2008 Summer Project Week

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Summer 2008


Logistics

Dates: June 23-27, 2008

Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.


Registration Fee: $TBD (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by TBD, 2008. 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 TBD/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

NA-MIC Project Week is a 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. This event is the seventh of the series. It is held in the summer at MIT (typically the last week of June), and a shorter version is held 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 capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
  • NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and 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 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

Preparation

  1. Please make sure that you are on the na-mic-programming-week mailing list
  2. May 22 TCON#1 at 3pm ET to discuss Engr Core Projects and Assign/Verify Teams
  3. May 29 TCON#2 at 3pm ET to discuss Projects and Assign/Verify Teams
  4. June 5 TCON#3 at 3pm ET to discuss outstanding projects and teams from previous week
  5. June 12: Create a Wiki page per project (the participants must do this, hopefully jointly)
  6. June 12, 2008: Create a directory for each project on the NAMIC Sandbox (Zack)
    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. (Zack)
  7. By 3pm ET on June 12, 2008: 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. 3pm ET on June 19, 2008: 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...

A History in Wiki Links

A history of all the programming/project events in NA-MIC is available by following this link.

Projects

Please note that the following list is for reference from last year. It will be updated in May 2008 for the upcoming project week.


DBP II

These are projects by the new set of DBPS:

  1. Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia (Harvard: Marek Kubicki, PI)
  2. Longitudinal MRI Study of Early Brain Development in Autism (UNC: Heather Hazlett, Joseph Piven, PI)
  3. Analysis of Brain Lesions in Lupus (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
  4. Segmentation and Registration Tools for Robotic Prostate Intervention (Queens/JHU: Gabor Fichtinger, PI):

Structural Analysis

  1. EMSegmentation Validation (Brad Davis Kitware, Sylvain Bouix BWH)
  2. Non-Rigid Groupwise Registration Tools for ITK (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)

Diffusion Image Analysis

  1. DTI population analysis (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose 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)
  5. Distortion Correction in DWI (Ran Tao, Utah)
  6. Fluid Mechanics Based Tractography (Nathan Hagemen UCLA)
  7. Sliced Multiple Glyphed Visualization for Volume Data (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)

Calibration/Validation

This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5

  1. Contrasting Tractography Measures (Marek Kubicki, Ross Whitaker, Guido Gerig, Randy Gollub)

NA-MIC Kit - Slicer 3

  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. Lightbox (James, Jim, Wendy, Alex)
  5. Support for Unstructured Grids (Curt, Nicole, Alex, Steve, Will, Vince)
  6. Python Support in Slicer 3 (Dan, Luca, Steve)
  7. CPack, CTest infrastructure Improvements (Katie, Steve, Bill Hoffman)
  8. Drafting Human Interface and Slicer Style Guidelines (Wendy,Yumin)
  9. Slicer Matlab Pipeline for Tensors (Katharina, Sylvain, Steve)
  10. Dendritic Spine Morphometrics (Bryan Smith)
  11. Review of Slicer3 CMake Files (Steve, Jim, Luca, Bill)
  12. ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)
  13. Lego Mindstorms Dissemination for IGT (Danielle Pace)
  14. Edge Detection in Slicer3 (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)

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. Collaboration/MGH/Radiation Therapy Radiation Therapy Planning (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
  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)
  8. MIND Clinical Imaging Study: conversion of mgh 60 direction sequence to nrrd (Jeremy Bockholt, Sumner Williams)

Non-Medical Collaborations

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

Attendee List

  1. Gary Christensen, The University of Iowa
  2. Jeffrey Hawley, Gary Christensen's student
  3. Kate Raising, Gary Christensen's student
  4. Nathan Fritze, Gary Christensen's student
  5. Paul Song, Gary Christensen's student

Pictures

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