2007 Project Half Week

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Results of this event will be summarized here after it is completed.

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. Scripts to run and visualize 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. SVM Shape Analysis (Brad, Polina, Martin)
  5. Parallelization of ITK for deformable registration (Stephen, Jim, Ross)
    1. Driving problem: Congealing with B-spline (Lilla, Stephen)
    2. Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
  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

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, 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


  1. Slicer3 Infrastructure Projects
    1. Architecture/Features (Steve Pieper, Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
    2. Data Model / libMRML (Alex, Steve)
    3. Execution Model / Command Line Modules (Jim Miller, Bill Lorensen)
    4. Interface Design and Usability (Wendy Plesniak, KWWidgets: Sebastien Barre, Yumin Yuan) 4-block PPT Jan 2007
      1. See Slicer3:UIEngineering
    5. Transition of Selected Slicer2.x Modules to Slicer3 (Nicole, Katie, Wendy, Mathieu)
      1. DTMRI: Raul, LMI
      2. Tractography: Lauren 4-block PPT Jan 2007
      3. Editor: Steve
      4. Colors, Fiducials, FreeSurfer, ModelMaker: Nicole
      5. IGT, Trackers: Haiying
      6. EMSegment Interface: Brad Davis
      7. SlicerDaemon Interface (for unu, matlab): Steve Pieper
    6. Build/Test/Deploy System (Andy, Katie)
    7. Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) File:2007 AHM Programming Half Week Slicer3 Launch.ppt
    8. Pipeline Integration (Jags)
    9. Grid Integration (Jeff Grethe, Neil)
    10. Slicer3:Performance Analysis (Katie)
  2. Grid Execution (Neil, Bill, Jim) 2007_Project_Half_Week_GridExecution.ppt
  3. Tractography in Slicer3 (Lauren, Raul)
  4. Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

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 2007
  2. Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) IGT Project page in NA-MIC wiki
  3. Radiology Workstation Module for Slicer3 (Pat, Steve)
  4. vmtk module for Slicer(Luca Antiga, Jim Miller)
  5. Hexahedral Voxel Meshing Slicer Module for collaboration grant (Nicole Grosland, Vincent Magnotta, Curt Lisle, Ritesh Bafna, Steve Pieper) Voxel Meshing 4 block PPT 2007

This following is a list of projects carried out at the last project week (summer 2006). For new attendees, these projects can be used as templates. For attendees involved in the last project week, please move projects from the list below to the list above if you intend to continue these projects. And please do add a new 4-block PPT for 2007.

2006 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): 4-block PPT 2006
  2. ITK statistical analysis using non-parametric permutation analysis and false discovery rate (Martin Styner, UNC): 4 block PPT 2006
  3. Local curvature based correspondence in ITK (Ipek Oguz, Martin Styner, UNC): 4 block PPT 2006
  4. Shape analysis of female SPD dataset (Jim Levitt, PNL, Marc Niethammer, PNL, Sylvain Bouix, PNL, Martin Styner, UNC): 4-block PPT 2006
  5. Mesh Untangling (Gheorghe Postelnicu, MGH, Bill Lorensen GE): 4 block PPT 2006
  6. MR Histology Registration (Gheorghe Postelnicu MGH, Bill Lorensen GE): 4 block PPT 2006

2006 Diffusion Image Analysis

  1. ITK DTI Image Processing Modules (Casey Goodlett UNC, Tom Fletcher Utah, Bill Lorensen GE, John Melonakos GT/GE): 4-block PPT 2006
  2. Fiber Tools / Slicer 3 Integration (Casey Goodlett UNC, Bill Lorensen GE): 4-block PPT 2006
  3. Stochastic Fiber Tracing Applications (C-F Westin, Marek Kubicki, Raul San-Jose, AW de Vries, All LMI): 4-block PPT 2006
  4. Slicer Fiber (Model) Labeling Interface (Lauren O'Donnell MIT, Marek Kubicki BWH) : 4-block PPT 2006

2006 FMRI Image Analysis

  1. Conformal Flattening in ITK(Yi Gao GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware, Marc Niethammer BWH): 4-block PPT 2006
  2. Spatial Regularization in fMRI Analysis(Wanmei Ou, Polina Golland, Sandy Wells, and Carsten) 4-block PPT 2006

2006 NA-MIC Kit

  1. Slicer3 Interface (Wendy Plesniak, Sebastien Barre, Steve Pieper, Mathieu Malaterre, Randy Gollub, Michael Halle), 4-block PPT 2006
  2. Migrating Slicer2.x Modules to Slicer3 (Nicole Aucoin, Mathieu Malaterre, Katie Hayes, Bill Lorensen): 4-block PPT 2006
  3. Slicer3 Packaging (Andy Cedilnik, Steve Pieper) 4-block PPT 2006
  4. Slicer3 Grid Integration (Jeff Grethe, Brendan Faherty, Steve Pieper, Katie Hayes), 4-block PPT 2006
  5. Slicer3 Pipeline Integration (Jagadeeswaran Rajendiran, Martin Styner, Steve Pieper), 4 block PPT 2006
  6. 2006 Project MGH File Format Converter(Gheorghe Postelnicu, Bill Lorensen) 4-block PPT 2006
  7. Volumetric Meshing (Kiran Shivanna, Vincent Magnotta, Nicole Grosland):4-block PPT 2006
  8. Dicom Query/Retrieve (Eduardo Suárez, Rafael Nebot, Steve Pieper, Jim Miller):4-block PPT 2006
  9. A Translation Station for Imaging (Pat Mongkolwat, Alex Kogan, Tom Lechner, Steve Pieper, Wendy Plesniak):4-block PPT 2006
  10. Converting vtkFMRIEngine and vtkMRAblation to Slicer3 modules (Noby Hata, Haiying Liu, Steve Pieper, Jim Miller): 4-block ppt 2006

2006 NA-MIC Kit Support for Non-Medical Data

  1. ITK IO support for reading astronomy data and coordinates from FITS files (Douglas Alan IIC, Michael Halle BWH/IIC, Luis Ibanez Kitware) 4-block PPT 2006


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-programming-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.