2007 Programming/Project Week MIT

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Logistics

Dates: June 25-29, 2007

Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.

Registration Fee: TBD (most likely $75 to subsidize 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:

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: 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. Summer is tourist season in Boston, so please book your rooms early.

Please Note

Programming/Project week is one of the major events in the NA-MIC calendar. This will be our third annual Summer Programmming/Project Week.

• Core 1 - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
• Core 2 - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
• Core 3 - 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 three or 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.

Background and Preparation

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

Goals

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

• Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
• 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.
• Submit any projects that you would like to work on during this week, and what type of help you might need for it.

Preparation for the workshop

1. Please make sure that you are on the na-mic-programming-week mailing list
2. May 3, 2007: Kickoff TCON#1 to discuss Engr 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 14, 2007: Complete the top half of this powerpoint template for each project. Upload and link to the right place.
8. June 14, 2007: TCON#3 Review of 4-Blocks (Structural, DTI, Collaboration, Other)
9. June 21, 2007: TCON#4 Review of 4-Blocks (NA-MIC Kit)
10. 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...

Results

Results of this event will be summarized here after it is completed.

Projects

DBP II

These are projects by the new set of DBPS:

• (MIND/UNM)
• (JHU)
• (Harvard)
• (UNC)

Structural Analysis

• EMSegmentation Validation (Brad Davis, Sylvain Bouix)
• vtkITK wrapper for rule based segmentation (Brad Davis, John Melonakis, Marek Kubiki)
  • Application of the Slicer2 module on DBP data
  • Conversion to Slicer3

NA-MIC Kit

• Slicer3
  • QDEC integration into Slicer3 (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
  • Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
  • MRML Scenes for the Execution Model, including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Steve Pieper)
  • Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
  • Python support in Slicer3 (depends on Dan's availability)
  • CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
• Slicer2

External Collaborations

• Meshing
  • Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
  • Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
• IGT
  • Tracker Integration (Noby, Haiying)
  • Collaboration/MGH/Radiation Therapy Radiation Therapy Planning (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics)
• Registration
  • Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
• vmtk (vmtk.sourceforge.net) integration within Slicer3 (Luca Antiga, MNI)
  • 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)

Attendee List

1. Kilian Pohl, BWH, Core 1
2. John Melonakos, Georgia Tech, Core 1
3. W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
4. Jim Miller, GE Core 2
5. Steve Pieper, Isomics, Core 2
6. Katie Hayes, BWH, Core 2
7. Dan Blezek, GE Core 2 (Tentative)
8. Tina Kapur, BWH, Core 6
9. Ron Kikinis, Core 7, PI
10. Peter Kazanzides, JHU, Collaborator
11. Wendy Plesniak, BWH, Collaborator
12. Luca Antiga, Mario Negri Institute, Collaborator
13. Sylvain Bouix, BWH, Core 3
14. Chris Wyatt, Virginia Tech, Collaborator
15. Nicole Aucoin, BWH, Core 2
16. Will Schroeder, Kitware, Core 2
17. Sebastien Barre, Kitware, Core 2
18. Brad Davis, Kitware, Core 2
19. Raimundo Sierra, BWH, Core 2
20. Clare Tempany, BWH Collaborator
21. Noby Hata, BWH Collaborator (June 25 only)
22. Haiying Liu, BWH Collaborator
23. Alex Yarmarkovich, Isomics, Core 2
24. Vincent Magnotta, University of Iowa, Collaborator
25. Hans Johnson, University of Iowa, Collaborator
26. Gary E. Christensen, University of Iowa, Collaborator
27. Joo Hyun (Paul) Song, University of Iowa, Gary's student
28. Xiujuan Geng, University of Iowa, Gary's student
29. Jake Nickel, University of Iowa, Gary's student
30. Nick Kiguta, University of Iowa, Gary's student
31. Kunlin Cao, University of Iowa, Gary's student
32. James Harris, University of Iowa, Gary's student
33. Rhiannon Carlson, University of Iowa, Gary's student
34. Jeff Hawley, University of Iowa, Gary's student
35. Skip Talbot, Northwestern University, Collaborator
36. Alex Kogan, Northwestern University, Collaborator
37. Vladimir Kleper, Northwestern University, Collaborator
38. Pat Mongkolwat, Northwestern University, Collaborator