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: $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. If you are attending for one day only, the registration fee is not required.
• Registration Method The event is full. Tkapur 18:12, 17 June 2008 (UTC)
• Hotel: We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the Hotel at MIT (now called Le Meridien). Please click here to reserve. This rate is good only through June 1.
• 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.
• 2008 Summer Project Week Template
• Last Year'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 in Utah -- January 5-9, 2009

Introduction to NA-MIC Project Week

Please read an introduction about these events here.

Agenda

• Monday
  • noon-1pm lunch
  • 1pm: Welcome (Ron Kikinis)
  • 1:05-3:30pm Introduce Projects using templated wiki pages (all Project Leads) (Wiki Template)
  • 3:30-5:30pm Start project work
• Tuesday
  • 8:30am breakfast
  • 9:00-9:45am: NA-MIC Software Process
  • 10-10:30am Slicer 3.0 Update (Jim Miller, Steve Pieper)
  • 11-12noon Performance tuning for Slicer 3.2 (Ron Kikinis)
  • noon lunch
  • 2:30-3:30pm: Project Week 2008 Special topic breakout: XNAT Database (Daniel Marcus)
  • 5:30pm adjourn for day
• Wednesday
  • 8:30am breakfast
  • 9:00-12pm Project Week 2008 Special topic breakout: ITK (Luis Ibanez)
  • noon lunch
  • 2:30-3:30pm: Project Week 2008 Special topic breakout: Non-rigid Registration (Stephen Aylward)
  • 5:30pm adjourn for day
• Thursday
  • 8:30am breakfast
  • noon lunch
  • 2:30-3:30pm Project Week 2008 Special topic breakout: GWE (Marco Ruiz)
  • 5:30pm adjourn for day
• Friday
  • 8:30am breakfast
  • 10am-noon: Project Progress using update Project Wiki pages
  • noon lunch boxes and adjourn. (Next one in Utah the week of Jan 5, 2009)

Projects

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)
   1. DWI Registration using Optimal Mass Transport (Sylvain Bouix BWH, Tauseef Rehman GATech)
   2. EPI-DWI Eddy Current distortion correction (Sylvain Bouix BWH, Ran Tao Utah)
   3. Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
   4. GM Long Distance Tractography (John Melonakos GATech, Marek Kubicki BWH)
   5. Group Analysis of DTI (Casey Goodlett Utah, Marek Kubicki BWH)
2. Longitudinal MRI Study of Early Brain Development in Autism (UNC: Heather Hazlett, Joseph Piven, PI)
   1. Work Flow Tool for regional cortical thickness pipeline (Clement Vachet UNC)
   2. NITRC registration of cortical thickness modules (Clement Vachet UNC)
   3. DWI DTI Prep Tools (Zhexing Liu UNC)
3. Analysis of Brain Lesions in Lupus (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
   1. Finish Roadmap Project
   2. Longitudinal Registration
   3. Beyond Lesions
4. Segmentation and Registration Tools for Robotic Prostate Intervention (Queens/JHU: Gabor Fichtinger, PI)
   1. Trans-Rectal Prostate Biopsy module (David Gobbi, Gabor Fichtinger, Queens/JHU)
   2. Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)
   3. Hardware/software overlay for percutaneous intervention (PERK Station) (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

Other Projects

1. Eddy current and head motion correction of DWIs (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
2. Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
3. CVS / SVN auto synchronization
4. 3D Widgets in Slicer (Nicole Aucoin, Will Schroeder)
   1. Issues with existing widgets
   2. Design of new widgets
5. Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
6. Module Chaining (Marco, Jim, Steve, Dan B., Luca)
7. Nonlinear transforms (Jim, Steve, Luis)
   1. TransformToWorld/TransformFromWorld, integration with slice viewing
8. Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien, Dan B.)
   1. Review and enrich use cases
9. Python in Slicer (Dan B., Michael Halle, Steve, Luca)
10. Performance Tuning of Fiducials using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
11. GUI Tweaking (Wendy, Sebastien) [1]
12. fMRI connectivity (Bryce Kim, MIT)
13. Atlas free Segmentation (Tammy Riklin-Raviv, MIT)
14. New Bias Field Correction in EM (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
15. Fluid Mechanics Based DTI Tractography (Nathan Hageman, UCLA)

External Collaborations

1. NA-MIC/Projects/Collaboration/UWA-Perth (Adam Wittek)
2. NA-MIC/Projects/Collaboration/MRSI Module for Slicer (Bjoern Menze)
3. NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation (Gary Christensen Group)
4. NA-MIC/Projects/Collaboration/Lung Atlas (Gary Christensen Group)
5. NA-MIC/Projects/Collaboration/Non-rigid image registration (Gary Christensen Group)
6. NA-MIC/Projects/Collaboration/SARP phantom (Keith Gunderson)
7. FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
8. NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction
9. NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration (Luca Antiga, Dan Blezek, Mike Halle, Steve Piper)
10. NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008 (Iowa Group)
11. NA-MIC/Projects/Collaboration/Carto_scar_BIDMC (Dana Peters Group)
12. NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3 (Junichi, Haiying and Noby - SPL, David - Queen's), Danielle - Robarts) )
13. NA-MIC/Projects/Collaboration/MGH RadOnc (Greg Sharp, MGH)
14. NA-MIC/Projects/External Collaboration/W&M CRTC Non-rigid registration for neurosurgery (Nikos Chrisochoides, Andriy Fedorov, College of William&Mary)
15. NA-MIC/Projects/Collaboration/SBIA UPenn Non-rigid DTI Registration(Ragini Verma, SBIA Upenn)

Non-Medical Collaborations

1. Astronomical Medicine (Harvard IIC: Douglas Alan, Michael Halle)

Preparation

1. Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list

1. May 08 and May 15 TCON DBPs ONLY at 3pm ET to discuss NA-MIC DBP Projects ONLY.
2. May 22 TCON#1 at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
3. May 29 TCON#2 at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot here. Projects will be discussed in order of the signups.
4. June 5 TCON#3 at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot here. Projects will be discussed in order of the signups.
5. June 12 TCON#4 at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot here. Projects will be discussed in order of the signups.
6. June 19 TCON#5 at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
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. By 3pm on June 19, 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)
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...