2006 Programming/Project Week MIT

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Welcome to the web page for the 3rd Project Week!

Summary

The 3rd NA-MIC Project event was was successfully concluded on June 30, 2006. The results of this week are summarized here.

Some statistics:

• 56 total attendees: 38 NA-MIC participants, 18 collaborators
  • 38 NA-MIC Participants breakdown by cores: Core 1 (11), Core 2 (13), Core 3 (9), Core 4 (2), Core 5 (2), Core 6 (1)
  • 18 Collaborators: Northwestern (3), Iowa (1), JHU (1), Harvard IIC (1), Canary Islands (2), MIT(3), BWH (7)
• 22 Projects: Structural Analysis (4), Diffusion Image Analysis (4), fMRI analysis (2), NA-MIC Kit (10), Astronomy Data(1)

A summary of all past Project Events.

Logistics

• Dates: June 26-30, 2006
• Location: MIT.

Please note that Monday lunch will be in the Allen Room, 36-462 (due to water damage in previously planned location). Entrance is still at 50 Vassar St., turn left inside the lobby (building 34), proceed to the elevators in building 36. Go to the 4th floor and exit to the RIGHT. Follow around the corner and the conference room is just a few steps down the hall.

Rest of the activities are in Grier Rooms A & B: 34-401A & 34-401B.

Registration Fee: $75 (to subsidize the cost of breakfast and lunch for the week). Due by Tuesday, June 20, 2006. 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.

Agenda

• Monday
  • noon-1pm lunch (Allen Room, 36-462)
  • 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 Execution Model (Jim Miller, Steve Pieper)
  • noon lunch
  • 1-2pm: Special topic: IGT Software Architecture at JHU (Peter Kazanzides)
  • 2-3pm: Special topic: Slicer UI Feature Request & Usability discussion (Wendy Plesniak)
  • 5:30pm adjourn for day
• Wednesday
  • 8:30am breakfast
  • 9-10am Insight Journal Submission Q&A (Luis Ibanez)
  • noon lunch
  • 1-2pm: Special topic: Calibrating Slicer's EM Segmenter (Kilian Pohl)
  • 5:30pm adjourn for day
  • 7:00pm Dinner and Music
• Thursday
  • 8:30am breakfast
  • noon lunch
  • 3:30-5pm Genetics 101 (Jim Kennedy, Aristotle Voineskos - UToronto/CAMH)
  • 5:30pm adjourn for day
• Friday
  • 8:30am breakfast
  • 10am-noon: Project Progress using 4-block slides
  • noon lunch boxes and adjourn

Background and Preparation

A difference between previous such weeks and this one is that we have decided to call it "Project Week" rather than "Programming Week" to better reflect the activity during the event - 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. In contrast to previous years, this event will involve programming, algorithm design, and clinical application development/testing.
• You do need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
• 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.

How will this week work?

Please note that:

• Everyone should bring a laptop. We will have three or four projectors.
• It looks like about half the time will be spent working on projects and the other half in project related discussions.

Preparation for the workshop

1. Please make sure that you are on the NA-MIC Project Week mailing list.
2. April 6: Kickoff TCON
3. April 19: Create a Wiki page per project (the participants must do this, hopefully jointly)
4. May 25: TCON#2 to discuss projects and assign teams
5. May 30: Create a directory for each project on the NAMIC Sandbox (Andy)
6. June:
   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 June 22 complete the top half of this powerpoint template for each project. Upload and link to the right place.
8. June 22: TCON#3 last preparation tcon
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...

A History in Wiki Links

• Programming Event#2: Programming Half Week in Utah, Jan 2006 and Summary of Results
• Programming Event#1: Programming Week at MIT, June 2005 and Summary of Results

Projects

All the project pages are available here.

Attendees

If you are interested in attending this week, please note your name here:

1. Martin Styner, UNC Core 1
2. Ipek Oguz, UNC Core 1
3. Casey Goodlett, UNC Core 1
4. Tom Fletcher, Utah Core 1
5. Ross Whitaker, Utah Core 1 (Wed-Fri - off and on)
6. Gheorghe Postelnicu, MGH Core 1
7. Polina Golland, MIT Core 1 (Wed-Thur)
8. Lauren O'Donnell, MIT Core 1 (Thur-Fri)
9. Wanmei Ou, MIT Core 1
10. Xavier Le Faucheur, GT Core 1
11. Yi Gao, GT Core 1
12. John Melonakos, GT/GE Core 1,2
13. Bill Lorensen, GE Core 2
14. Jim Miller, GE Core 2
15. Luis Ibanez, Kitware Core 2
16. Will Schroeder, Kitware Core 2,4
17. Mathieu Malaterre, Kitware Core 2
18. Andy Cedilnik, Kitware Core 4 (Tue, Wed, Thu, Fri)
19. Sebastien Barre, Kitware Core 2
20. Steve Pieper, Isomics Core 2,6
21. Alex Yarmarkovich, Isomics Core 2 (Tue, Wed, Thu)
22. Katie Hayes, BWH Core 2
23. Nicole Aucoin, BWH Core 2
24. Wendy Plesniak, BWH Core 2
25. Brendan Faherty, UCSD Core 2
26. Jagadeeswaran Rajendiran, UCLA - Core 2
27. Katharina Quintus, PNL Core 3.1 (Tue)
28. Doug Markant, PNL Core 3.1 (Tue)
29. Lillian Hsu, PNL Core 3.1 (Tue)
30. Marc Niethammer, PNL Core 3.1 (Mon, Thurs)
31. Sylvain Bouix, PNL core 3.1 (Mon, Tue, Thurs)
32. Marek Kubicki, PNL core 3.1
33. John West, Dartmouth Medical School, Core 3.1 (Wed)
34. Aristotle Voineskos, University of Toronto, Core 3.2 (Thursday)
35. James Kennedy, University of Toronto, Core 3.2 (Thursday)
36. Randy Gollub, MGH Core 5- as needed to develop supporting materials and/or teach neuro and/or help with fMRI
37. Sonia Pujol, BWH Core 5- as needed to develop supporting materials
38. Tina Kapur, Epiphany Medical, Core 6
39. Pat Mongkolwat, Northwestern Collaborator
40. Thomas Lechner, Northwestern Collaborator
41. Alex Kogan, Northwestern Collaborator
42. Kiran Shivanna, Iowa Collaboration
43. Peter Kazanzides, Johns Hopkins University Collaborator (Tuesday)
44. Haiying Liu, BWH IGT Collaborator
45. C-F Westin, LMI, NAC, BWH, Collaborator
46. AW de Vries, LMI, BWH, Collaborator
47. Raul San Jose, BWH, Collaborator
48. Gordon Kindlmann, BWH, Collaborator (Wed+Thu)
49. Michael Halle, BWH, Harvard Initiative in Innovative Computing
50. Kilian Pohl, BWH Collaborator (Mon, Tue, Wed)
51. Douglas Alan, Harvard IIC, Collaborator
52. Rafael Nebot, Canary Islands Technological Institute Collaborator (Tue-Thu)
53. Eduardo Suárez, Canary Islands Technological Institute Collaborator (Tue-Thu)
54. Lilla Zollei, MIT Collaborator
55. Clare Poynton, MIT, BWH Collaborator
56. Ulas Ziyan, MIT Collaborator