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.

Draft Agenda

Please note that this agenda is a draft and will be finalized by June 15th.

• 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
  • 9-10am: NA-MIC Software Process (Bill Hoffman - TBC)
  • 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
  • 11-12pm: Special topic breakout: IGT for Prostate
  • noon lunch
  • 1-2pm: Special topic breakout: Non-Linear Registration
  • 2-3pm: Special topic breakout: DWI/DTI
  • 3-4pm: Special topic breakout: KWWidgets
  • 4-5pm: Special topic breakout: Atlases
  • 5:30pm adjourn for day
• Wednesday
  • 8:30am breakfast
  • 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:

• Longitudinal Classification of White Matter Lesions in Lupus (MIND/UNM)
• Segmentation and Registration Tools for Robotic Prostate Interventions (JHU/Queen's)
• Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study (UNC)
• Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia (Harvard)

Structural Analysis

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

Diffusion Image Analysis

• DTI population analysis (Casey Goodlett)
• Slicer3 Whole brain Seeding platform: data representation and pipeline execution (Raul San Jose, Lauren O'Donnell)
• Slicer3 Tractography editor (Lauren O'Donnell, Raul San Jose)

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)
  • Drafting Human Interface and Slicer Style Guidelines (Wendy)
  • Slicer Matlab Pipeline for scalars and tensors (Katharina, Sylvain, 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, Katie Hayes BWH)
  • Collaboration/MGH/Radiation Therapy Radiation Therapy Planning (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
  • Brachytherapy needle positioning robot integration (Csaba Csoma JHU, David Gobbi Queen's, Katie Hayes BWH)
  • RadVision and Tracker Integration (Jack Blevins, Noby)
• Registration
  • Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
  • Developing Electronic Atlas Software using NA-MIC Kit (Gary Christensen UIowa, Jeff Grethe)
  • Developing a GUI for non-rigid image registration programs using NA-MIC Kit (Gary Christensen UIowa, Yumin Kitware)
• vmtk (vmtk.sourceforge.net) integration within Slicer3 (Luca Antiga, MNI, Dan Blezek(GE))
• A Translation Station(Skip, Alex, Vlad, Pat, Alex, Steve)
• Applying EMSegmenter to NonHuman Primate Neuroimaging(Chris Wyatt VT, Kilian Pohl BWH)
• 3D+t Cells Lineage:GoFigure (Alex G, Yumin)

Attendee List

1. Kilian Pohl, BWH, Core 1
2. John Melonakos, Georgia Tech, Core 1, (Hotel at MIT request)
3. Tauseef Rehman, Georgia Tech, Core 1
4. Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
5. W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
6. Jim Miller, GE Core 2, Booked at the Hotel At MIT
7. Steve Pieper, Isomics, Core 2
8. Katie Hayes, BWH, Core 2
9. Dan Blezek, GE Core 2, Booked at the Hotel At MIT
10. Tina Kapur, BWH, Core 6
11. Ron Kikinis, Core 7, PI
12. Peter Kazanzides, JHU, Collaborator
13. Wendy Plesniak, BWH, Collaborator
14. Luca Antiga, Mario Negri Institute, Collaborator
15. Sylvain Bouix, BWH, Core 3
16. Marek Kubicki, BWH, Core 3
17. Chris Wyatt, Virginia Tech, Collaborator
18. Nicole Aucoin, BWH, Core 2
19. Will Schroeder, Kitware, Core 2
20. Yumin Yuan, Kitware, Core 2
21. Brad Davis, Kitware, Core 2
22. Stephen Aylward, Kitware, Collaborator
23. Raimundo Sierra, BWH, Core 2
24. Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
25. Noby Hata, BWH Collaborator (Monday, June 25th only)
26. Haiying Liu, BWH Collaborator
27. Alex Yarmarkovich, Isomics, Core 2
28. Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
29. Hans Johnson, University of Iowa, Collaborator
30. Gary E. Christensen, University of Iowa, Collaborator
31. Joo Hyun (Paul) Song, University of Iowa, Gary's student
32. Xiujuan Geng, University of Iowa, Gary's student
33. Jake Nickel, University of Iowa, Gary's student
34. Nick Kiguta, University of Iowa, Gary's student
35. Kunlin Cao, University of Iowa, Gary's student
36. James Harris, University of Iowa, Gary's student
37. Rhiannon Carlson, University of Iowa, Gary's student
38. Jeff Hawley, University of Iowa, Gary's student
39. Skip Talbot, Northwestern University, Collaborator
40. Alex Kogan, Northwestern University, Collaborator
41. Vladimir Kleper, Northwestern University, Collaborator
42. Pat Mongkolwat, Northwestern University, Collaborator
43. Csaba Csoma, Johns Hopkins University, Collaborator
44. David Gobbi, Queen's University, Collaborator
45. Kai Ding, University of Iowa, Gary's student
46. H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
47. Mark Scully, The MIND Institute, DBP2:MIND software engineer
48. Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
49. Greg Sharp, MGH, Collaborator
50. Lauren O'Donnell, BWH
51. Raul San Jose, BWH
52. Katharina Quintus, BWH, Core 3
53. Marc Niethammer, BWH. Core 3
54. Kevin Teich, MGH
55. Michael Halle, BWH/IIC
56. James Ross, GE
57. Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)