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,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

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 Kit 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 Kitand 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

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

• Monday June 25
  • noon-1pm lunch
  • 1-3:30pm Introduce Projects using templated wiki pages (all Project Leads) (Wiki Template)
  • 3:30-5:30pm Start project work
  • 4:30-5:30pm Special topic breakout: New DBP Introduction to NA-MIC Engineering
• Tuesday June 26
  • 8:30am breakfast
  • 9:00-9:45am: NA-MIC Software Process (Bill Hoffman)
  • 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: KWWidgets
  • 2-3pm: Special topic breakout: Non-Linear Registration
  • 3-4pm: Special topic breakout: Atlases
  • 4-5pm: Special topic breakout: DWI/DTI
  • 5:30pm adjourn for day
• Wednesday June 27
  • 8:30am breakfast
  • noon lunch
  • 1-2pm: Special topic breakout: Plan for Long Lead Time Items
  • 5:30pm adjourn for day
• Thursday June 28
  • 8:30am breakfast
  • noon lunch
  • 3:30-5pm Special topic breakout: TBD
  • 5:30pm adjourn for day
• Friday June 29
  • 8:30am breakfast
  • 10am-noon: Project Progress using update Project Wiki pages
  • noon lunch boxes and adjourn. (Next one in Utah the week of Jan 7, 2008)

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 - Please use this template intead of the 4-block ppts.

DBP II

These are projects by the new set of DBPS:

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

Structural Analysis

1. EMSegmentation Validation (Brad Davis Kitware, Sylvain Bouix BWH)
2. vtkITK wrapper for rule based segmentation (John Melonakos GATech, Tauseef Rehman GATech, Brad Davis Kitware, Marek Kubicki BWH)

Diffusion Image Analysis

1. DTI population analysis (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki 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)

NA-MIC Kit

1. Slicer3
   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. Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
   5. Python Support in Slicer 3 (Luca, Steve, Dan)
   6. CPack, CTest infrastructure Improvements (Bill Hoffman, Katie, Steve)
   7. Drafting Human Interface and Slicer Style Guidelines (Wendy,Yumin)
   8. Slicer Matlab Pipeline for Scalars and Tensors (Katharina, Sylvain, Steve)
   9. Dendritic Spine Morphometrics (Bryan Smith)
2. Slicer2

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. Image-Guided Therapy
   1. Collaboration/BWH/Tracker Integration (Noby, Haiying, Katie Hayes BWH)
   2. Collaboration/MGH/Radiation Therapy Radiation Therapy Planning (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
   3. Brachytherapy needle positioning robot integration (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
   4. RadVision and Tracker Integration (Jack Blevins, Noby)
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)

Non-Medical Collaborations

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

Attendee List

1. Kilian Pohl, BWH, Core 1
2. John Melonakos, Georgia Tech, Core 1
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)
66. Clif Burdette (Acousticmed, Collaborator)
67. Jack Blevins (Acousticmed, Collaborator)
68. Lilla Zollei (MGH)
69. Serdar K Balci (MIT)