ABC|Efficient co-registration of multiple MR modalities using the ABC (atlas-based classification) framework, joint visualization of multiple co-registered modalities]] (Bo Wang, Jack Van Horn, Marcel Prastawa, Guido Gerig).
* [[2011_Winter_Project_Week:DTI_MRI_Registration|DTI MRI Registration- Evaluation of registration schemes]] (Anuja Sharma, Guido Gerig)
* Registration of CT and MRI volumes for Adaptive Radiotherapy (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:Atlas_Registration_in_Slicer3|Atlas Registration in Slicer3]] (Daniel Haehn, Dominik Meier, Kilian Pohl, Ryan Eckbo)
* Registration in the presence of anatomic variation (aka. Sliding organ registration) (Danielle Pace, Marc Niethammer, Petter Risholm, Tina Kapur, Sandy Wells, Stephen Aylward)
* [[2011_Winter_Project_Week:UncertaintyVisualization|Visualizing registration uncertainty in Slicer3]] (Petter Risholm, William Wells)
* [[2011_Winter_Project_Week:LandmarkRegularization|Landmark-based registration with analytic regularization]] (Nadya Shusharina, Gregory Sharp)
* [[2011_Winter_Project_Week:DTIPipeline|DTI registration/processing pipeline in Slicer3]] (Francois Budin, Clement Vachet)

=== IGT ===
*Open IGT Link 2.0 (Junichi Tokuda, Nobuhiko Hata)
*[[2011_Winter_Project_Week:Osteomark|Osteormark, navigation tool for Osteotomy]] (Laurent Chauvin, Nobuhiko Hata)
*[[2011_Winter_Project_Week:Intra-ProceduralProstateMotion|Detection and compensation for prostate motion during MR-guided prostate biopsy]] (A.Fedorov, Andras Lasso)
*[[2011_Winter_Project_Week:ThinClientQtInterfaceForIGT|Thin Client QT Interface for IGT]] (Nicholas Herlambang, Steve Pieper, Julien Finet, JC)
*[[2011_Winter_Project_Week:TransformRecorderAndProcedureAnnotation|Transform recorder and (surgical) procedure annotation module]] (Tamas Ungi, Junichi Tokuda)
*[[2011_Winter_Project_Week:SurgicalToolsTracking|Surgical Tools Tracking]] (Martin Rajchl, Feng Li)

=== Radiotherapy ===
* User controlled segmentation of head and neck structures for Adaptive Radiotherapy (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:DicomRtExport|DICOM-RT export]] (Greg Sharp, Steve Pieper)

=== Analysis ===
* [[2011_Winter_Project_Week:GAMBITCorticalThicknessAnalysis |GAMBIT - Cortical thickness analysis]] - Clement Vachet, Martin Styner
* [[2011_Winter_Project_Week:ParticleShapeAnalysis|Particle shape analysis incorporating surface normals ]] - Beatriz Paniagua, Martin Styner
* [[2011_Winter_Project_Week:NAMICShapeAnalysis |NAMIC shape analysis pipeline in Slicer 3]] - Lucile Bompard, Martin Styner, Clement Vachet, Chris Gloschat
* Particle Systems for Shape Analysis - Josh Cates, Manasi Datar, Ross Whitaker
* [[2011_Winter_Project_Week:MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] - Bjoern Menze, Jason Crane, Beck Olson, Polina Golland

=== Informatics ===
* [[2011_Winter_Project_Week:UIowaTHPDTIData|Share all UIowa Traveling Human Phantom DTI data with NAMIC]] - Mark Scully, Hans Johnson, Zack M.
* Ontology-augmented MRI brain atlas - Michael Halle, Jim Miller, Samira Farough
* Functional brain atlas (version 2) - Michael Halle, Jim Miller

=== Diffusion ===
* [[2011_Winter_Project_Week:DicomToNrrdTestSuite |Test suite for DicomToNrrdConverter]] - Mark Scully, Zach Mullen, Xiaodong Tao, Hans Johnson
* [[2011_Winter_Project_Week:DicomToNrrdRefactoring |Requirements gathering for refactoring DicomToNrrdConverter]] - Mark Scully, Xiaodong Tao, Hans Johnson
* [[2011_Winter_Project_Week:DTIPrepDocumentation |Documentation and 1st Draft Tutorial for DTIPrep]] - Clement Vachet, Mark Scully, Hans Johnson
* Voxelwise fiber distribution from tractography - Yinpeng Li, Martin Styner
* [[2011_Winter_Project_Week:TwoTensorTracts |Two-tensor full brain tractography pipeline]] - Lauren O'Donnell, Yogesh Rathi, C-F Westin
* [[2011_Winter_Project_Week:FreeWaterElimination |Free-water elimination]] - Ofer Pasternak, Demian Wassermann, C-F Westin
* Finsler tractography in ITK - Antonio Tristan-Vega, C-F Westin
* Statistical analysis of Cingulum extracted using Volumetric framework - Gopal Veni, Ross Whitaker

=== NA-MIC Kit Internals ===

* Command line module logic redesign (passing paramenters, tie into workflows) - Jim, Steve
* 64bit Windows Builds - Dave P
* Dashboards: Factory machine, subprojects, and CDash@Home - Dave P, Zack M, Steve, and Stephen
* MIDAS for data hosting - Zach M and Hans
* vtkWidgets - JC and Will, Nicole Aucoin
* [[2011_Winter_Project_Week:Annotation_module_in_Slicer4_Display_widget_intersections|Annotation module in Slicer4: Display widget intersections]] (Daniel Haehn, Nicole Aucoin, Steve Pieper)
* [[2011_Winter_Project_Week: Python and Slicer4| Python and Slicer4]]: Workflows, Scripting, and Porting - JC, Jim, Steve, and Danielle
* [[2011_Winter_Project_Week: Slice View Performance| Improve Performance of Slice Rendering in slicer3 and slicer4]] (Steve, Will, Jc, J2, Jim, Luca)
* [[2011_NAMIC_Project_week:_Real-Time_Volume_Rendering_for_Virtual_Colonoscopy| Real-Time Volume Rendering for Virtual Colonoscopy]] (Steve, Alex)

=== Execution Model ===
* Extract SlicerExecutionModel (SEM) into separate entity. SEM is the only component needed to build modules compatible with Slicer3D, so it should be easy incorporate into external applications without all of Slicer3D. Jim, Hans
* [[2011_Winter_Project_Week:ExtendSEMXml|Extend SEM xml]] to include sections for explicit grant acknowledgements, pointers to documentation, and pointers to examples. - Hans, Andriy
* [[2011_Winter_Project_Week:SEMXMLSchema|Create a formal schema for the SEM xml so that eternal tools (i.e. nipype) can validate the xml.]] - Hans Johnson, Jim Miller, Tim Olsen
* [[2011_Winter_Project_Week:XMLToMediaWiki|Improve documentation extractor script that converts XML to MediaWiki format so that it can directly push this information into the Slicer3D MediaWiki.]] - (Wiki Systems Admin), Hans Johnson
* [[2011_Winter_Project_Week:ExternalToolsMergingStrategies | Improve merging strategies between software that is part of externals tools and part of Slicer.]] - Mark Scully, Hans Johnson

=== Workflows and Integration ===
* Workflows and Service Oriented Architecture Solutions for Slicer3 Modules. - Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis

=== 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 28th, 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 28: Engineering Infrastructure Projects
#*November 4: Engineering Infrastructure Projects
#*November 11: DPB Projects: Iowa, Outcomes from Alg Core Retreat
#*November 18: DPB Projects: MGH
#*November 25: DBP Projects, Funded External Collaborations
#*December 2: Funded External Collaborations
#*December 9: Other External Collaborations
#*December 16:Finalize Engineering Projects
#*January 6: Loose Ends
#By December 16, 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 16, 2010: 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 Summer Project Week

2010-06-03T19:38:58Z

Fli: /* IGT */

__NOTOC__

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

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

==Background==

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

==Projects==

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

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

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, ?)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)

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

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

=== Shape Analysis ===
* Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)
=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)

=== Python ===
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

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

=== Execution Model ===

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

== Preparation ==

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

==Attendee List==

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

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

2010 Summer Project Week

2010-06-03T19:38:21Z

Fli: /* 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]]

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

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

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

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

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

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

==Projects==

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

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

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, ?)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton)

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

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

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

=== Shape Analysis ===
* Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)
=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)

=== Python ===
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

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

=== Execution Model ===

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

== Preparation ==

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

==Attendee List==

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

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

2010 Summer Project Week

2010-06-03T19:37:45Z

Fli: /* 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]]

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

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

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

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

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

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

==Projects==

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

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

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, ?)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton)

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

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

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

=== Shape Analysis ===
* Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)
=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)

=== Python ===
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

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

=== Execution Model ===

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

== Preparation ==

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

==Attendee List==

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

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