Difference between revisions of "2007 Programming/Project Week MIT"

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Back to [[Engineering:Programming_Events|Programming/Project Events]]
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__NOTOC__
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Back to [[Events]]
  
== Logistics ==
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[[Image:ProjectWeek-2007.png|200px]]
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=Welcome to the web page for the 5th Project Week!=
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[[Image:Mit.jpg|thumb|right|400px|Photo taken by Jeffrey Hawley. More [http://woofton.rivendel.net/gallery2/main.php?g2_itemId=3945 photos ] taken by Jeffrey Hawley.]]
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==Summary==
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The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 48 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.
  
'''Dates:''' June 25-29, 2007
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Statistics at a glance:
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* 85 Registered Attendees:  35 NA-MIC participants, 48 collaborators, 2 EAB+NIH
 +
**  35 NA-MIC Participants breakdown by cores: Core 1 (7), Core 2 (14), Core 3 (10), Core 4-5-6-7 (4)
 +
** 46 Collaborators: Acoustic Med (2), BWH (19), Caltech (2), GE (1), Harvard IIC (1), JHU (1), Kitware (1), Knowledge Vis (1), Mario Negri (1), MGH (2), NWU (4), University of Iowa(12), Virginia Tech (1)
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*  41 Projects: DBP-II(6), Structural Analysis (2), Diffusion Image Analysis (7), NA-MIC Kit (14), External Collaborations (12)
  
'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
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A summary of all past NA-MIC Project Events is available [[Project_Events#Past_Project_Weeks|here]].
  
'''Registration Fee:''' $200 (this will cover the cost of breakfast and lunch for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:  
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== Logistics ==
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*Dates: June 25-29, 2007.
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*Location: MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
 +
 
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'''Registration Fee:''' $200 (this will cover the cost of breakfast, lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:  
 
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139
 
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139
  
 
If you are attending for one day only, the registration fee is not required.
 
If you are attending for one day only, the registration fee is not required.
  
'''Hotel:''' There is no official hotel for the meeting. Here is some information about 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.
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'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) 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.
 +
 
 +
([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])
  
 
===Introduction to NA-MIC Project Week===
 
===Introduction to NA-MIC Project Week===
  
This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).   
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NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).   
 
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.   
 
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.   
  
 
* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
 
* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
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* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
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* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
 
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
 
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
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* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
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* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
 
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu).  Please note that the event is open to people outside NA-MIC, subject to availability.
 
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu).  Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
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* Everyone should '''bring a laptop'''. We will have four projectors.
 
* About half the time will be spent working on projects and the other half in project related discussions.
 
* About half the time will be spent working on projects and the other half in project related discussions.
 
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
 
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
 
 
  
 
=== Agenda===
 
=== Agenda===
 
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* Monday June 25
* Monday
 
 
** noon-1pm lunch  
 
** noon-1pm lunch  
** 1-3:30pm Introduce Projects using 4-block slides (all Project Leads)
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**1pm: Welcome (Ron Kikinis)
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** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])  
 
** 3:30-5:30pm Start project work
 
** 3:30-5:30pm Start project work
* Tuesday
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** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
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* Tuesday June 26
 
** 8:30am breakfast
 
** 8:30am breakfast
** 9-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
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** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
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*** [[Media:NAMICSoftwareProcess.ppt|Bill's presentation]], [[Media:Boost Process.ppt|David's presentation]]
 +
** 10-10:30am [[Project Week 2007 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
 +
** 11am [[Special topic breakout: Grid Computing]] (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
 +
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
 
** noon lunch
 
** noon lunch
** 1-2pm: Special topic breakout: Non-Linear Registration (Stephen)
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** 1:30-2:30pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: Special topic breakout: DWI/DTI (?)
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** 2:30-3:30pm: [[Special topic breakout: Non-Linear Registration]]
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** 3:30-4:30pm: [[Special topic breakout: Atlases]]
 +
** 4:30-5:30pm: [[Special topic breakout: DWI/DTI]]
 
** 5:30pm adjourn for day
 
** 5:30pm adjourn for day
* Wednesday
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* Wednesday June 27
 
** 8:30am breakfast
 
** 8:30am breakfast
** 9-10am Special topic breakout:  
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** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
 
** noon lunch
 
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items|  Plan for Long Lead Time Items]]
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** 4-5pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items|  Plan for Long Lead Time Items]]
 
** 5:30pm adjourn for day
 
** 5:30pm adjourn for day
* Thursday
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* Thursday June 28
 
** 8:30am breakfast
 
** 8:30am breakfast
 
** noon lunch
 
** noon lunch
** 3:30-5pm Special topic breakout: TBD
 
 
** 5:30pm adjourn for day
 
** 5:30pm adjourn for day
* Friday
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* Friday June 29
 
** 8:30am breakfast
 
** 8:30am breakfast
** 10am-noon: Project Progress using 4-block slides
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** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn
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** noon lunch boxes and adjourn.  (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])
  
 
=== Preparation ===
 
=== Preparation ===
  
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
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# 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].
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
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# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engineer Core Projects and Assign/Verify Teams]]
 
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
 
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
 
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
 
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
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## 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.)
 
## 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. (Andy)
 
## 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. (Andy)
# By 3pm ET on June 14, 2007: Complete the top half of [[media:NA-MIC_Latest_4-Block_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
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# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/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.
# [[Engineering:TCON_2007#2005-06-14|June 14, 2007: TCON#3 Review of 4-Blocks (Structural, DTI, Collaboration, Other)]]
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# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Review of 4-Blocks (NA-MIC Kit)]]
 
 
# 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...
 
# 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...
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== A History in Wiki Links ==
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A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].
  
 
== Projects ==
 
== Projects ==
 
 
===DBP II===
 
===DBP II===
 
These are projects by the new set of DBPS:
 
These are projects by the new set of DBPS:
*(MIND/UNM)
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#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
*[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU)
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#* [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
*(Harvard)
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#*[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
*(UNC)
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#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
 +
#*[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
 +
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
 +
#*[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
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#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
 +
#*[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
 +
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)
  
 
===Structural Analysis===
 
===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
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#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
*vtkITK wrapper for rule based segmentation (Brad Davis, John Melonakis, Marek Kubiki)
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#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)
** Application of the Slicer2 module on DBP data
 
** Conversion to Slicer3
 
  
 
===Diffusion Image Analysis===
 
===Diffusion Image Analysis===
 +
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)
 +
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
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# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
 +
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
 +
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
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# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)
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# [[Projects/Diffusion/2007_Project_Week_Glyphed_Visualization_For_Volume_Data|Sliced Multiple Glyphed Visualization for Volume Data]] (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)
  
===NA-MIC Kit===
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===Calibration/Validation===
* Slicer3
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This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
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#[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Ross Whitaker, Guido Gerig, Randy Gollub)
** Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
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** MRML Scenes for the Execution Model, including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Steve Pieper)
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===NA-MIC Kit - Slicer 3===
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
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#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** Python support in Slicer3 (Luca, Steve, depends on Dan's availability)
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#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
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# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
** GUI Lightbox mode (Wendy)
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# [[Projects/Slicer3/2007_Project_Week_Lightbox|Lightbox]] (James, Jim, Wendy, Alex)
* Slicer2
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# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Curt, Nicole, Alex, Steve, Will, Vince)
 +
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
 +
# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Katie, Steve, Bill Hoffman)
 +
# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
 +
# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
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# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
 +
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
 +
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)
 +
# [[Projects/Slicer3/2007_Project_Week_Lego Mindstorms dissemination for IGT | Lego Mindstorms Dissemination for IGT]] (Danielle Pace)
 +
# [[Projects/Slicer3/2007_Project_Week_EdgeDetection | Edge Detection in Slicer3]] (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)
  
 
===External Collaborations===
 
===External Collaborations===
* Meshing
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# Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
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## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
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## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
*IGT
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# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
** Tracker Integration (Noby, Haiying)
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# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics)
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# Registration
** Brachytherapy needle positioning robot integration (Csaba Csoma JHU, David Gobbi Queen's)
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## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
** RadVision and Tracker Integration (Jack Blevins, Noby)
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## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
* Registration
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## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
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# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
** Developing Electronic Atlas Software using NA-MIC Kit (Gary Christensen UIowa)
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# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
** Developing a GUI for non-rigid image registration programs using NA-MIC Kit (Gary Christensen UIowa)
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# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
* vmtk (vmtk.sourceforge.net) integration within Slicer3 (Luca Antiga, MNI, Dan Blezek(GE))
+
# MIND Clinical Imaging Study: [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)
** Solve issues with consistency of transforms
 
** Exploiting the Python shell
 
* A Translation Station
 
** Integrating 3D Slicer version 3 into a radiological workstation (Skip, Alex, Vlad, Pat, Alex, Steve)
 
  
 
===Non-Medical Collaborations===
 
===Non-Medical Collaborations===
 +
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)
  
 
==Attendee List==
 
==Attendee List==
#Kilian Pohl, BWH, Core 1
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===Core1===
#John Melonakos, Georgia Tech, Core 1
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#John Melonakos, Georgia Tech, Core 1  
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
+
#Tauseef Rehman, Georgia Tech, Core 1  
#Jim Miller, GE Core 2
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#Casey Goodlett, UNC, Core 1
#Steve Pieper, Isomics, Core 2
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#Serdar K Balci, MIT, Core 1
#Katie Hayes, BWH, Core 2
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#Elliot Uvero, MIT, Core 1
#Dan Blezek, GE Core 2
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#Ran Tao, Utah, Core 1
#Tina Kapur, BWH, Core 6
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#Kevin Teich, MGH, Core 1
#Ron Kikinis, Core 7, PI
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===Core2===
#Peter Kazanzides, JHU, Collaborator
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#W. Bryan Smith, UCSD/NCMIR, Core 2  
#Wendy Plesniak, BWH, Collaborator
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#Jeffrey Grethe, UCSD, Core 2
#Luca Antiga, Mario Negri Institute, Collaborator
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#Marco Ruiz, UCSD, Core 2
#Sylvain Bouix, BWH, Core 3
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#Neil Jones, UCSD, Core 2
#Marek Kubicki, BWH, Core 3  
+
#Jim Miller, GE Core 2
#Chris Wyatt, Virginia Tech, Collaborator
+
#Dan Blezek, GE Core 2  
#Nicole Aucoin, BWH, Core 2
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#Steve Pieper, Isomics, Core 2  
#Will Schroeder, Kitware, Core 2
+
#Alex Yarmarkovich, Isomics, Core 2  
#Sebastien Barre, Kitware, Core 2
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#Will Schroeder, Kitware, Core 2
#Brad Davis, Kitware, Core 2
+
#Yumin Yuan, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
+
#Brad Davis, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
+
#Luis Ibanez, Kitware, Core 2
#Clare Tempany, BWH Collaborator
+
#Bill Hoffman, Kitware, Core 2 (Mon, Tue)
#Noby Hata, BWH Collaborator (June 25 only)
+
#Nathan Hageman, UCLA, Core 2 (Tue, Wed)
#Haiying Liu, BWH Collaborator
+
 
#Alex Yarmarkovich, Isomics, Core 2
+
===Core3-I&II===
#Vincent Magnotta, University of Iowa, Collaborator
+
#Sylvain Bouix, BWH, Core 3
#Hans Johnson, University of Iowa, Collaborator
+
#Katharina Quintus, BWH, Core 3
#Gary E. Christensen, University of Iowa, Collaborator
+
#Marc Niethammer, BWH. Core 3  
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
+
#Marek Kubicki, BWH, Core 3 (II)  (One-day)
#Xiujuan Geng, University of Iowa, Gary's student
+
#Clement Vachet, UNC Core 3 (II) 
#Jake Nickel, University of Iowa, Gary's student
+
#David Gobbi, Queen's University, Core 3 (II)
#Nick Kiguta, University of Iowa, Gary's student
+
#Csaba Csoma, Johns Hopkins University, Core 3 (II)
#Kunlin Cao, University of Iowa, Gary's student
+
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II)
#James Harris, University of Iowa, Gary's student
+
#Mark Scully, The MIND Institute, Core 3 (II)
#Rhiannon Carlson, University of Iowa, Gary's student
+
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01
#Jeff Hawley, University of Iowa, Gary's student
+
===Core 4,5,6,7===
#Skip Talbot, Northwestern University, Collaborator
+
#Zack Galbreath, Kitware, Core 4 (Mon, Tue)
 +
#Randy Gollub, MGH, COre 5
 +
#Tina Kapur, BWH, Core 6
 +
#Ron Kikinis, Core 7, PI
 +
===Collaborators===
 +
#Chris Wyatt, Virginia Tech, Collaborator R01
 +
#Vincent Magnotta, University of Iowa, Collaborator R01
 +
#Kiran Shivanna, University of Iowa, Collaborator R01
 +
#Hans Johnson, University of Iowa, Collaborator  
 +
#Gary E. Christensen, University of Iowa, Collaborator  
 +
#Joo Hyun (Paul) Song, University of Iowa, Gary's student  
 +
#Xiujuan Geng, University of Iowa, Gary's student  
 +
#Jake Nickel, University of Iowa, Gary's student  
 +
#Nick Kiguta, University of Iowa, Gary's student  
 +
#Kunlin Cao, University of Iowa, Gary's student  
 +
#James Harris, University of Iowa, Gary's student  
 +
#Kai Ding, University of Iowa, Gary's student  
 +
#Jeffrey Hawley, University of Iowa, Gary's student  
 +
#Luca Antiga, Mario Negri Institute, Collaborator
 +
#Stephen Aylward, Kitware, Collaborator
 +
#Peter Kazanzides, JHU, Collaborator  (One-day)
 +
#Skip Talbot, Northwestern University, Collaborator  
 
#Alex Kogan, Northwestern University, Collaborator
 
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
+
#Vladimir Kleper, Northwestern University, Collaborator  
#Pat Mongkolwat, Northwestern University, Collaborator
+
#Pat Mongkolwat, Northwestern University, Collaborator  
#Csaba Csoma, Johns Hopkins University, Collaborator
+
#Greg Sharp, MGH, Collaborator  
#David Gobbi, Queen's University, Collaborator
+
#Lilla Zollei, MGH, Collaborator  (One-day)
#Kai Ding, University of Iowa, Gary's student
+
#James Ross, GE, Collaborator
 +
#Alex Gouaillard, CEGS Caltech, Collaborator
 +
#Sean Megason, CEGS caltech, Collaborator
 +
#Clif Burdette, Acousticmed, Collaborator
 +
#Jack Blevins, Acousticmed, Collaborator
 +
#Curtis Lisle, KnowledgeVis, Collaborator
 +
#Douglas Alan, Harvard IIC, Collaborator
 +
#Michael Halle, BWH/IIC, Collaborator
 +
#Katie Hayes, BWH, Core 2
 +
#Nicole Aucoin, BWH, Core 2
 +
#Wendy Plesniak, BWH, Collaborator
 +
#Kilian Pohl, BWH Collaborator
 +
#Raimundo Sierra, BWH, Collaborator
 +
#Lauren O'Donnell, BWH, Collaborator
 +
#Raul San Jose, BWH, Collaborator
 +
#C-F Westin, BWH, Collaborator
 +
#Demian Wassermann, BWH/INRIA , Collaborator
 +
#Danielle Pace, BWH , Summer Intern
 +
#Sandy Wells, BWH, Collaborator
 +
#Haiying Liu, BWH Collaborator
 +
#Clare Tempany, BWH Collaborator (One-day) 
 +
#Noby Hata, BWH Collaborator  (One-day)
 +
#Hong Xiang, BWH Collaborator  (One-day)
 +
#Kim Lawson, BWH Collaborator  (One-day)
 +
#Junichi Tokuda, BWH Collaborator  (One-day)
 +
#Robert Cormack, BWH Collaborator (One-day)
 +
 
 +
===NIH, EAB===
 +
#Zohara Cohen, NIH (One-day)
 +
#Bill Lorensen, EAB (One-day)
 +
 
 +
'''We have reached capacity of this workshop.  Any changes made to this list at this point do not translate into space at this meeting.  Apologies.  If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''
 +
 
 +
==Pictures==
 +
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=3945 PICTURES!] taken by Jeffrey Hawley

Latest revision as of 19:47, 11 April 2023

Home < 2007 Programming < Project Week MIT

Back to Events

ProjectWeek-2007.png

Welcome to the web page for the 5th Project Week!

Photo taken by Jeffrey Hawley. More photos taken by Jeffrey Hawley.

Summary

The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 48 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.

Statistics at a glance:

  • 85 Registered Attendees: 35 NA-MIC participants, 48 collaborators, 2 EAB+NIH
    • 35 NA-MIC Participants breakdown by cores: Core 1 (7), Core 2 (14), Core 3 (10), Core 4-5-6-7 (4)
    • 46 Collaborators: Acoustic Med (2), BWH (19), Caltech (2), GE (1), Harvard IIC (1), JHU (1), Kitware (1), Knowledge Vis (1), Mario Negri (1), MGH (2), NWU (4), University of Iowa(12), Virginia Tech (1)
  • 41 Projects: DBP-II(6), Structural Analysis (2), Diffusion Image Analysis (7), NA-MIC Kit (14), External Collaborations (12)

A summary of all past NA-MIC Project Events is available here.

Logistics

Registration Fee: $200 (this will cover the cost of breakfast, lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

Hotel: We have a group rate of $209/night at the Hotel at MIT. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: Boston_Hotels. Summer is tourist season in Boston, so please book your rooms early.

(This is a checklist for the onsite planning items)

Introduction to NA-MIC Project Week

NA-MIC Project Week is a hands on activity -- programming using the NA-MIC Kit, algorithm design, and clinical application -- that has become one of the major events in the NA-MIC Kit calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

  • NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
  • Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
  • This is not an introduction to the components of the NA-MIC Kit.
  • NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
  • NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the NA-MIC Kit capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
  • NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
  • External Collaborators - if you are working on a project that uses the NA-MIC kit, and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
  • Everyone should bring a laptop. We will have four projectors.
  • About half the time will be spent working on projects and the other half in project related discussions.
  • You do need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

Agenda

Preparation

  1. Please make sure that you are on the NA-MIC Project Week mailing list.
  2. May 3, 2007: Kickoff TCON#1 to discuss Engineer Core Projects and Assign/Verify Teams
  3. May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams
  4. May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week
  5. May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
  6. May 31, 2007: Create a directory for each project on the NAMIC Sandbox (Andy)
    1. 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)
    2. 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.)
    3. 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. (Andy)
  7. By 3pm ET on June 21, 2007: 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.
  8. June 21, 2007: TCON#4 Final Call before showtime...
  9. 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...


A History in Wiki Links

A history of all the programming/project events in NA-MIC is available by following this link.

Projects

DBP II

These are projects by the new set of DBPS:

  1. Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia (Harvard: Marek Kubicki, PI)
  2. Longitudinal MRI Study of Early Brain Development in Autism (UNC: Heather Hazlett, Joseph Piven, PI)
  3. Analysis of Brain Lesions in Lupus (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
  4. Segmentation and Registration Tools for Robotic Prostate Intervention (Queens/JHU: Gabor Fichtinger, PI):

Structural Analysis

  1. EMSegmentation Validation (Brad Davis Kitware, Sylvain Bouix BWH)
  2. Non-Rigid Groupwise Registration Tools for ITK (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)

Diffusion Image Analysis

  1. DTI population analysis (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)
  2. Geodesic Tractography (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
  3. Slicer3 Whole brain Seeding platform: data representation and pipeline execution (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
  4. Slicer 3 Tractography Editor (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
  5. Distortion Correction in DWI (Ran Tao, Utah)
  6. Fluid Mechanics Based Tractography (Nathan Hagemen UCLA)
  7. Sliced Multiple Glyphed Visualization for Volume Data (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)

Calibration/Validation

This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5

  1. Contrasting Tractography Measures (Marek Kubicki, Ross Whitaker, Guido Gerig, Randy Gollub)

NA-MIC Kit - Slicer 3

  1. QDEC Integration into Slicer3(Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
  2. Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
  3. MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
  4. Lightbox (James, Jim, Wendy, Alex)
  5. Support for Unstructured Grids (Curt, Nicole, Alex, Steve, Will, Vince)
  6. Python Support in Slicer 3 (Dan, Luca, Steve)
  7. CPack, CTest infrastructure Improvements (Katie, Steve, Bill Hoffman)
  8. Drafting Human Interface and Slicer Style Guidelines (Wendy,Yumin)
  9. Slicer Matlab Pipeline for Tensors (Katharina, Sylvain, Steve)
  10. Dendritic Spine Morphometrics (Bryan Smith)
  11. Review of Slicer3 CMake Files (Steve, Jim, Luca, Bill)
  12. ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)
  13. Lego Mindstorms Dissemination for IGT (Danielle Pace)
  14. Edge Detection in Slicer3 (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)

External Collaborations

  1. Meshing
    1. Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3 (Will, Vince, Kiran, Curt)
    2. Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
  2. Applying EMSegmenter to NonHuman Primate Neuroimaging(Chris Wyatt VT, Kilian Pohl BWH)
  3. Collaboration/MGH/Radiation Therapy Radiation Therapy Planning (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
  4. Registration
    1. Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
    2. Developing Electronic Atlas Software using NA-MIC Kit (Gary Christensen UIowa, Jeff Grethe, Wendy)
    3. Developing a GUI for non-rigid image registration programs using NA-MIC Kit (Gary Christensen UIowa, Yumin Kitware)
  5. vmtk (vmtk.sourceforge.net) integration within Slicer3 (Luca Antiga, MNI, Dan Blezek GE)
  6. A Translation Station(Skip, Alex, Vlad, Pat, Alex, Steve)
  7. 3D+t Cells Lineage:GoFigure (Alex G, Yumin)
  8. MIND Clinical Imaging Study: conversion of mgh 60 direction sequence to nrrd (Jeremy Bockholt, Sumner Williams)

Non-Medical Collaborations

  1. Collaboration/Harvard IIC/AstroMed (Michael Halle, Douglas Alan)

Attendee List

Core1

  1. John Melonakos, Georgia Tech, Core 1
  2. Tauseef Rehman, Georgia Tech, Core 1
  3. Casey Goodlett, UNC, Core 1
  4. Serdar K Balci, MIT, Core 1
  5. Elliot Uvero, MIT, Core 1
  6. Ran Tao, Utah, Core 1
  7. Kevin Teich, MGH, Core 1

Core2

  1. W. Bryan Smith, UCSD/NCMIR, Core 2
  2. Jeffrey Grethe, UCSD, Core 2
  3. Marco Ruiz, UCSD, Core 2
  4. Neil Jones, UCSD, Core 2
  5. Jim Miller, GE Core 2
  6. Dan Blezek, GE Core 2
  7. Steve Pieper, Isomics, Core 2
  8. Alex Yarmarkovich, Isomics, Core 2
  9. Will Schroeder, Kitware, Core 2
  10. Yumin Yuan, Kitware, Core 2
  11. Brad Davis, Kitware, Core 2
  12. Luis Ibanez, Kitware, Core 2
  13. Bill Hoffman, Kitware, Core 2 (Mon, Tue)
  14. Nathan Hageman, UCLA, Core 2 (Tue, Wed)

Core3-I&II

  1. Sylvain Bouix, BWH, Core 3
  2. Katharina Quintus, BWH, Core 3
  3. Marc Niethammer, BWH. Core 3
  4. Marek Kubicki, BWH, Core 3 (II) (One-day)
  5. Clement Vachet, UNC Core 3 (II)
  6. David Gobbi, Queen's University, Core 3 (II)
  7. Csaba Csoma, Johns Hopkins University, Core 3 (II)
  8. H. Jeremy Bockholt, The MIND Institute, Core 3 (II)
  9. Mark Scully, The MIND Institute, Core 3 (II)
  10. Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01

Core 4,5,6,7

  1. Zack Galbreath, Kitware, Core 4 (Mon, Tue)
  2. Randy Gollub, MGH, COre 5
  3. Tina Kapur, BWH, Core 6
  4. Ron Kikinis, Core 7, PI

Collaborators

  1. Chris Wyatt, Virginia Tech, Collaborator R01
  2. Vincent Magnotta, University of Iowa, Collaborator R01
  3. Kiran Shivanna, University of Iowa, Collaborator R01
  4. Hans Johnson, University of Iowa, Collaborator
  5. Gary E. Christensen, University of Iowa, Collaborator
  6. Joo Hyun (Paul) Song, University of Iowa, Gary's student
  7. Xiujuan Geng, University of Iowa, Gary's student
  8. Jake Nickel, University of Iowa, Gary's student
  9. Nick Kiguta, University of Iowa, Gary's student
  10. Kunlin Cao, University of Iowa, Gary's student
  11. James Harris, University of Iowa, Gary's student
  12. Kai Ding, University of Iowa, Gary's student
  13. Jeffrey Hawley, University of Iowa, Gary's student
  14. Luca Antiga, Mario Negri Institute, Collaborator
  15. Stephen Aylward, Kitware, Collaborator
  16. Peter Kazanzides, JHU, Collaborator (One-day)
  17. Skip Talbot, Northwestern University, Collaborator
  18. Alex Kogan, Northwestern University, Collaborator
  19. Vladimir Kleper, Northwestern University, Collaborator
  20. Pat Mongkolwat, Northwestern University, Collaborator
  21. Greg Sharp, MGH, Collaborator
  22. Lilla Zollei, MGH, Collaborator (One-day)
  23. James Ross, GE, Collaborator
  24. Alex Gouaillard, CEGS Caltech, Collaborator
  25. Sean Megason, CEGS caltech, Collaborator
  26. Clif Burdette, Acousticmed, Collaborator
  27. Jack Blevins, Acousticmed, Collaborator
  28. Curtis Lisle, KnowledgeVis, Collaborator
  29. Douglas Alan, Harvard IIC, Collaborator
  30. Michael Halle, BWH/IIC, Collaborator
  31. Katie Hayes, BWH, Core 2
  32. Nicole Aucoin, BWH, Core 2
  33. Wendy Plesniak, BWH, Collaborator
  34. Kilian Pohl, BWH Collaborator
  35. Raimundo Sierra, BWH, Collaborator
  36. Lauren O'Donnell, BWH, Collaborator
  37. Raul San Jose, BWH, Collaborator
  38. C-F Westin, BWH, Collaborator
  39. Demian Wassermann, BWH/INRIA , Collaborator
  40. Danielle Pace, BWH , Summer Intern
  41. Sandy Wells, BWH, Collaborator
  42. Haiying Liu, BWH Collaborator
  43. Clare Tempany, BWH Collaborator (One-day)
  44. Noby Hata, BWH Collaborator (One-day)
  45. Hong Xiang, BWH Collaborator (One-day)
  46. Kim Lawson, BWH Collaborator (One-day)
  47. Junichi Tokuda, BWH Collaborator (One-day)
  48. Robert Cormack, BWH Collaborator (One-day)

NIH, EAB

  1. Zohara Cohen, NIH (One-day)
  2. Bill Lorensen, EAB (One-day)

We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.

Pictures

PICTURES! taken by Jeffrey Hawley