NAMIC Wiki - User contributions [en]

2011 Summer Project Week DICOM Networking

2011-06-24T14:22:49Z

Nherlambang:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-dicomtent-2011-06-02.png|Current prototype (not fully functional) with DCMTK/Qt-based ctkDICOM widgets in Slicer4
Image:CtkDICOM-20110624.png|Latest ctkDICOM widgets (2011-6-24)
</gallery>

==Key Investigators==
* BWH: Nicole Aucoin, Noby Hata
* Isomics: Steve Pieper
* AZE: Nicholas Herlambang

Goal is to define use cases and test current implementations of DICOM networking.

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

<h3>Objective</h3>
Come away with a specific design for GUI and functionality of Slicer4's DICOM networking support.

Collect concrete use cases.

</div>

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

<h3>Approach, Plan</h3>

Review current prototypes and functionality available in various toolkits (CTK, DCMTK).
* [http://www.commontk.org/index.php/CTK-Hackfest-Feb-2011#ctkDICOM CTK DICOM work]

</div>

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

<h3>Progress</h3>
* Discussed concrete use cases with key customers
** DICOM-RT (Greg Sharp)
** Prostate Therapy (Andrey Fedorov)
* Reviewed mapping of DICOM and Displayable Hierarchies
* Some progress on ctkDICOM
** Better inter-connectivity between widgets
** Window/Level and zoom function in image previewer
** Cool new cine display in ctkDICOM!
** Defined some TODOs:
*** Multiple selections on data list
*** Show the number of images for each series in data list
*** Cine display accross series/studies
*** Implement search function on local SQLite database
*** Tool-tip previewing

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in: yes, a core part of slicer4
##Extension -- commandline: Maybe, if needed
##Extension -- loadable: no

File:CtkDICOM-20110624.png

2011-06-24T14:21:36Z

Nherlambang:

2011 Summer Project Week DICOM Networking

2011-06-24T13:28:53Z

Nherlambang: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-dicomtent-2011-06-02.png|Current prototype (not fully functional) with DCMTK/Qt-based ctkDICOM widgets in Slicer4
</gallery>

==Key Investigators==
* BWH: Nicole Aucoin, Noby Hata
* Isomics: Steve Pieper
* AZE: Nicholas Herlambang

Goal is to define use cases and test current implementations of DICOM networking.

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

<h3>Objective</h3>
Come away with a specific design for GUI and functionality of Slicer4's DICOM networking support.

Collect concrete use cases.

</div>

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

<h3>Approach, Plan</h3>

Review current prototypes and functionality available in various toolkits (CTK, DCMTK).
* [http://www.commontk.org/index.php/CTK-Hackfest-Feb-2011#ctkDICOM CTK DICOM work]

</div>

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

<h3>Progress</h3>
* Discussed concrete use cases with key customers
** DICOM-RT (Greg Sharp)
** Prostate Therapy (Andrey Fedorov)
* Reviewed mapping of DICOM and Displayable Hierarchies
* Some progress on ctkDICOM
** Better inter-connectivity between widgets
** Window/Level and zoom function in image previewer
** Cool new cine display in ctkDICOM!
** Defined some TODOs:
*** Multiple selections on data list
*** Show the number of images for each series in data list
*** Cine display accross series/studies
*** Implement search function on local SQLite database
*** Tool-tip previewing

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in: yes, a core part of slicer4
##Extension -- commandline: Maybe, if needed
##Extension -- loadable: no

2011 Summer Project Week DICOM Networking

2011-06-24T13:27:40Z

Nherlambang: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-dicomtent-2011-06-02.png|Current prototype (not fully functional) with DCMTK/Qt-based ctkDICOM widgets in Slicer4
</gallery>

==Key Investigators==
* BWH: Nicole Aucoin, Noby Hata
* Isomics: Steve Pieper
* AZE: Nicholas Herlambang

Goal is to define use cases and test current implementations of DICOM networking.

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

<h3>Objective</h3>
Come away with a specific design for GUI and functionality of Slicer4's DICOM networking support.

Collect concrete use cases.

</div>

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

<h3>Approach, Plan</h3>

Review current prototypes and functionality available in various toolkits (CTK, DCMTK).
* [http://www.commontk.org/index.php/CTK-Hackfest-Feb-2011#ctkDICOM CTK DICOM work]

</div>

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

<h3>Progress</h3>
* Discussed concrete use cases with key customers
** DICOM-RT (Greg Sharp)
** Prostate Therapy (Andrey Fedorov)
* Reviewed mapping of DICOM and Displayable Hierarchies
* Some progress on ctkDICOM
** Better inter-connectivity between widgets
** Window/Level and zoom function in image previewer
** Cool new cine display in ctkDICOM!
** Defined some TODOs:
*** Multiple selections in data list
*** Show the number of images for each series in data list
*** Cine display accross series/studies
*** Implement search function on local SQLite database

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in: yes, a core part of slicer4
##Extension -- commandline: Maybe, if needed
##Extension -- loadable: no

2011 Summer Project Week DICOM Networking

2011-06-24T13:13:19Z

Nherlambang: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-dicomtent-2011-06-02.png|Current prototype (not fully functional) with DCMTK/Qt-based ctkDICOM widgets in Slicer4
</gallery>

==Key Investigators==
* BWH: Nicole Aucoin, Noby Hata
* Isomics: Steve Pieper
* AZE: Nicholas Herlambang

Goal is to define use cases and test current implementations of DICOM networking.

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

<h3>Objective</h3>
Come away with a specific design for GUI and functionality of Slicer4's DICOM networking support.

Collect concrete use cases.

</div>

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

<h3>Approach, Plan</h3>

Review current prototypes and functionality available in various toolkits (CTK, DCMTK).
* [http://www.commontk.org/index.php/CTK-Hackfest-Feb-2011#ctkDICOM CTK DICOM work]

</div>

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

<h3>Progress</h3>
* Discussed concrete use cases with key customers
** DICOM-RT (Greg Sharp)
** Prostate Therapy (Andrey Fedorov)
* Reviewed mapping of DICOM and Displayable Hierarchies
* Some progress on ctkDICOM
** Better inter-connectivity between widgets
** Window/Level and zoom function in image previewer
** Cool new cine display in ctkDICOM!
** Defined some TODOs:
*** Multiple selection in data list
*** Show the number of images for each series in data list
*** Cine display accross series/studies
*** Search function on local SQLite database

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in: yes, a core part of slicer4
##Extension -- commandline: Maybe, if needed
##Extension -- loadable: no

2011 Winter Project Week:ThinClientQtInterfaceForIGT

2011-01-14T15:57:11Z

Nherlambang: /* Key Investigators */

__NOTOC__
<gallery>

</gallery>

== Key Investigators ==
* AZE: Nicholas Herlambang
* BWH: Nobuhiko Hata
* Isomics: Steve Pieper
* Kitware: Julien Finet, JC

<div style="margin: 20px;">
<div style="width: 33%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Considering the space available in operating room, one ideal scenario for IGT is to have processing power of a workstation on a smaller form-factor devices such as laptop PC. By separating GUI from the processing engine, it is possible to use laptop PC in the operating room, while the processing workstation is put outside the operating room.
Our objective is to develop a thin-client for IGT that provides visualization from and receive user input to be passed to the server (3D Slicer). We will use Qt to built the thin-client GUI, and define a messaging protocol for passing images from the server and user input to the server.

</div>
<div style="width: 30%; float: left;">

<h3>Approach, Plan</h3>
* Build thin-client GUI with Qt
* Define messaging protocol for data transfer between the thin-client and server (3D Slicer)
* Build a simple viewer application for preliminary assessment
</div>
<div style="width: 33%; float: left;">

<h3>Progress</h3>
* Preliminary system design
** Use Slicer4
** Separate GUI and processing engine at MRML layer
** Server-Client communication using Python scripting
** Utilize OpenIGTLink for transfer protocol
*** Python scripting over OpenIGTLink
*** Implementation of Remote Frame Buffer over OpenIGTLink
** vtkWindowToImageFilter for screen grabbing

</div>
</div>

2011 Winter Project Week:ThinClientQtInterfaceForIGT

2011-01-14T14:45:20Z

Nherlambang: /* Key Investigators */

__NOTOC__
<gallery>

</gallery>

== Key Investigators ==
* AZE: Nicholas Herlambang
* BWH: Nobuhiko Hata
* Isomics: Steve Pieper
* Kitware: Julien Finet, JC

<div style="margin: 20px;">
<div style="width: 33%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Considering the space available in operating room, one ideal scenario for IGT is to have processing power of a workstation on a smaller form-factor devices such as laptop PC. By separating GUI from the processing engine, it is possible to use laptop PC in the operating room, while the processing workstation is put outside the operating room.
Our objective is to develop a thin-client for IGT that provides visualization from and receive user input to be passed to the server (3D Slicer). We will use Qt to built the thin-client GUI, and define a messaging protocol for passing images from the server and user input to the server.

</div>
<div style="width: 30%; float: left;">

<h3>Approach, Plan</h3>
* Build thin-client GUI with Qt
* Define messaging protocol for data transfer between the thin-client and server (3D Slicer)
* Build a simple viewer application for preliminary assessment
</div>
<div style="width: 33%; float: left;">

<h3>Progress</h3>
* Preliminary system design
** Use Slicer4
** Separate GUI and processing engine at MRML layer
** Server-Client communication using Python scripting
** vtkWindowToImageFilter for screen grabbing
** Utilize OpenIGTLink for transfer protocol
*** Python scripting over OpenIGTLink
*** Implementation of Remote Frame Buffer over OpenIGTLink

</div>
</div>

2011 Winter Project Week:ThinClientQtInterfaceForIGT

2011-01-14T11:24:27Z

Nherlambang: /* Key Investigators */

__NOTOC__
<gallery>

</gallery>

== Key Investigators ==
* AZE: Nicholas Herlambang
* BWH: Nobuhiko Hata
* Isomics: Steve Pieper
* Kitware: Julien Finet, JC

<div style="margin: 20px;">
<div style="width: 33%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Considering the space available in operating room, one ideal scenario for IGT is to have processing power of a workstation on a smaller form-factor devices such as laptop PC. By separating GUI from the processing engine, it is possible to use laptop PC in the operating room, while the processing workstation is put outside the operating room.
Our objective is to develop a thin-client for IGT that provides visualization from and receive user input to be passed to the server (3D Slicer). We will use Qt to built the thin-client GUI, and define a messaging protocol for passing images from the server and user input to the server.

</div>
<div style="width: 30%; float: left;">

<h3>Approach, Plan</h3>
* Build thin-client GUI with Qt
* Define messaging protocol for data transfer between the thin-client and server (3D Slicer)
* Build a simple viewer application for preliminary assessment
</div>
<div style="width: 33%; float: left;">

<h3>Progress</h3>
* Preliminary system design
** Use Slicer4
** Separate GUI and processing engine at Python layer
** vtkWindowToImageFilter for screen grabbing
** Utilize OpenIGTLink
*** Python scripting over OpenIGTLink
*** Implementation of Remote Frame Buffer over OpenIGTLink

</div>
</div>

2011 Winter Project Week:ThinClientQtInterfaceForIGT

2011-01-10T14:25:00Z

Nherlambang: /* Key Investigators */

__NOTOC__
<gallery>

</gallery>

== Key Investigators ==
* AZE: Nicholas Herlambang
* BWH: Nobuhiko Hata
* Isomics: Steve Pieper
* Kitware: Julien Finet, JC

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

<h3>Objective</h3>
Considering the space available in operating room, one ideal scenario for IGT is to have processing power of a workstation on a smaller form-factor devices such as laptop PC. By separating GUI from the processing engine, it is possible to use laptop PC in the operating room, while the processing workstation is put outside the operating room.
Our objective is to develop a thin-client for IGT that provides visualization from and receive user input to be passed to the server (3D Slicer). We will use Qt to built the thin-client GUI, and define a messaging protocol for passing images from the server and user input to the server.

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

<h3>Approach, Plan</h3>
* Build thin-client GUI with Qt
* Define messaging protocol for data transfer between the thin-client and server (3D Slicer)
* Build a simple viewer application for preliminary assessment
</div>

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

</div>
</div>
<div style="width: 95%; float: left;">

2011 Winter Project Week:ThinClientQtInterfaceForIGT

2010-12-16T00:55:10Z

Nherlambang: Created page with '__NOTOC__ <gallery> </gallery> == Key Investigators == * AZE: Nicholas Herlambang <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Ob…'

__NOTOC__
<gallery>

</gallery>

== Key Investigators ==
* AZE: Nicholas Herlambang

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

<h3>Objective</h3>
Considering the space available in operating room, one ideal scenario for IGT is to have processing power of a workstation on a smaller form-factor devices such as laptop PC. By separating GUI from the processing engine, it is possible to use laptop PC in the operating room, while the processing workstation is put outside the operating room.
Our objective is to develop a thin-client for IGT that provides visualization from and receive user input to be passed to the server (3D Slicer). We will use Qt to built the thin-client GUI, and define a messaging protocol for passing images from the server and user input to the server.

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

<h3>Approach, Plan</h3>
* Build thin-client GUI with Qt
* Define messaging protocol for data transfer between the thin-client and server (3D Slicer)
* Build a simple viewer application for preliminary assessment
</div>

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

</div>
</div>
<div style="width: 95%; float: left;">

2011 Winter Project Week

2010-12-16T00:33:35Z

Nherlambang: /* 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 ===
* Extension of ABC (Atlas-Based Classification) to detect pathology categories, with tests on TBI images (Bo Wang, 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)
* The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper)
*TubeTK for vascular image segmentation and analysis (Stephen Aylward, Danielle Pace)
* A stenosis detector in Slicer4 using VMTK (Suares Tamekue, Daniel Haehn, Luca Antiga)
* [[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)

=== 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)
* Efficient co-registration of multiple MR modalities using the ABC (atlas-based classification) framework, joint visualization of multiple co-registered modalities (Bo Wang, Guido Gerig)
* DTI-MRI registration: Evaluation of large deformation diffeomorphic mapping (LDDMM) with other nonlinear registration schemes (Anuja Sharma, Guido Gerig)
* Registration of CT and MRI volumes for Adaptive Radiotherapy (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
* Atlas Registration in Slicer3 (Daniel Haehn, Dominik Meier, Kilian Pohl)
* 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)
*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)
*Transform recorder and (surgical) procedure annotation module (Tamas Ungi, Junichi Tokuda)

=== 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, Chris Gloschat
* Particle Systems for Shape Analysis - Josh Cates, Manasi Datar, Ross Whitaker

=== 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
* Annotation module in Slicer4: Display widget intersections (Daniel Haehn, Nicole Aucoin, Steve Pieper)

=== 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
* Two-tensor full brain tractography pipeline - Lauren O'Donnell, Yogesh Rathi, C-F Westin
* 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: 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, Luca)

=== 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 Implementing Open IGT Link to Virtual Place for research support

2010-06-25T15:11:46Z

Nherlambang: /* Key Investigators */

==Key Investigators==
*AZE: Nicholas Herlambang, Masakatsu Hoashi
*BWH: Noby Hata, Junichi Tokuda

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

<h3>Objective</h3>

Our objective is to add Open IGT Link support into AZE Virtual Place(VP) for research support. We would like to enable users to do image processing outsite VP and visualization with VP.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop Open IGT Link plugin in Virtual Place similar to Open IGT Link module in Slicer3. We would like to add MATLAB connectivity through Open IGT Link.

</div>

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

<h3>Progress</h3>
Preparation:<br>
Prototype plug-in that acts as Open IGT Link server has been developed. MATLAB code that acts as Open IGT Link client has also been developed. We will focus on performance and stability during this Project Week. <br><br>
Progress during Project Week: <br>
We successfully connect MATLAB and VirtualPlace through OpenIGTLink. A usage example: MATLAB get a 3D image data from VirtualPlace, perform FFT transform, low-pass filter, and reverse FFT transform in MATLAB, and then send back the result image to VirtualPlace to be visualized with volume rendering immediately. A stability issue was pointed out and solved during Project Week. "One more thing": We tried connection through OpenIGTLink interface of BioImage Suite to BrainLAB system, and successfully received tracking data from BrainLAB system.

</div>
</div>

[[File:VPMatlab-before.jpg|100px]]
[[File:Matlab-fig1.jpg|100px]]
[[File:Matlab-fig2.jpg|100px]]
[[File:Matlab-fig3.jpg|100px]]
[[File:Matlab-fig4.jpg|100px]]
[[File:VPMatlab-after.jpg|100px]]

File:VPMatlab-after.jpg

2010-06-25T15:10:55Z

Nherlambang: uploaded a new version of "File:VPMatlab-after.jpg"

Visualization of 3D data in VirtualPlace after low pass filtering done in MATLAB

File:VPMatlab-before.jpg

2010-06-25T15:07:27Z

Nherlambang: uploaded a new version of "File:VPMatlab-before.jpg"

Visualization of 3D data in VirtualPlace before filtering.

2010 Summer Project Week

2010-06-25T14:22:06Z

Nherlambang: /* IGT */

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

[[Image:PW-MIT2010.png|500px|right]]

__TOC__
<br>
[http://www.smugmug.com/gallery/12687574_DsJjF '''Photos ''']
<br>
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 21
!width="250px"|Tuesday, June 22
!width="250px"|Wednesday, June 23
!width="250px"|Thursday, June 24
!width="250px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am:''' [[Media:NAMIC Kit-2010-6-22.ppt|NA-MIC Kit Update]] (Jim Miller)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''9:20am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am:''' Superbuild Demo (Dave Partyka)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10:15am:''' Break
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10:30-11am:''' [[Media:2010_Project_Week_OpenIGTLink.ppt|OpenIGTLink Update]] (Junichi Tokuda)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''11am-12pm:''' [[2010_Summer_Project_Week_Slicer_Hands-on_Workshop|Slicer Hands-on Workshop]] (Randy Gollub, Sonia Pujol)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font>
<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Stephen Aylward)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
<br>[[MIT_Project_Week_Rooms#Kiva|Kiva Room]]
<br>----------------------------------------<br>
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)
<br>[[MIT_Project_Week_Rooms#32-261|32-261 Room]]
<br>----------------------------------------<br>
<br>'''5pm: <font color="#4020ff">Reception'''</font><br>
<br>[[MIT_Project_Week_Rooms#R&D Pub|R&D Pub]]
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
<br>----------------------------------------<br>
'''2-3pm:''' Simple Git (Steve Pieper) [[media:Simple Git-pieper-2010-06-24.ppt|(Slides)]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

Please note:
*We need to empty room by 1:30pm on Friday. 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| January 3-7, 2011, Salt Lake City, Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week_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_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Johannes Schick, Steve Pieper, Ron Kikinis)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[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_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward, Andriy Fedorov)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

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

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

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi Tokuda, Tamas Ungi, Haiying Liu, Sam Song)]]
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Masakatsu Hoashi, Junichi Tokuda, Noby Hata)
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, Noby Hata)

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

=== Analysis ===
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner, Andriy Fedorov)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_Summer_Project_Week_Quantification_Of_Lesion_Diffusion_Disruption| Quantification of Lesion Diffusion Disruption]](M Scully, H J Bockholt)
#[[2010_Summer_Project_Week_Lupus_Lesion_Segmentation_and_Review_Statistics|Lupus Lesion Segmentation and Review Statistics]](M Scully, H J Bockholt)

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

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

=== Workflows and Integration ===
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

==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]]

== 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>

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

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-25T14:12:54Z

Nherlambang:

==Key Investigators==
*AZE: Nicholas Herlambang, Masakatsu Hoashi
*BWH: Noby Hata, Junichi Tokuda

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

<h3>Objective</h3>

Our objective is to add Open IGT Link support into AZE Virtual Place(VP) for research support. We would like to enable users to do image processing outsite VP and visualization with VP.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop Open IGT Link plugin in Virtual Place similar to Open IGT Link module in Slicer3. We would like to add MATLAB connectivity through Open IGT Link.

</div>

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

<h3>Progress</h3>
Preparation:<br>
Prototype plug-in that acts as Open IGT Link server has been developed. MATLAB code that acts as Open IGT Link client has also been developed. We will focus on performance and stability during this Project Week. <br><br>
Progress during Project Week: <br>
We successfully connect MATLAB and VirtualPlace through OpenIGTLink. A usage example: MATLAB get a 3D image data from VirtualPlace, perform FFT transform, low-pass filter, and reverse FFT transform in MATLAB, and then send back the result image to VirtualPlace to be visualized with volume rendering immediately. A stability issue was pointed out and solved during Project Week. "One more thing": We tried connection through OpenIGTLink interface of BioImage Suite to BrainLAB system, and successfully received tracking data from BrainLAB system.

</div>
</div>

[[File:VPMatlab-before.jpg|600px]]

[[File:Matlab-fig1.jpg|300px]]
[[File:Matlab-fig2.jpg|300px]]

[[File:Matlab-fig3.jpg|300px]]
[[File:Matlab-fig4.jpg|300px]]

[[File:VPMatlab-after.jpg|600px]]

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-25T14:04:32Z

Nherlambang:

==Key Investigators==
*AZE: Nicholas Herlambang, Masakatsu Hoashi
*BWH: Noby Hata, Junichi Tokuda

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

<h3>Objective</h3>

Our objective is to add Open IGT Link support into AZE Virtual Place(VP) for research support. We would like to enable users to do image processing outsite VP and visualization with VP.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop Open IGT Link plugin in Virtual Place similar to Open IGT Link module in Slicer3. We would like to add MATLAB connectivity through Open IGT Link.

</div>

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

<h3>Progress</h3>
Preparation:<br>
Prototype plug-in that acts as Open IGT Link server has been developed. MATLAB code that acts as Open IGT Link client has also been developed. We will focus on performance and stability during this Project Week. <br><br>
Progress during Project Week: <br>
We successfully connect MATLAB and VirtualPlace through OpenIGTLink. A usage example: MATLAB get a 3D image data from VirtualPlace, perform FFT transform, low-pass filter, and reverse FFT transform in MATLAB, and then send back the result image to VirtualPlace to be visualized with volume rendering immediately. A stability issue was pointed out and solved during Project Week. "One more thing": We tried connection through OpenIGTLink interface of BioImage Suite to BrainLAB system, and successfully received tracking data from BrainLAB system.

</div>
</div>

[[File:VPMatlab-before.jpg|1000px]]

[[File:Matlab-fig1.jpg|500px]]
[[File:Matlab-fig2.jpg|500px]]
[[File:Matlab-fig3.jpg|500px]]
[[File:Matlab-fig4.jpg|500px]]

[[File:VPMatlab-after.jpg|1000px]]

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-25T13:58:52Z

Nherlambang:

==Key Investigators==
*AZE: Nicholas Herlambang, Masakatsu Hoashi
*BWH: Noby Hata, Junichi Tokuda

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

<h3>Objective</h3>

Our objective is to add Open IGT Link support into AZE Virtual Place(VP) for research support. We would like to enable users to do image processing outsite VP and visualization with VP.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop Open IGT Link plugin in Virtual Place similar to Open IGT Link module in Slicer3. We would like to add MATLAB connectivity through Open IGT Link.

</div>

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

<h3>Progress</h3>
Preparation:<br>
Prototype plug-in that acts as Open IGT Link server has been developed. MATLAB code that acts as Open IGT Link client has also been developed. We will focus on performance and stability during this Project Week. <br><br>
Progress during Project Week: <br>
We successfully connect MATLAB and VirtualPlace through OpenIGTLink. A usage example: MATLAB get a 3D image data from VirtualPlace, perform FFT transform, low-pass filter, and reverse FFT transform in MATLAB, and then send back the result image to VirtualPlace to be visualized with volume rendering immediately. A stability issue was pointed out and solved during Project Week. "One more thing": We tried connection through OpenIGTLink interface of BioImage Suite to BrainLAB system, and successfully received tracking data from BrainLAB system.

</div>
</div>

<div style="width:500px">
[[File:VPMatlab-before.jpg]]
</div>

[[File:Matlab-fig1.jpg]]
[[File:Matlab-fig2.jpg]]
[[File:Matlab-fig3.jpg]]
[[File:Matlab-fig4.jpg]]

[[File:VPMatlab-after.jpg]]

File:Matlab-fig4.jpg

2010-06-25T13:56:52Z

Nherlambang: cross-sectional image of 3D data (after low pass filtering)

cross-sectional image of 3D data (after low pass filtering)

File:Matlab-fig3.jpg

2010-06-25T13:55:36Z

Nherlambang: cross-sectional image in frequency domain (after low pass filtering)

cross-sectional image in frequency domain (after low pass filtering)

File:Matlab-fig2.jpg

2010-06-25T13:55:05Z

Nherlambang: cross-sectional image in frequency domain (before filtering)

cross-sectional image in frequency domain (before filtering)

File:Matlab-fig1.jpg

2010-06-25T13:54:01Z

Nherlambang: Cross-sectional view (before filtering)

Cross-sectional view (before filtering)

File:VPMatlab-after.jpg

2010-06-25T13:52:39Z

Nherlambang: Visualization of 3D data in VirtualPlace after low pass filtering done in MATLAB

Visualization of 3D data in VirtualPlace after low pass filtering done in MATLAB

File:VPMatlab-before.jpg

2010-06-25T13:51:53Z

Nherlambang: Visualization of 3D data in VirtualPlace before filtering.

Visualization of 3D data in VirtualPlace before filtering.

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-25T13:50:30Z

Nherlambang:

==Key Investigators==
*AZE: Nicholas Herlambang, Masakatsu Hoashi
*BWH: Noby Hata, Junichi Tokuda

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

<h3>Objective</h3>

Our objective is to add Open IGT Link support into AZE Virtual Place(VP) for research support. We would like to enable users to do image processing outsite VP and visualization with VP.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop Open IGT Link plugin in Virtual Place similar to Open IGT Link module in Slicer3. We would like to add MATLAB connectivity through Open IGT Link.

</div>

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

<h3>Progress</h3>
Preparation:<br>
Prototype plug-in that acts as Open IGT Link server has been developed. MATLAB code that acts as Open IGT Link client has also been developed. We will focus on performance and stability during this Project Week. <br><br>
Progress during Project Week: <br>
We successfully connect MATLAB and VirtualPlace through OpenIGTLink. A usage example: MATLAB get a 3D image data from VirtualPlace, perform FFT transform, low-pass filter, and reverse FFT transform in MATLAB, and then send back the result image to VirtualPlace to be visualized with volume rendering immediately. A stability issue was pointed out and solved during Project Week. "One more thing": We tried connection through OpenIGTLink interface of BioImage Suite to BrainLAB system, and successfully received tracking data from BrainLAB system.

</div>
</div>

[[File:VPMatlab-before.jpg]]

[[File:Matlab-fig1.jpg]]
[[File:Matlab-fig2.jpg]]
[[File:Matlab-fig3.jpg]]
[[File:Matlab-fig4.jpg]]

[[File:VPMatlab-after.jpg]]

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-25T10:10:23Z

Nherlambang: /* Key Investigators */

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-25T10:10:05Z

Nherlambang: /* Key Investigators */

==Key Investigators==
*AZE: Nicholas Herlambang, Masakatsu Hoashi
*BWH: Noby Hata, Junichi Tokuda

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

<h3>Objective</h3>

Our objective is to add Open IGT Link support into AZE Virtual Place(VP) for research support. We would like to enable users to do image processing outsite VP and visualization with VP.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop Open IGT Link plugin in Virtual Place similar to Open IGT Link module in Slicer3. We would like to add MATLAB connectivity through Open IGT Link.

</div>

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

<h3>Progress</h3>
Preparation:<br>
Prototype plug-in that acts as Open IGT Link server has been developed. MATLAB code that acts as Open IGT Link client has also been developed. We will focus on performance and stability during this Project Week. <br><br>
Progress during Project Week: <br>
We successfully connect MATLAB and VirtualPlace through OpenIGTLink. A usage example: MATLAB get a 3D image data from VirtualPlace, perform FFT transform, low-pass filter, and reverse FFT transform in MATLAB, and then send back the result image to VirtualPlace to be visualized with volume rendering immediately. A stability issue was pointed out and solved during Project Week. "One more thing": We tried connection through OpenIGTLink interface of BioImage Suite to BrainLAB system, and successfully receive tracking data from BrainLAB system.

</div>
</div>

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-25T10:08:48Z

Nherlambang: /* Key Investigators */

==Key Investigators==
*AZE: Nicholas Herlambang, Masakatsu Hoashi
*BWH: Noby Hata, Junichi Tokuda

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

<h3>Objective</h3>

Our objective is to add Open IGT Link support into AZE Virtual Place(VP) for research support. We would like to enable users to do image processing outsite VP and visualization with VP.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop Open IGT Link plugin in Virtual Place similar to Open IGT Link module in Slicer3. We would like to add MATLAB connectivity through Open IGT Link.

</div>

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

<h3>Progress</h3>
Preparation:<br>
Prototype plug-in that acts as Open IGT Link server has been developed. MATLAB code that acts as Open IGT Link client has also been developed. We will focus on performance and stability during this Project Week. <br><br>
Progress during Project Week: <br>
We successfully connect MATLAB and VirtualPlace through OpenIGTLink. A usage example: MATLAB get a 3D image data from VirtualPlace, perform FFT transform, low-pass filter, and reverse FFT transform in MATLAB, and then send back the result image to VirtualPlace to be visualized with volume rendering immediately. A stability issue was pointed out and solved during Project Week. "One more thing": We tried connection through OpenIGTLink interface of BioImage Suite to Brain Lab system, and successfully receive tracking data from Brain Lab system.

</div>
</div>

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-21T19:45:42Z

Nherlambang: /* Key Investigators */

2010 Summer Project Week Breakout Session: Volume Rendering

2010-06-21T17:53:44Z

Nherlambang: /* Participants */

[[2010_Summer_Project_Week|Back to Project Week 2010]]

= Breakout session on Volume Rendering =
Goal of this session is to compare and contrast various volume rendering approaches in the context of clinical application scenarios. This will mainly be done through hands-on demos and group discussion.

* When: 3pm Thursday June 24
* Where: at a projector in the project week room.

Systems to examine:
* VTK GPU Raycasting in slicer 3.6 (GLSL)
* NCI GPU Raycasting in slicer 3.6 (GLSL)
* Microsoft research volume rendering demo (CUDA, closed source)
* Others?

Scenarios:
* Virtual Colonoscopy
* PET-CT
* Microscopy

== Preparation ==
Earlier in the project week we will work on getting the same datasets loaded on the various systems.

== Participants ==
Please add your name to the list if you are interested in participating in this session
# Steve Pieper, Isomics, Inc.
# Julien Finet, Kitware Inc.
# Alex Yarmarkovich, Isomics, Inc.
# Yanling Liu, SAIC-Frederick/NCI-Frederick.
# Jim Barabas, MIT Media Lab.
# Arnaud Gelas, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Andriy Fedorov, SPL
# Curtis Lisle, KnowledgeVis
# Nicholas Herlambang, AZE, Ltd.

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-16T10:22:15Z

Nherlambang:

==Key Investigators==
*AZE: Nicholas Herlambang
*BWH: Noby Hata

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

<h3>Objective</h3>

Our objective is to add Open IGT Link support into AZE Virtual Place(VP) for research support. We would like to enable users to do image processing outsite VP and visualization with VP.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop Open IGT Link plugin in Virtual Place similar to Open IGT Link module in Slicer3. We would like to add MATLAB connectivity through Open IGT Link.

</div>

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

<h3>Progress</h3>

Prototype plug-in that acts as Open IGT Link server has been developed. MATLAB code that acts as Open IGT Link client has also been developed. We will focus on performance and stability during this Project Week.

</div>
</div>

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-10T01:02:22Z

Nherlambang: /* Key Investigators */

2010 Summer Project Week Implementing Open IGT Link to Virtual Place for research support

2010-06-10T00:29:44Z

Nherlambang: Created page with '==Key Investigators== *AZE: Nicholas Herlambang *BWH: Noby Hata <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Objective</h3> </…'

==Key Investigators==
*AZE: Nicholas Herlambang
*BWH: Noby Hata

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

<h3>Objective</h3>

</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>

</div>
</div>

2010 Summer Project Week

2010-06-10T00:24:36Z

Nherlambang: /* 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 Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

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

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

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

==Projects==

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

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

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi)
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith)
*[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

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

=== 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
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
* [[Particle Based Shape Regression ]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)

=== 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)
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Ross Whitaker)

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

*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Ron Kikinis)
*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.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# 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
#Fritscher, Karl, UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Haehn Daniel , University of Pennsylvania
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
#Halle, Michael, BWH
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# 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
# Marcus Daniel , Washington University
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# 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, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , Brigham and Women's Hospital
# Tao Xiaodong , GE Research
#Tokuda, Junichi, BWH
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
#Weinrich, Adam, Nokia
# Wells Sandy , BWH
# Wu Guorong , University of North Carolina at Chapel Hill
#Yarmarkovich, Alexander, ISOMICS

2010 Summer Project Week

2010-06-10T00:00:23Z

Nherlambang: /* 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 Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

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

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

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

==Projects==

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

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

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
* [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi)
*[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith)
*Implementing Open IGT Link to Virtual Place for research support(Nicholas Herlambang, Noby Hata)

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

=== 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
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
* [[Particle Based Shape Regression ]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)

=== 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)
*[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
*[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Ross Whitaker)

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

*[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Ron Kikinis)
*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.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# 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
#Fritscher, Karl, UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Haehn Daniel , University of Pennsylvania
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
#Halle, Michael, BWH
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# 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
# Marcus Daniel , Washington University
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# 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, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , Brigham and Women's Hospital
# Tao Xiaodong , GE Research
#Tokuda, Junichi, BWH
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
#Weinrich, Adam, Nokia
# Wells Sandy , BWH
# Wu Guorong , University of North Carolina at Chapel Hill
#Yarmarkovich, Alexander, ISOMICS