Engineering:Programmers Half Week Jan 2006

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To All Hands on Project Events

To AHM 2006

Welcome to the web page for the 2nd Project Week!

A summary of results from this programming half week is available here.

Logistics

Dates and Schedule

• Starts on Tuesday, Jan 10th afternoon and ends on Friday, January 13th by noon.
• We expect to start around 8am and end at 5:30pm on Wednesday, and Thursday.

Location/Hotel Same as hotel for AHM.

Agenda

AHM 2006 Agenda

List of Registered Attendees

This is a list of all those who have already registered for the various events related to NAMIC AHM 2006 (Workshop, Main AHM, Programming Half Week). If you have not registered yet, please follow the AHM 2006 Registered Attendee List - Please do not edit.

Goals

The main goal of this week is to move forward the software deliverables of NAMIC. All programers in NAMIC are welcome.

• 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 related project, using the NA-MIC kit, 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 time will be spent programming and the other half in programming related discussions.

Preparation for the workshop

1. Please make sure that you are on the na-mic-programming-week mailing list
2. November 17: Kickoff TCON. Details sent to mailing list.
3. November 20: Create a Wiki page per project (the participants must do this, hopefully jointly)
4. December 1st: TCON#2 to continue discussion of projects and teams.
5. Sometime in December: Create a directory for each project on the NAMIC Sandbox (Andy)
6. Sometime in December:
   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. Jan 5: last preparation tcon
8. By Jan 5:Complete the top half of this powerpoint template for each project. Upload and link to project page.
9. General note1: program, email, call, program (maybe take breaks to think in between...)
10. Please note that by the time we get to the programming event, 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".

Projects

Please add a page for your project in Engineering:Project:2006 AHM Programming:Name, and add a link here. After you have a reasonable definition of your project, please fill in this powerpoint template (thanks to Gordon Kindlmann in helping prepare the template), upload, and link to your project page. We will review these powerpoints in a tcon on Jan 5th, and also at the programming week itself.

1. Define Joint Registration and Segmentation Framework (Kilian Pohl- MIT/BWH)
2. Affine Invariant Anisotropic Smoothing ITK Filter (John Melonakos-GT, Delphine Nain-GT, Jim Miller-GE)
3. Rule Based Segmentation Slicer Module (John Melonakos-GT, Delphine Nain-GT, Ramsey Al-Hakim-GT, Shawn Lankton-GT, Alex Yarmakovich-Isomics)
4. Basic image processing filters for DTI data (Saurav Basu-Utah, Casey Goodlett-UNC, Tom Fletcher-Utah,Karthik Krishnan-Kitware, Xiaodong Tao-GE)
5. Automated image mosaicking and feature tracking for Electron Microscopy data (Tolga Tasdizen-Utah, Liz Jurrus-Utah, Paul Koshevoy-Utah, Ross Whitaker-Utah)
6. Slicer 3
   1. Slicer 3 Architecture Powerpoint
   2. Slicer 3's web presence (Nicole Aucoin-BWH, Andy Cedilnik-KW)
   3. Define / Code API for communication between command line executables and GUI's (Dan Blezek-GE, Jeff Grethe-UCSD, Brendan Faherty-UCSD)
   4. Slicer 3's Data Model (Mike Halle, Luis Ibanez, Alex Yarmarkovich, Xiaodong Tao)
   5. Slicer 3's UI (Sebastien Barre, Mathieu Malaterre, Wendy Plesniak, Mike Halle)
   6. Slicer 3 and IGSTK integration (Nobuhiko Hata, Luis Ibanez, Patrick Cheng)
   7. Slicer 3 and Grid Integration (Jeff Grethe - UCSD, Brendan Faherty - UCSD)
7. Angular Smoothing and Interpolation of DW-MRI(Xiaodong Tao, GE; Dennis Jen, MGH)
8. Tissue Classification from MRI with Neighborhood Statistics(Tolga Tasdizen-Utah, Ross Whitaker-Utah, Suyash Awate-Utah, Liz Jurrus-Utah)
9. Development of Automated Segmentation and Volumetric Mesh Generation for Orthopeadic Applications (Vincent Magnotta-Iowa Kiran Shivanna-Iowa)
10. Incorporating KWWidgets into our shape analysis visualization tool, and extending the functionality (Ipek Oguz, Martin Styner - UNC, Sebastien Barre - Kitware)
11. Improved DTMRI module tract display (Lauren O'Donnell - MIT, C-F Westin, BWH, Raul San Jose, BWH)
12. itku: Command-line ITK interface (Raul San Jose, Gordon Kindlmann - BWH)
13. Graphical framework to construct/ execute complex scientific analyses of data (Michael Pan, UCLA)
14. Simple to use UNC shape analysis LONI pipeline (Martin Styner, UNC)
15. Non-rigid intrasubject registration of T2 EPI to T1 conventional (Josh Snyder, MGH; Xiaodong Tao, GE; Alex Yarmarkovich, BWH; Dennis Jen, MGH)
16. Client-Server based Time Series Navigation for fMRI Statistical Analysis ( Sonia Pujol, BWH)
17. Integrating Tube Visualization for Tractography Generated in Slicer (Tom Lechner, NWU)
18. Coding into Itk of Block Matching Based Registration Algorithm (Eduardo Suárez, Izzat Sabbagh, Juan Ruiz-Alzola, Instituto Tecnológico de Canarias - Spain)

Computer Resources

• All participants should bring laptops with development software and sample data loaded.

• See, for example, the instructions for the Feb 17-18, 2005 Dissemination Workshop at UCSD for background material.

• Some cluster computing resources are being prepared.
  • AHM 2006 Cluster Resources.
  • Example code and data for testing is here.

Results from Previous Programming Week

Results from Programming Week#1, MIT, Summer 2005