2007 Project Half Week

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Welcome to the web page for the 4th Project Week!


This event was successfully concluded on January 12, 2007 in conjunction with the third NA-MIC AHM. The AHM recorded 96 total attendees, 56 of whom were NA-MIC participants, 32 were collaborators, and 8 represented the EAB and the NIH. During the project event, 38 projects were actively pursued by the participants.

A summary powerpoint for this event is available here.

Some statistics at a glance

For the AHM:

  • 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
    • 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
    • 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), University of Iowa(6), Virginia Tech (1).
  • 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

A summary of all past Project Events.

Please note

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


This is the list of projects discussed in the preparation tcons on December 7 and December 14, 2006. Each project lead (first name in the list) needs to complete a new 4-block PPT, and upload and link it to this page.

Structural Analysis

  1. ITK Spherical Wavelet Transform Filter (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): 4-block PPT Summer 2006, 4-block PPT Jan 2007
  2. UNC shape analysis with Spherical Wavelet Features (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): 4-block PPT Jan 2007
  3. EMSegmenter Software Development (Kilian, Brad) 4-block PPT Jan 2007
  4. Data assimilation for NAMIC (Stephen) 4 block PPT Jan 2007
  5. Parallelization of ITK for deformable registration (Stephen, Jim, Ross) 4-block PPT Jan 2007
  6. Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), 4-block PPT Jan 2006, 4-block PPT Jan 2007
  7. Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), 4-block PPT Jan 2007
  8. Genus Zero Slicer3 Module (Marc, Sylvain, Steve), 4-block PPT Jan 2007
  9. Thickness Slicer3 Module (Marc, Sylvain, Steve), 4-block PPT Jan 2007

Diffusion Image Analysis

  1. Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): 4-block PPT Jan 2007
  2. Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): 4-block PPT Jan 2007
  3. Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): 4-block PPT Jan 2007
  4. Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): 4-block PPT Jan 2007
  5. ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), 4-block PPT Jan 2007
  6. Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), 4-block PPT Jan 2007
  7. ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), 4-block PPT Jan 2007


  1. Slicer3:Architecture/Features (Steve Pieper, Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) 4-block ppt
  2. Slicer3: Data Model / libMRML (Alex, Steve) 4 block:MRML Feedback, 4 block:MRML Hierarchy Representation
  3. Slicer3: Execution Model / Command Line Modules (Jim Miller, Bill Lorensen)
  4. Slicer3: Interface Design and Usability (Wendy Plesniak, KWWidgets: Sebastien Barre, Yumin Yuan) 4-block PPT Jan 2007
  5. Slicer3: Transition of Selected Slicer2.x Modules to Slicer3 (Nicole, Katie, Wendy, Mathieu)
    1. DTMRI Raul, LMI File:2007 Project Half Week DTI.ppt
    2. Tractography Lauren 4-block PPT Jan 2007
    3. Editor Steve 4-block ppt
    4. Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker Nicole 4 block:Colors, 4 block:Fiducials, 4 block:FreeSurfer, 4 block:ModelMaker
  6. Build/Test/Deploy System (Andy, Katie) 4-block PPT 4-block PPT Feb 2007
  7. Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) 4-block PPT
  8. Slicer3: Pipeline Integration (Jags) 4-block PPT
  9. Slicer3: Grid Integration (Neil, Bill, Jim) 4-block PPT Jan 2007
  10. Slicer3:Performance Analysis (Katie) 4-block PPT Jan 2007 4-block PPT Feb 2007
  11. Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), 4-block PPT Jan 2007

External Collaborations

  1. Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) 4 block PPT Jan 2007
  2. Slicer3: IGT, Trackers Haiying 4 block PPT Jan 2007
  3. IGT Workflow for Slicer3: Interventional Imaging (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) 4 block PPT Jan 2007
  4. Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex) 4 block PPT Jan 2007
  5. vmtk module for Slicer (Luca Antiga, Jim Miller) 4 block PPT Jan 2007 discussion on reference systems
  6. Hexahedral Voxel Meshing into Slicer3 for collaboration grant
    1. Voxel meshing as an execuation module in Slicer3 - Voxel Meshing 4 block PPT Jan 2007 (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
    2. Mesh Quality Visualization Development - Mapped Quality 4 block PPT Jan 2007 (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
    3. Bounding Box Projection Meshing - Bounding Box 4 block PPT Jan 2007 (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
    4. Tetrahedral Mesh Generation Tools in VTK - VTK Tetrahedral Meshing 4 block PPT Jan 2007 (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
    5. Mapped Meshing Using ITK - ITK FEM Registration Mapped Meshing Jan 2007 (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
  7. Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) File:2007 Project Half Week AlcoholExposureStructuralImaging.ppt
  8. Slicer Enhancements for Astronomical Data Cubes (Douglas Alan IIC, Mike Halle BWH/IIC, Bill Lorensen GE, Jim Miller GE, Wendy Plesniak BWH), 4-block PPT June 2006, 4-block PPT Jan 2007


Dates: January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

Registration Fee: Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please follow this link.

Background and Preparation

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". 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.


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. This event involves programming, algorithm design, and clinical application development/testing.
  • The event is open to people outside NA-MIC, subject to availability.
  • 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.

Preparation for the workshop

  1. Please make sure that you are on the NA-MIC Project Week mailing list.
  2. December 7: Kickoff TCON
  3. December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
  4. December 14: TCON#2 to discuss projects and verify teams
  5. December: Create a directory for each project on the NAMIC Sandbox (Andy)
    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)
  6. January 4, 2007: TCON#3 last preparation tcon
  7. By January 9th: Complete the top half of this powerpoint template for each project. Upload and link to the right place.
  8. 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.