Difference between revisions of "2008 Summer Project Week"

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* Tuesday  
* Tuesday  
** 8:30am breakfast
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 9:00-9:45am: Work
** 10-10:30am [http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 Slicer 3.2 Update] (Jim Miller, Steve Pieper)
** 10-10:30am [http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 Slicer 3.2 Update] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Jackson Room 38-466) (Ron Kikinis)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Jackson Room 38-466) (Ron Kikinis)

Revision as of 13:37, 24 June 2008

Home < 2008 Summer Project Week

Back to Programming/Project Events

Summer 2008


  • 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.




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. Parcellation of 3T MR data(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. Lesion Classification Module (Mark Scully MIND)
    2. Longitudinal Registration and time course analyses in white matter lesions (Mark Scully and Jeremy Bockholt, MIND)
    3. Enhancements and extension of white matter lesion classification using DTI scalars (Jeremy Bockholt, MIND)
  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. Porting groupwise registration project into NAMIC-kit (Serdar Balci, Brad Davis)
  4. CVS / SVN auto synchronization (Sebastien, Steve, Jim, Will, Bill)
  5. 3D Widgets in Slicer (Nicole Aucoin, Will Schroeder)
    1. Issues with existing widgets
    2. Design of new widgets
  6. Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
  7. Module Chaining (Marco, Jim, Steve, Dan B., Luca)
  8. Nonlinear transforms (Jim, Steve, Luis)
    1. TransformToWorld/TransformFromWorld, integration with slice viewing
  9. Slicer3, XNAT integration and XCEDE Web Services (Dan M., Wendy, Steve, Julien, Dan B.)
    1. Review and enrich use cases (developing use case ppt)
  10. Python in Slicer (Dan B., Michael Halle, Steve, Luca)
  11. Performance Tuning of Fiducials using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
  12. Focused GUI Refinement and Strategies for Consistency (Wendy, Sebastien) [1]
  13. fMRI connectivity (Bryce Kim, MIT)
  14. Atlas free Segmentation (Tammy Riklin-Raviv, MIT)
  15. New Bias Field Correction in EM (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
  16. Fluid Mechanics Based DTI Tractography (Nathan Hageman, UCLA)

External Collaborations

  1. NA-MIC/Projects/Collaboration/UWA-Perth (Grand Joldes)
  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 Pieper)
  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 and Siddharth - 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 DTI and HARDI Analysis tools(Ragini Verma, SBIA Upenn)
  16. Projects/Diffusion/2008 Project Week DiffusionMRI QBall Diffusion QBall framework integration( Demian Wassermann, Rachid Deriche, Odyssée INRIA, CF Westin, LMI

Non-Medical Collaborations

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


  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...

Attendee List

  1. Jack Blevins Acoustic Med
  2. Pratik Patel Brainlab
  3. Mark Anderson BWH
  4. Nicole Aucoin BWH
  5. Sylvain Bouix BWH
  6. Michael Halle BWH
  7. Nobuhiko Hata BWH
  8. Katie Hayes BWH
  9. Scott Hoge BWH
  10. Marianna Jakab BWH
  11. Tina Kapur BWH
  12. Ron Kikinis BWH
  13. Jacek Kukluk BWH
  14. Haying Liu BWH
  15. Bjoern Menze BWH
  16. Wendy Plesniak BWH
  17. Kilian Pohl BWH
  18. Sonia Pujol BWH
  19. Carlos Sánchez Mendoza BWH
  20. Priya Srinivasan BWH
  21. Junichi Tokuda BWH
  22. Demian Wassermann BWH (INRIA)
  23. C-F Westin BWH
  24. Xiaodong Tao GE
  25. Dirk Padfield GE
  26. Jim Miller GE
  27. Surprise Guest from EAB
  28. Viswanath Avasarala GE
  29. John Melonakos GA Tech
  30. Yi Gao GA Tech
  31. Tauseef Rehman GA Tech
  32. Sean Megason Harvard Med
  33. Alex Gouaillard Harvard Med
  34. Kishore Mosaliganti Harvard Med
  35. Arnaud Gelas Harvard Med
  36. Dana Peters Harvard Med
  37. Jason Taclas Harvard Med
  38. Douglas Alan Harvard
  39. Toru Higaki Hiroshima U
  40. Daniel Blezek Isomics
  41. Curtis Lisle Isomics
  42. Steve Pieper Isomics
  43. Alex Yarmarkovich Isomics
  44. Csaba Csoma JHU
  45. Peter Kazanzides JHU
  46. Will Schroeder Kitware
  47. Sebastien Barre Kitware
  48. Julien Jomier Kitware
  49. Bill Hoffman Kitware
  50. Luis Ibanez Kitware
  51. Luca Antiga Mario Negri Inst
  52. Randy Gollub MGH
  53. Silas Mann MGH
  54. Greg Sharp MGH
  55. Marta Peroni MGH
  56. Serdar Balci MIT
  57. Bryce Kim MIT
  58. Clare Poynton MIT
  59. Tammy Riklin Raviv MIT
  60. Polina Golland MIT
  61. Jeremy Bockholt MRN Lupus DBP
  62. Mark Scully MRN Lupus DBP
  63. Gabor Fichtinger Queen's
  64. David Gobbi Queen's
  65. Purang Abolmaesumi Queen's
  66. Siddharth Vikal Queen's
  67. Zhen Qian Rutgers
  68. Jinghao Zhou Rutgers
  69. Jeffrey Grethe UCSD
  70. Marco Ruiz UCSD
  71. Chris Churas UCSD
  72. Nathan Hageman UCLA
  73. Keith Gunderson U Iowa
  74. Gary Christensen U Iowa
  75. Jeffrey Hawley U Iowa
  76. Kate Raising U Iowa
  77. Nathan Fritze U Iowa
  78. Paul Song U Iowa
  79. Cheng Zhang U Iowa
  80. Ying Wei U Iowa
  81. Nathan Burnette U Iowa
  82. Hans Johnson U Iowa
  83. Vincent Magnotta U Iowa
  84. Clement Vachet UNC
  85. Zhexing Liu UNC
  86. Ragini Verma U Penn
  87. Luke Bloy U Penn
  88. Yang Li U Penn
  89. Ran Tao Utah
  90. Marcel Prastawa Utah
  91. Casey Goodlett Utah
  92. Ross Whitaker Utah
  93. John Hale U Tulsa
  94. Cody Pollet U Tulsa
  95. Nikeisha Schimke U Tulsa
  96. Adam Wittek Western Australia
  97. Grand Joldes Western Australia
  98. Jamie Berger Western Australia
  99. Carling Cheung Western Ontario
  100. Danielle Pace Western Ontario
  101. Vidya Rajagopalan VA Tech
  102. Nikos Chrisochoides William and Mary
  103. Andriy Fedorov William and Mary
  104. Dan Marcus Washington U
  105. Tim Olsen Washington U
  106. Kevin Archie Washington U
  107. Misha Milchenko Washington U
  108. Xenophon Papademetris Yale U
  109. John Onofrey Yale U
  110. Yifeng Jiang Yale U
  111. Dustin Scheinost Yale U
    • Please note that Registration is closed. Do not add names here. Tkapur 18:19, 19 June 2008 (UTC)