2009 Winter Project Week

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To AHM 2009


Welcome to the web page for the 8th Project Week!


The eighth NA-MIC Project event was held on January 5-9, 2009, in connection with the 2009 NA-MIC AHM. The AHM recorded 98 registered attendees. During the project event, 51 projects were actively pursued by the participants.

Statistics at a glance:

  • 98 Registered Attendees: 63 NA-MIC participants, 35 collaborators
    • 63 NA-MIC Participants breakdown by cores: Core 1 (21), Core 2 (18), Core 3 (10), Core 5 (2), Core 7 (2), EABS-NIH (10)
    • 35 Collaborators: Funded by NCBC program (10), Other (25)
  • 51 Projects: DBP Roadmap Projects (11), NA-MIC infrastructure algorithms and engineering Projects (32), External Collaborations (8)

A summary of all past Project Events.

Introduction to NA-MIC Project Week

Please read an introduction about these events here.


Please click here for Dates, Venue, and Registration for this event.


Please click here for the agenda for AHM 2009 and Project Week.


Please note:

The following is a list of all projects that will be pursued at this meeting. (Session notes for the moderators)

NA-MIC DBP Roadmap Projects

Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

  1. Harvard Roadmap Project: Stochastic Tractography for VCFS
    1. Tubular Surface Segmentation for fiber bundle extraction (Vandana Mohan GATech, Allen Tannenbaum GATech, Marek Kubicki BWH, Stephen Aylward Kitware)
    2. Stochastic Tractograhy Tool for Slicer (Marek Kubicki BWH, Julien de Siebenthal BWH, Steve Pieper Isomics)
    3. Evaluation of basic Slicer 3.0 Functionality from a User Perspective (Doug Terry BWH, Marek Kubicki BWH, Sylvain Bouix BWH, Steve Pieper, Wendy Plesniak, Nicole Aucoin)
    4. Group analysis of DTI fiber bundles (Casey Goodlett, Guido Gerig, Marek Kubicki, Sylvain Bouix)
  2. UNC Roadmap Project: Cortical Thickness Measurement for Autism
    1. Local Cortical Thickness Pipeline (Clement Vachet, Martin Styner, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz)
    2. Regional Cortical Thickness Pipeline (Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett)
  3. MIND Roadmap Project: Brain Lesion Analysis in Lupus
    1. Slicer High Level Wizard Project(Steve Pieper, Mark Scully, Jeremy Bockholt)
    2. Review of Lesion Algorithms(Ross Whitaker, Vincent Magnotta, Marcel Prastawa, Mark Scully, Jeremy Bockholt)
    3. Determine Requirements of Longitudinal Lesion Analyses(Jeremy Bockholt, Marcel Prastawa, Mark Scully, Andriy Fedorov)
    4. Optimize the new segmentation method for speed, memory use, and multi-threading(Jeremy Bockholt, Steve Piper, Mark Scully)
  4. JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention
    1. Prostate segmentation module for Slicer3 (Siddharth Vikal, Gabor Fichtinger, Queens University, Katie Hayes, Brigham and Women's Hospital, Yi Gao, Allen Tannenbaum, Georgia Tech)

Other NA-MIC Projects

  1. Fluid mechanics tractography and visualization (Nathan Hageman UCLA, Steve Pieper and Alex Yarmarkovich Isomics)
  2. UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning (Nathan Hageman UCLA)
  3. Development of FEM / FVM solver library in ITK/VTK/Python (Nathan Hageman UCLA, Vince, Nicole Grosland, Luca, Steve)
  4. Transform Management(Jim Miller)
  5. Interactive 3D Widgets - Introduce new interactors into Slicer; extensions to current widgets to support Slicer (Karthik, Will Schroeder, Nicole Aucoin)
  6. Using ITK in VTK Pipelines (Jim, Steve)
  7. User Interface Flexible Layouts (Wendy, Jim, Steve, Sebastien, Ron)
  8. Python interface completion and packaging - Fortran and openssl problems (Luca, Steve, Demian)
  9. Two-tensor tractography in Slicer using Python and Teem (Madeleine Seeland, C-F Westin, Xiaodong Tao)
  10. Diffusion Tensor Invariant gradients and rotation tangents in Python and Teem (Peter Savadjiev, C-F Westin, Luis Ibanez)
  11. Tractography Segmentation by Nonparametric Bayesian Clustering (Xiaogang Wang, C-F Westin)
  12. KWWidgets and Slicer automated GUI testing (Sebastien, Yumin, Interested User: Vince)
  13. Slicer Colors Module update (Nicole)
  14. MRSI Module for Slicer (Bjoern Menze)
  15. Volume Rendering (Alex, Curt, Nicholas)
  16. XNAT Desktop BatchMake integration & Slicer interface (Dan Marcus, Stephen Aylward, Wendy Plesniak, Curt Lisle)
  17. Cortical correspondence using DTI (Ipek, Martin, Xiaodong)
  18. Command Line Program Testing (Lorensen, Ron)
  19. Compiler Warnings:Slicer3's Graffiti (Lorensen, NA-MIC)
  20. Vessel Segmentation in Slicer using VMTK (Daniel Haehn, Luca Antiga)
  21. Exploring Functional Connectivity in fMRI via Clustering (Archana Venkataraman, Marek Kubicki, Polina Golland)
  22. Measuring dynamics of tumor growth in Slicer3 with ChangeTracker (Andriy Fedorov, Jim Miller, Alex Yarmarkovich, Wendy Plesniak, Marcel Prastawa)
  23. GWE integration with catalog files (Marco Ruiz, TBD from XNAT group)
  24. ITK level set solution for cell segmentation in microscopy datasets (part of Gofigure) (Kishore mosaliganti)
  25. ITK surface processing filters: Smoothing, spherical parameterization (part of Gofigure) (Alex. Gouaillard)
  26. VTK widgets for manual segmentation and manual validation of segmentation (part of Gofigure) (Arnaud Gelas)
  27. Integration of Utah registration and segmentation methods as Slicer plugins (Marcel Prastawa)
  28. DWI to MRI Registration Using Optimat Mass Transport (Sylvain Bouix, Ivan Kolesov GATech)
  29. Lung Imaging Platform (James Ross, Raul San Jose)
  30. Brain Atlases for Segmentation (Michal Depa, Koen Van Leemput, Mert Rory Sabuncu, Polina Golland)
  31. Particle-based Shape Analysis Pipeline (Manasi Datar, Josh Cates, Ross Whitaker, Stephen Aylward, Martin Styner)
  32. EPI Geometric Distortion Correction (Ran Tao, Tom Fletcher, Ross Whitaker)

External Collaborations

  1. Iowa Meshing Project 2009: Iowa Meshing Tutorial
  2. Wake Forest - Virginia Tech: Move to All Slicer3 Workflow
  3. Georgetown U: Prototype RF Lesion Ablation Workflow prototyped in Slicer
  4. UNC: MR-image registration and white matter lesion segmentation algorithms to be extended and added to namic kit
  5. Stanford SIMBIOS: Whole Body Segmentation for Simulation
  6. NCI Evaluating NA-MIC Tools for Image Analysis
  7. Lung Lesion Sizing Toolkit
  8. MGH Radiation Oncology


  1. Please make sure that you are on the NA-MIC Project Week mailing list.
  2. Starting Thursday, October 16th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
    • October 16: Engineering Infrastructure Projects
    • October 23: Funded External Collaboration Projects
    • November 6: DPB Projects
    • November 20: New Collaborations
    • December 4: Other Projects
    • December 18: Loose Ends
  3. By December 17, 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.
  4. By December 17, 2008: Create a directory for each project on the NAMIC Sandbox (Zack)
    1. Ask Zack for a Sandbox account
    2. 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)
    3. 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.)
    4. 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)
  5. FINAL TCON: December 18th 3pm ET to tie loose ends
  6. 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...

Previous Project Events

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