2009 Winter Project Week

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Introduction to NA-MIC Project Week

Please read an introduction about these events here.

Dates.Venue.Registration

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

Agenda

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

Projects

Please note:

• Please use the 2009 Project Week Template to create a page for your project(s)
• Last Event's Projects as a reference
• For hosting projects, we are planning to make use of the NITRC resources. See Information about NITRC Collaboration
• Next Project Week is at MIT -- June 22-26, 2009

The following is a list of all projects that will be pursued at this meeting.

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)
   2. Stochastic Tractograhy Tool for Slicer (Marek Kubicki BWH, Julien de Siebenthal BWH)
   3. Evaluation of basic Slicer 3.0 Functionality from a User Perspective (Doug Terry BWH, Marek Kubicki BWH)
2. UNC Roadmap Project: Cortical Thickness Measurement for Autism
3. MIND Roadmap Project: Brain Lesion Analysis in Lupus
4. JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention

Other NA-MIC Projects

1. Fluid mechanics tractography and visualization (Nathan Hageman UCLA)
2. UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning - using Slicer and its link to BrainLab to investigate whether different tractography methods aid in preoperative planning of tumor resection.(Nathan Hageman UCLA)
3. Development of FEM / FVM solver library in ITK/VTK (and/or Python?) (Nathan Hageman UCLA, Vince, Luca, Steve)
4. Transform Management(Jim Miller)
5. Interactive 3D Widgets - Introduce new interactors into Slicer (Karthik)
6. Using ITK in VTK Pipelines (Jim, Steve)
7. User Interface Flexible Layouts (Wendy, Jim, Steve)
8. Packaging Python Interface - Fortran and openssl problems(Luca, Steve)
9. Two-tensor tractography in Slicer using Python and Teem (Madeleine Seeland, C-F Westin)
10. Diffusion Tensor Invariant gradients and rotation tangents in Python and Teem(Peter Savadjiev and C-F Westin)
11. xnat and batchmake integration (Julien, Dan Marcus)
12. Automated GUI testing (Sebastien, Interested User: Vince)
13. Slicer Colors Module update (Nicole)
14. Volume Rendering (Alex, Curt, Nicholas)
15. XNAT Dekstop & File Repository prototypes (Dan Marcus, Wendy Plesniak)
16. Cortical correspondence using DTI (Ipek, Martin)
17. Command Line Program Testing (Lorensen, NA-MIC)
18. Vessel Segmentation in Slicer using VMTK (Daniel Haehn, Luca Antiga)
19. Exploring Functional Connectivity in fMRI via Clustering (Archana Venkataraman, Marek Kubicki, Polina Golland)
20. Compiler Warnings:Slicer3's Graffiti (Lorensen, NA-MIC)

External Collaborations

• Iowa Meshing Tutorial
  • (the work is likely to be completed by the AHM)
• Wake Forest - Virginia Tech
  • Move to All Slicer3 Workflow
  • Development of deformation based morphometry module
• Georgetown U: Prototype RF Lesion Ablation Workflow prototyped in Slicer
• UNC:
  • MR-image registration algorithm to be extended and added to namic kit
  • white matter lesion segmentation
• Mario Negri
• Stanford SIMBIOS: segmentation of knee joint
• MRSI Module for Slicer (Bjoern Menze)

Preparation

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.