Difference between revisions of "2009 Summer Project Week"

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#Sylvain Jaume, MIT
 
#Sylvain Jaume, MIT
 
#Alex Yarmarkovich, Isomics
 
#Alex Yarmarkovich, Isomics
 +
#Marco Ruiz, UCSD
  
 
== Logistics ==
 
== Logistics ==

Revision as of 19:25, 23 April 2009

Home < 2009 Summer Project Week

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Introduction to the FIRST JOINT PROJECT WEEK

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the NA-MIC Kit, algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of NA-MIC, NCIGT, NAC, Harvard Catalyst, and CIMIT. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available here.

Agenda

Projects

The list of projects for this week will go here.

  • Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
  • 4D Imaging - currently used for Lung Perfusion (Junichi, Dan Blezek?, Steve, Alex G?)
  • Liver Ablation in Slicer (Haiying, Georgetown?)
  • SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
  • Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
  • gpu based registration acceleration (James Balter?, Greg Sharp, Alark Joshi, Dave Gustafson, Aditya K., Yogesh Rathi?, Sandy Wells, Tina Kapur)
  • Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
  • Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)
  • xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
  • Xnat user clinic - combine with data clinic
  • xnat programmer clinic
  • Grid Wizard+xnat clinic (Clement)
  • ?Fluid Mechanincs Module (Nathan Hageman)
  • ?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
  • Cortical Thickness Pipeline (Clement, Ipek)
  • Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)

IGT Projects:

  • port 4d gated ultrasound code to Slicer - (Danielle)
  • integration of stereo video into Slicer (Robarts)
  • multi-spectral toolbox for MR T1, T2, fmri, DTI data (robarts, sylvain jaume, nicholas, noby)
  • neuroendoscope workflow presentation (sebastien barre)
  • slicer integration of mri compatible prostate biopsy robot(sid, queens)

Preparation

  1. Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
  2. Join the kickoff TCON on April 16, 3pm ET.
  3. June 18 TCON at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
  4. By 3pm ET on June 11, 2009: 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.
  5. By 3pm on June 18, 2009: 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)
  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...

Attendee List

If you plan to attend, please add your name here.

  1. Ron Kikinis, BWH
  2. Ferenc Jolesz, BWH
  3. Clare Tempany, BWH
  4. Tina Kapur, BWH
  5. Steve Pieper, Isomics Inc
  6. Jim Miller, GE Research
  7. Bill Lorensen, EAB
  8. Randy Gollub, MGH
  9. Nicole Aucoin, BWH
  10. Dan Marcus, WUSTL
  11. Junichi Tokuda, BWH
  12. Alex Gouaillard, Harvard Systems Biology
  13. Arnaud Gelas, Harvard Systems Biology
  14. Kishore Mosanliganti, Harvard Systems Biology
  15. Lydie Souhait, Harvard Systems Biology
  16. Luis Ibanez, Kitware Inc
  17. Vincent Magnotta, UIowa
  18. Xenios Papademetris, Yale
  19. Gregory S. Fischer, WPI (Mon, Tue, Wed)
  20. Daniel Blezek, Mayo (Tue-Fri)
  21. Danielle Pace, Robarts Research Institute / UWO
  22. Clement Vachet, UNC-Chapel Hill
  23. Dave Welch, UIowa
  24. Demian Wassermann, Odyssée lab, INRIA, France
  25. Manasi Ramachandran, UIowa
  26. Greg Sharp, MGH
  27. Rui Li, MGH
  28. Mehdi Esteghamatian, Robarts Research Institute / UWO
  29. Misha Milchenko, WUSTL
  30. Kevin Archie, WUSTL
  31. Tim Olsen, WUSTL
  32. Wendy Plesniak BWH
  33. Haiying Liu BWH
  34. Curtis Lisle, KnowledgeVis / Isomics
  35. Diego Cantor, Robarts Research Institute / UWO
  36. Daniel Haehn, BWH
  37. Nicolas Rannou, BWH
  38. Sylvain Jaume, MIT
  39. Alex Yarmarkovich, Isomics
  40. Marco Ruiz, UCSD

Logistics

  • Dates: June 22-26, 2009
  • 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 12th, 2009. 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 this is your first event and you are attending for only one day, the registration fee is waived. Please let us know, so that we can cover the costs with one of our grants.
  • Registration Method Add your name to the Attendee List section of this page
  • Hotel: We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). 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.
  • 2009 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
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