2007 Programming/Project Week MIT

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Summer 2007

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.

(This is a checklist for the onsite planning items)

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.

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 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...

Projects

Template

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template

DBP II

These are projects by the new set of DBPS:

Structural Analysis

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

Diffusion Image Analysis

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

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)
    • 2007_Project_Week_MIT_MRML_Scenes_for_the_Execution_Model, including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
    • Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
    • Python support in Slicer3 (Luca, Steve, Dan)
    • CPack, Ctest infrastructure improvements (Bill Hoffman, Katie, Steve)
    • Drafting Human Interface and Slicer Style Guidelines (Wendy,Yumin)
    • Slicer Matlab Pipeline for scalars and tensors (Katharina, Sylvain, Steve)
  • Slicer2

External Collaborations

Non-Medical Collaborations

  • AstroMed (Michael Halle, Douglas Alan)

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
  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. Luis Ibanez, Kitware, Core 2
  24. Bill Hoffman, Kitware, Core 2
  25. Raimundo Sierra, BWH, Core 2
  26. Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
  27. Noby Hata, BWH Collaborator (Monday, June 25th only)
  28. Haiying Liu, BWH Collaborator
  29. Alex Yarmarkovich, Isomics, Core 2
  30. Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
  31. Hans Johnson, University of Iowa, Collaborator
  32. Gary E. Christensen, University of Iowa, Collaborator
  33. Joo Hyun (Paul) Song, University of Iowa, Gary's student
  34. Xiujuan Geng, University of Iowa, Gary's student
  35. Jake Nickel, University of Iowa, Gary's student
  36. Nick Kiguta, University of Iowa, Gary's student
  37. Kunlin Cao, University of Iowa, Gary's student
  38. James Harris, University of Iowa, Gary's student
  39. Kai Ding, University of Iowa, Gary's student
  40. Jeff Hawley, University of Iowa, Gary's student
  41. Skip Talbot, Northwestern University, Collaborator (Hotel at MIT request)
  42. Alex Kogan, Northwestern University, Collaborator (Hotel at MIT request)
  43. Vladimir Kleper, Northwestern University, Collaborator (Hotel at MIT request)
  44. Pat Mongkolwat, Northwestern University, Collaborator (Hotel at MIT request)
  45. Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
  46. David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
  47. H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
  48. Mark Scully, The MIND Institute, DBP2:MIND software engineer
  49. Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
  50. Greg Sharp, MGH, Collaborator
  51. Lauren O'Donnell, BWH
  52. Raul San Jose, BWH
  53. Katharina Quintus, BWH, Core 3
  54. Marc Niethammer, BWH. Core 3
  55. Kevin Teich, MGH
  56. Michael Halle, BWH/IIC
  57. James Ross, GE
  58. Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
  59. Douglas Alan, Harvard IIC
  60. Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
  61. Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
  62. Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)
  63. Ran Tao, Utah, Core 1
  64. Alex. Gouaillard, CEGS caltech Software Engineer, QuadEdgeMesh project Lead (ITK)
  65. Sean Megason, CEGS caltech PI, (not full week)
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