Engineering:Programmers Week Summer 2005

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=Welcome to the web page for the 1st Project Week!

Summary

The first NA-MIC Programming Week was successfully concluded on July 1, 2005 at MIT. Results are summarized here.

Logistics

Dates and Schedule Monday, June 27 - Friday, July 1st, 2005.

  • Starting on Monday at noon, and ending on Friday at 2pm.
  • We expect to start at 9am each day and end around 5:30pm.

Location

Hotel University Hotel at MIT

Interactive map of Hotel@MIT and MIT

Registration Fee $75. (This includes breakfast every day and lunch most days.)

Please make checks out to "Massachusetts Institute of Technology" and mail to:


Donna Kaufman
MIT
77 Massachusetts Ave., 38-409b
Cambridge, MA 02139


by Monday, June 20, 2005

You may contact Donna at 617.253.4624 or dkauf@mit.edu

Goals

The main goal of this week is to move forward the software deliverables of NAMIC. All NAMIC programmers, whether they are faculty, researcher, student, administrator, engineer, or anything else in their day job, are welcome to join us. Some key points:

  • You don't need to be in core 1 or 2 to attend, even though most of the attendees are likely to be from these cores.
  • You do need to be actively programming on a NAMIC 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 have an algorithm that needs to be moved into the NAMIC Kit, and those who can help make it happen.
  • This is not an introduction to ITK or Slicer or LONI pipeline. If you have not had any introductory exposure to at least one of these three yet, and want to attend, please make sure that you have done all the programming exercises that were introduced in the NAMIC dissemination workshops.
  • The following types of projects are included in this week:
    • core 1 projects that need support from core 2
    • core 2 projects on the NAMIC Toolkit
    • core 2 project on the kickoff of the next generation of Slicer infrastructure
  • 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?

The agenda below gives an idea of how the week will be structured. In addition, please note that:

  • Everyone should bring a laptop. We will have three or four projectors.
  • It looks like about half the week will be programming and the other half discussions.
  • There is an optional DTI workshop hosted by Core 1 on Monday morning.
  • Wednesday afternoon is open touring Boston and boxed lunches will be provided. Conference rooms (and coffee) will be supplied for those who prefer to continue working.

Preparation for the workshop

This is being prepared right now, so please check it often for changes. Tkapur 00:26, 10 Jun 2005 (EDT)

  1. Please make sure that you are on the na-mic-programming-week mailing list
  2. Thursday, April 14 at 3pm EST: Programming week Kickoff TCON. Details sent to mailing list.
  3. By Thursday April 21: Create a Wiki page per project (the participants must do this, hopefully jointly)
  4. By Friday April 22: Create a directory for each project on the NAMIC Sandbox (Andy)
  5. By Friday April 29: 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)
  6. By Friday April 29: 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.)
  7. By Friday May 6th: 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)
  8. Two TCONS: Thursday June 16th at 3pm EST, and Thursday June 23rd at 3pm EST... if you don't have the details for these, add yourself to the programming week mailing list.
  9. Until June 27th: program, email, call, program (maybe take breaks to think in between...)
  10. Please note that by the time we get to Boston, we shouldn't be talking about which method to use, and what is the purpose of the application. At that point we should be talking about "how much computation time it took to run method A in image #5", and "how that compares to the results of method B in image #7".

Agenda

Monday (Star, Kiva) Tuesday (Star, Kiva) Wednesday (Grier A and B) Thursday (Grier A and B) Friday (Grier A and B)
Goal Set the stage, share each team's goals for the week, make sure programming environment is functional Goal: Write code in small teams, start discussion of slicer 3.0 Work... Tour Boston Mostly finish up programming goals for the week. Report One Highlight. Tie loose ends. Wrap-up week.
8:30-9am Breakfast in the R&D Dining Room Breakfast in the R&D Dining Room Breakfast in Grier Breakfast in Grier Breakfast in Grier
9-10:30am

Mathematics of Diffusion Workshop in Star(optional)

Meet in Kiva for 15 minutes, and then continue work in teams.

Meet for 15 minutes, and then Slicer 3.0 continue in Grier A, and other teams continue in Grier B.

One "mid-week" highlight by each project team TBD based on feedback on Thursday evening
10:30-11am Coffee in the R&D Dining Room Coffee in the R&D Dining Room Coffee in Grier Coffee in Grier Coffee in Grier
11am-12pm

Mathematics of Diffusion Workshop in Star(optional)

Continue... Continue... Continue to work in teams. Continue...
12-1pm

Welcome/Lunch in R&D Dining Room (Grimson, Kikinis)

Lunch in R&D Dining Room Lunch Boxes in Grier Go out for lunch Wrap-up week (Lorensen, Kapur)
1-2:15pm

Programming Week Kickoff in Kiva(Lorensen, Kapur, Pieper, Schroeder). 1:50pm: On requirements gathering (Tuch). 2:05pm: Sample Training Document(Pujol)

Training Presentation

Documentation Template

Slicer 3.0 in Kiva for the afternoon. Other Project Teams continue in Star for the afternoon.

Take a break to tour Boston (optional) Continue ...
2:15-3:30pm Core 1 Projects Overview by Team Leads (10 min each) Continue... Continue ... Continue ...
3:30-4pm Coffee in the R&D Dining Room Coffee in the R&D Dining Room Coffee in Grier Coffee in Grier
4-5:30pm Computer/Env Setup Continue ... Continue ... Continue ...
5:30-6pm Wrap-up for Day in Kiva (Lorensen, Kapur) Wrap-up for Day in Kiva (Lorensen, Kapur) Continue ... Wrap-up for Day in Grier and identify critical items for Friday morning (Lorensen, Kapur)
6:30pm

Licensing Discussion over Dinner (Hosts:Ibanez, Kindlmann)

Participants

We are now beyond capacity (35) for this workshop. Please don't add any more names to this list. If you are still interested in attending, please identify the team that you will work with and send an email to tkapur at epiphanymedical com and hopefully we will be able to figure something out.

When you add a name to this list, please also make sure that you are on the NA-MIC Programming Week mailing list.

  1. John Melonakos (Georgia Tech, Core 1)
  2. Ramsey Al-Hakim (Georgia Tech, Core 1)
  3. Casey Goodlett (UNC, Core 1)
  4. Ipek Oguz (UNC, Core 1)
  5. Christine Xu (UNC, Core 1)
  6. Martin Styner (UNC, Core 1)
  7. Isabelle Corouge (UNC, Core 1)
  8. Tom Fletcher (Utah, Core 1)
  9. Josh Snyder (MGH, Core 1)
  10. Mahnaz Maddah (MIT, Core 1)
  11. Lauren O'Donnell (MIT, Core 1)
  12. Steve Pieper (BWH, Core 2)
  13. Jags (UCLA, Core 2)
  14. Luis Ibanez (Kitware, Core 2)
  15. Andy Cedilnik (Kitware, Core 2)
  16. Sebastien Barre (Kitware, Core 2)
  17. Andinet Enquobahrie (Kitware, Core 2)
  18. Berk Geveci (Kitware, Core 2 ParaView expert)
  19. Rick Avila (Kitware, Core 2)
  20. Alex Yarmarkovich (BWH, Core 2)
  21. Jim Miller (GE, Core 2)
  22. Xiaodong Tao (GE, Core 2)
  23. Bill Lorensen (GE, Core 2 PI)
  24. Jason Gerk(UCSD, Core 2)
  25. Jeff Grethe(UCSD, Core 2)
  26. Sylvain Bouix (Harvard, Core 3)
  27. Will Schroeder (Kitware, Core 4 PI)
  28. Randy Gollub (MGH, Core 5)
  29. Sonia Pujol (BWH, Core 5)
  30. Tina Kapur (Epiphany Medical, Core 6)
  31. Katie Hayes (BWH, Collaborator)
  32. Raul San Jose Estepar (BWH, Collaborator)
  33. Karl Krissian (BWH, Collaborator)
  34. Chand John (Stanford, Collaborator)
  35. Michael Halle (BWH, Collaborator)
  36. Nicole Aucoin (BWH, Collaborator)
  37. Besam Khidhir (BWH, Collaborator)
  38. Neculai Archip (BWH, Collaborator)
  39. Bryn Lloyd (BWH, Collaborator)
  40. Andriy Fedorov (College of William and Mary/BWH, Collaborator)
  41. Torsten Rohlfing (SRI, Collaborator introduction to Torsten's fields of work)
  42. Neil Weisenfeld (BWH, Collaborator)
  43. Ron Kikinis (BWH, PI)
  44. Eric Grimson (MIT, Core 1 PI)

Projects

Applications

(Kiva) Non-rigid EPI registration using ITK (Snyder, Tuch, Ibanez)

(Star) Prototype ITK system for Quantitative Fiber Tract Analysis (Casey - UNC, Xiaodong - GE), Isabelle - UNC

(Star)Processing modules and visualization tools for shape analysis (Ipek Oguz, Christine Xu, Martin Styner - UNC, Jim Miller - GE Research)

(Star)Object population desription and general feature analysis framework (Martin Styner - UNC, Tom Fletcher - Utah, Jim Miller - GE Research)

(Kiva)Addition of Bayesian Segmentation Module to ITK (John Melonakos, Ibanez)

(Kiva)Wrap motion robust matching code using ITK (Khidhir, Warfield, Archip, Lorensen)

(Kiva)DLPFC Semi-Automatic Segmentor (Ramsey Al-Hakim, Alex Yarmakovich)

(Star)Flux Diffusion in ITK (Karl Krissian)

(Star) ITKu, minimalist commandline tools using ITK (Raul San Jose, Gordon Kindlmann)

(Star) nrrd ITK IO, read and write nrrd tensor data with ITK (Gordon Kindlmann)

(Kiva) Slicer DTMRI module nightly testing (Lauren O'Donnell, Raul San Jose Estepar, Andy Cedilnik)

(Kiva) Spectral Clustering in ITK (Lauren O'Donnell, Luis Ibanez)

(Kiva) ITK Wrap Intensity Correction and Normalization Methods (Weisenfeld, Warfield)

(Star)LONI pipeline for UNC script based shape analysis pipeline (Martin Styner, Ipek Oguz - UNC, Jags Rajendiran - UCLA)

(Kiva)3D Adaptive Tetrahedral Mesh Generation in ITK (Fedorov, Chrisochoides, Warfield, Schroeder)

(Kiva)2D/3D Point landmark detection in ITK (Lloyd, Warfield)

(Star)Large Scale Algorithm Job Submission via Condor(Jason, Jeff, Pieper)

(Star)Pipelining ITK modules(Jags, Pieper)

Slicer3.0 Architecture Kickoff

Computer Resources

  • All participants should bring laptops with development software and sample data loaded.
  • Some cluster computing resources are being prepared.
    • More details to follow here.
    • Example code and data for testing is here.

Social stuff