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.

Collaboration Projects

  1. 2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images
  2. 4D Imaging (Perfusion, Cardiac, etc.) (Junichi, Dan Blezek?, Steve, Alex G?)
  3. Liver Ablation in Slicer (Haiying, Ziv, Noby)
  4. SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
  5. Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
  6. Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
  7. Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
  8. Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
  9. xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
  10. Grid Wizard+xnat clinic (Clement Vachet)
  11. Fluid mechanics tractography and visualization (Nathan Hageman UCLA)
  12. ?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
  13. Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
  14. Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman)
  15. Skull Stripping (Xiaodong, Snehashis Roy)
  16. HAMMER Registration (Guorong Wu, Xiaodong Tao, Jim Miller)
  17. White Matter Lesion segmentation (Minjeong Kim, Xiaodong Tao, Jim Miller)
  18. FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)
  19. Meningioma growth simulation (Fedorov, Marcel, Ron)
  20. Automatic brain MRI processing pipeline (Marcel, Hans)
  21. XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
  22. Spherical Mesh Diffeomorphic Demons Registration (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
  23. MRSI Module (Bjoern Menze, Jeff Yager, Vince Magnotta)
  24. Measuring Alcohol Stress Interaction (Vidya Rajgopalan, Andrey Fedorov)
  25. DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)

IGT Projects:

  1. Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
  2. port 4d gated ultrasound code to Slicer - (Danielle)
  3. integration of stereo video into Slicer (Mehdi)
  4. multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
  5. neuroendoscope workflow presentation (sebastien barre)
  6. breakout session on Dynamic Patient Models (James Balter)
  7. 2d/3d Registration (and GPGPU acceleration) for Radiation Therapy (Sandy Wells, Jim Balter, and others)

NA-MIC Engineering Projects

  1. DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
  2. Using ITK in python (Steve, Demian, Jim)
  3. Taking advantage of multicore machines & clusters with python (Julien de Siebenthal, Sylvain Bouix)
  4. Deferring heavy computational tasks with python (Julien de Siebenthal, Sylvain Bouix)
  5. Developing realtime feedback using CUDA (Julien de Siebenthal, Sylvain Bouix)
  6. VTK 3d Widgets in Slicer3 (Nicole, Karthik, Sebastien, Wendy)
  7. Updates to Slicer3 Colors module (Nicole)
  8. EM Segmenter (Sylvain Jaume, Nicolas Rannou)
  9. Plug-in 3D Viewer based on XIP (Lining)
  10. IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
  11. Slicer3 Informatics Workflow Design & XNAT updates for Slicer (Wen, Steve, Dan M, Dan B)
  12. BSpline Registration in Slicer3 (Samuel Gerber,Jim Miller, Ross Whitaker)
  13. EPI Correction in Slicer3 (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
  14. Registration reproducibility in Slicer3 (Andriy, Luis, Bill, Jim, Steve)
  15. The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn)

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...
  7. People doing Slicer related projects should come to project week with slicer built on your laptop.
    1. Projects to develop extension modules should work with the Slicer-3-4 branch (new code should not be checked into the branch).
    2. Projects to modify core behavior of slicer should be done on the trunk.

Attendee List

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

  1. Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
  2. Ferenc Jolesz, BWH (NCIGT, NAC)
  3. Clare Tempany, BWH (NCIGT)
  4. Tina Kapur, BWH (NA-MIC, NCIGT)
  5. Steve Pieper, Isomics Inc
  6. Jim Miller, GE Research
  7. Xiaodong Tao, GE Research
  8. Randy Gollub, MGH
  9. Nicole Aucoin, BWH (NA-MIC)
  10. Dan Marcus, WUSTL
  11. Junichi Tokuda, BWH (NCIGT)
  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. Hans Johnson, UIowa
  19. Xenios Papademetris, Yale
  20. Gregory S. Fischer, WPI (Mon, Tue, Wed)
  21. Daniel Blezek, Mayo (Tue-Fri)
  22. Danielle Pace, Robarts Research Institute / UWO
  23. Clement Vachet, UNC-Chapel Hill
  24. Dave Welch, UIowa
  25. Demian Wassermann, Odyssée lab, INRIA, France
  26. Manasi Ramachandran, UIowa
  27. Greg Sharp, MGH
  28. Rui Li, MGH
  29. Mehdi Esteghamatian, Robarts Research Institute / UWO
  30. Misha Milchenko, WUSTL
  31. Kevin Archie, WUSTL
  32. Tim Olsen, WUSTL
  33. Wendy Plesniak BWH (NAC)
  34. Haiying Liu BWH (NCIGT)
  35. Curtis Lisle, KnowledgeVis / Isomics
  36. Diego Cantor, Robarts Research Institute / UWO
  37. Daniel Haehn, BWH
  38. Nicolas Rannou, BWH
  39. Sylvain Jaume, MIT
  40. Alex Yarmarkovich, Isomics
  41. Marco Ruiz, UCSD
  42. Andriy Fedorov, BWH (NA-MIC)
  43. Harish Doddi, Stanford University
  44. Saikat Pal, Stanford University
  45. Scott Hoge, BWH (NCIGT)
  46. Vandana Mohan, Georgia Tech
  47. Ivan Kolosev, Georgia Tech
  48. Behnood Gholami, Georgia Tech
  49. James Balter, U Michigan
  50. Dan McShan, U Michigan
  51. Zhou Shen, U Michigan
  52. Maria Francesca Spadea, Italy
  53. Lining Yang, Siemens Corporate Research
  54. Beatriz Paniagua, UNC-Chapel Hill
  55. Bennett Landman, Johns Hopkins University
  56. Snehashis Roy, Johns Hopkins University
  57. Marta Peroni, Politecnico di Milano
  58. Sebastien Barre, Kitware, Inc.
  59. Samuel Gerber, SCI University of Utah
  60. Ran Tao, SCI University of Utah
  61. Marcel Prastawa, SCI University of Utah
  62. Katie Hayes, BWH (NA-MIC)
  63. Sonia Pujol, BWH (NA-MIC)
  64. Andras Lasso, Queen's University
  65. Yong Gao, MGH
  66. Minjeong Kim, UNC-Chapel Hill
  67. Guorong Wu, UNC-Chapel Hill
  68. Jeffrey Yager, UIowa
  69. Yanling Liu, SAIC/NCI-Frederick
  70. Ziv Yaniv, Georgetown
  71. Bjoern Menze, MIT
  72. Vidya Rajagopalan, Virginia Tech
  73. Sandy Wells, BWH (NAC, NCIGT)
  74. Lilla Zollei, MGH (NAC)
  75. Lauren O'Donnell, BWH
  76. Florin Talos, BWH (NAC)
  77. Nobuhiko Hata, BWH (NCIGT)
  78. Alark Joshi, Yale
  79. Yogesh Rathi, BWH
  80. Jimi Malcolm, BWH
  81. Dustin Scheinost, Yale
  82. Dominique Belhachemi, Yale
  83. Sam Song, JHU
  84. Nathan Cho, JHU
  85. Julien de Siebenthal, BWH
  86. Peter Savadjiev, BWH
  87. Carl-Fredrik Westin, BWH
  88. John Melonakos, AccelerEyes (Wed & Thu morning)
  89. Yi Gao, Georgia Tech
  90. Sylvain Bouix, BWH
  91. Zhexing Liu, UNC-CH
  92. Eric Melonakos, BWH
  93. Lei Qin, BWH
  94. Giovanna Danagoulian, BWH
  95. Andrew Rausch, BWH (1st day only)
  96. Haytham Elhawary, BWH
  97. Jayender Jagadeesan, BWH
  98. Marek Kubicki, BWH
  99. Doug Terry, BWH
  100. Nathan Hageman, LONI (UCLA)

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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