2006 Programming/Project Week MIT

Logistics

• Dates: June 26-30, 2006
• Location: MIT Stata Center
• Hotel: We are not booking a block of rooms at any hotel. 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 Draft

• Monday: start at noon
• Tue: 9-5
• Wed: 9-5
• Thurs: 9-5
• Fri: 9-noon

Background and Preparation

A difference between previous such weeks and this one is that we have decided to call it "Project Week" to reflect what actually goes on in these sessions - along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and we'd like the name to reflect that. What does this mean to you: if you are participating in a NA-MIC project 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-programming-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: TCON#2 to discuss projects and assign teams
5. May ?: 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 22nd: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

Instructions Please use the following protocol to add your project(s) to this list, under the appropriate category:

Project Title (Team Names) 2006_Project_Week_MIT_ProjectName, 1-slide summary

i.e.

• create a line for each project with the above text
• create a page for your project named 2006_Project_Week_MIT_<Project Name> and link it to the text "project page"
• download File:2006 Summer Project Week Template.ppt, summarize the project in it, and upload it to the wiki under the filename 2006_Project_Week_MIT_<ProjectName>.ppt

List of Projects

Structural Analysis

1. ITK Spherical Wavelet Transform Filter (Xavier Le Faucheur, GT, Delphine Nain, GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez, Kitware): 3D Shape Analysis Using Spherical Wavelets, <4-block ppt>

Diffusion Image Analysis

1. ITK DTI Image Processing Modules (Casey Goodlett UNC), DTI Software and Algorithm Infrastructure, <4-block ppt>

FMRI Image Analysis

1. ITK Conformal Flattening Filter (Yi Gao GT, Delphine Nain GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware): Conformal Flattening for fMRI Visualization. <4-block ppt>

NA-MIC Kit

1. NA-MIC cluster package (Jeff Grethe), <Project Page>, <4-block ppt>
2. MRML Lib (Alex Yarmarkovich, Mathieu Malaterre, Xiaodong Tao), <Project Page>, <4-block ppt>
3. Slicer3 Interface (Wendy Plesniak, Sebastient Barre), <Project Page>, <4-block ppt>
4. Slicer3 Execution Model (Dan Blezek, Mike Halle, Jim Miller), <Project Page>, <4-block ppt>
5. Migrating Slicer2.x Modules to Slicer3 (Nicole Aucoin, Mathieu Malaterre, Katie Hayes), <Project Page>, <4-block ppt>
6. Slicer3 Build/Test/Pack (Andy Cedilnik, Katie Hayes), <Project Page>, <4-block ppt>
7. Slicer3 Grid Integration (Jeff Grethe, Brendan Faherty), 2006_Project_Week_MIT_Grid_Integration, <4-block ppt>
8. Slicer3 Pipeline Integration (Jagadeeswaran Rajendiran), <Project Page>, <4-block ppt>

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. Kilian Pohl, BWH Core 1
5. Xavier Le Faucheur, GT Core 1
6. Delphine Nain, GT Core 1 (for some of the week)
7. Yi Gao, GT Core 1
8. John Melonakos, GT/GE Core 1,2
9. Bill Lorensen, GE Core 2
10. Jim Miller, GE Core 2
11. Dan Blezek, GE Core 2
12. Xiaodong Tao, GE Core 2
13. Luis Ibanez, Kitware Core 2
14. Will Schroeder, Kitware Core 2,4
15. Mathieu Malaterre, Kitware Core 2
16. Andy Cedilnik, Kitware Core 4
17. Sebastien Barre, Kitware Core 2
18. Steve Pieper, Isomics Core 2,6
19. Katie Hayes, BWH Core 2
20. Nicole Aucoin, BWH Core 2
21. Wendy Plesniak, BWH Core 2
22. Randy Gollub, MGH Core 5- as needed to develop supporting materials and/or teach neuro and/or help with fMRI
23. Sonia Pujol, BWH Core 5- as needed to develop supporting materials
24. Tina Kapur, Epiphany Medical, Core 6
25. Haiying Liu, BWH IGT Collaborator
26. Brendan Faherty, UCSD Core 2
27. Pat Mongkolwat, Northwestern Collaborator
28. Vincent Magnotta, Iowa Collaboration
29. Kiran Shivanna, Iowa Collaboration
30. Tom Fletcher + student, Utah Core 1