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: $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: 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.

Introduction to NA-MIC Project Week

This is a week of 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 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). 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 capabiliities, integrate Core 1 algorithms, and refine worflows 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 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.

Agenda

• Monday
  • noon-1pm lunch
  • 1-3:30pm Introduce Projects using 4-block slides (all Project Leads)
  • 3:30-5:30pm Start project work
• Tuesday
  • 8:30am breakfast
  • 9-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
  • noon lunch
  • 1-2pm: Special topic breakout: Non-Linear Registration (Stephen)
  • 2-3pm: Special topic breakout: DWI/DTI (?)
  • 5:30pm adjourn for day
• Wednesday
  • 8:30am breakfast
  • 9-10am Special topic breakout:
  • noon lunch
  • 1-2pm: Special topic breakout: Plan for Long Lead Time Items
  • 5:30pm adjourn for day
• Thursday
  • 8:30am breakfast
  • noon lunch
  • 3:30-5pm Special topic breakout: TBD
  • 5:30pm adjourn for day
• Friday
  • 8:30am breakfast
  • 10am-noon: Project Progress using 4-block slides
  • noon lunch boxes and adjourn

Preparation

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...

Projects

DBP II

These are projects by the new set of DBPS:

• (MIND/UNM)
• Segmentation and Registration Tools for Robotic Prostate Interventions (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 (Luca, Steve, 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, Alex, Steve)

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
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. Stephen Aylward, Kitware, Collaborator
20. Raimundo Sierra, BWH, Core 2
21. Clare Tempany, BWH Collaborator
22. Noby Hata, BWH Collaborator (June 25 only)
23. Haiying Liu, BWH Collaborator
24. Alex Yarmarkovich, Isomics, Core 2
25. Vincent Magnotta, University of Iowa, Collaborator
26. Hans Johnson, University of Iowa, Collaborator
27. Gary E. Christensen, University of Iowa, Collaborator
28. Joo Hyun (Paul) Song, University of Iowa, Gary's student
29. Xiujuan Geng, University of Iowa, Gary's student
30. Jake Nickel, University of Iowa, Gary's student
31. Nick Kiguta, University of Iowa, Gary's student
32. Kunlin Cao, University of Iowa, Gary's student
33. James Harris, University of Iowa, Gary's student
34. Rhiannon Carlson, University of Iowa, Gary's student
35. Jeff Hawley, University of Iowa, Gary's student
36. Skip Talbot, Northwestern University, Collaborator
37. Alex Kogan, Northwestern University, Collaborator
38. Vladimir Kleper, Northwestern University, Collaborator
39. Pat Mongkolwat, Northwestern University, Collaborator
40. Csaba Csoma, Johns Hopkins University, Collaborator
41. David Gobbi, Queen's University, Collaborator