2008 Summer Project Week

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Welcome to the web page for the 7th Project Week!


The seventh NA-MIC Project event was held on June 23-27, 2008 at MIT. There were 114 registered participants for this meeting who worked on 58 projects. 14 of these projects were directly related to the NA-MIC DBPs, 19 to External Collaborations, and 15 to NA-MIC Infrastructure.

A summary of all past Project Events.

More pictures (taken by Jeffrey Hawley).

Introduction to NA-MIC Project Week

Please read an introduction about these events here.




These are projects by the current 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, Serdar Balci MIT, Sylvain Bouix BWH, 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. Porting groupwise registration project into NAMIC-kit (Serdar Balci, Brad Davis)
  3. CVS / SVN auto synchronization (Sebastien, Steve, Jim, Will, Bill)
  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 XCEDE Web Services (Dan M., Wendy, Steve, Julien, Dan B.)
    1. Review and enrich use cases (developing use case ppt)
  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. Focused GUI Refinement and Strategies for Consistency (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 (Vidya Rajagopalan, Chris Wyatt, Kilian Pohl)
  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. 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. 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. Diffusion QBall Framework Integration (Demian Wassermann, Rachid Deriche, Odyssée INRIA, CF Westin, LMI
  17. IGT Projects Discussion
  18. NA-MIC/Projects/Collaboration/Slicer3 Theme (Iowa Group)

Non-Medical Collaborations

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


  1. Please make sure that you are on the NA-MIC Project Week mailing list.
  2. May 08 and May 15 TCON DBPs ONLY at 3pm ET to discuss NA-MIC DBP Projects ONLY.
  3. May 22 TCON#1 at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
  4. 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.
  5. 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.
  6. 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.
  7. June 19 TCON#5 at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
  8. 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.
  9. 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)
  10. 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. Purang Abolmaesumi :: Queen's University
  2. Douglas Alan :: Harvard Medical School
  3. Mark Anderson :: Brigham and Women's Hospital
  4. Luca Antiga :: Mario Negri Institute
  5. Kevin Archie :: Washington University in St. Louis
  6. Neculai Archip :: Brigham and Women's Hospital
  7. Nicole Aucoin :: Brigham and Women's Hospital
  8. Viswanath Avasarala :: General Electric
  9. Stephen Aylward :: Kitware, Inc.
  10. Serdar K Balci :: Massachusetts Institute of Technology
  11. Sebastien Barre :: Kitware, Inc.
  12. Jamie Berger :: University of Western Australia
  13. Jack Blevins :: Acoustic Med
  14. Daniel Blezek :: Isomics, Inc.
  15. Luke Bloy :: University of Pennsylvania
  16. Jeremy Bockholt :: The MIND Institute
  17. Sylvain Bouix :: Brigham and Women's Hospital
  18. Nathan Burnette :: University of Iowa
  19. Carling Cheung :: University of Western Ontario
  20. Nikos Chrisochoides :: College of William and Mary
  21. Gary E. Christensen :: University of Iowa
  22. Chris Churas :: UCSD
  23. Csaba Csoma :: Johns Hopkins University
  24. Andriy Fedorov :: College of William and Mary
  25. Gabor Fichtinger :: Queen's University
  26. Nathan Fritze :: University of Iowa
  27. Yi Gao :: Georgia Institute of Technology
  28. Arnaud Gelas :: Harvard Medical School
  29. David Gobbi :: Queen's University
  30. Polina Golland :: Massachusetts Institute of Technology
  31. Randy Gollub :: Massachusetts General Hospital
  32. Casey Goodlett :: University of Utah
  33. Alexandre Gouaillard :: Harvard Medical School
  34. Jeffrey Grethe :: UCSD
  35. Keith Gunderson :: University of Iowa
  36. Nathan Hageman :: UCLA
  37. John Hale :: University of Tulsa
  38. Michael Halle :: Brigham and Women's Hospital
  39. Nobuhiko Hata :: Brigham and Women's Hospital
  40. Jeffrey Hawley :: University of Iowa
  41. Kathryn Hayes :: Brigham and Women's Hospital
  42. Toru Higaki :: Hiroshima
  43. Bill Hoffman :: Kitware, Inc.
  44. Scott Hoge :: Brigham and Women's Hospital
  45. Luis Ibanez :: Kitware, Inc.
  46. Marianna Jakab :: Brigham and Women's Hospital
  47. Yifeng Jiang :: Yale University
  48. Hans Johnson :: University of Iowa
  49. Grand Joldes :: University of Western Australia
  50. Julien Jomier :: Kitware, Inc.
  51. Tina Kapur :: Brigham and Women's Hospital
  52. Peter Kazanzides :: Johns Hopkins University
  53. Ron Kikinis :: Brigham and Women's Hospital
  54. Bryce Kim :: Massachusetts Institute of Technology
  55. Jacek Kukluk :: Brigham and Women's Hospital
  56. Yang Li :: University of Pennsylvania
  57. Curtis Lisle :: Isomics, Inc.
  58. Haying Liu :: Brigham and Women's Hospital
  59. Zhexing Liu :: University of North Carolina
  60. Vincent Magnotta :: University of Iowa
  61. Silas Mann :: Massachusetts General Hospital
  62. Daniel Marcus :: Washington University in St. Louis
  63. Sean Megason :: Harvard Medical School
  64. John Melonakos :: Georgia Institute of Technology
  65. Carlos Sánchez Mendoza :: Brigham and Women's Hospital
  66. Bjoern Menze :: Brigham and Women's Hospital
  67. Mikhail Milchenko :: Washington University in St. Louis
  68. James Miller :: General Electric
  69. Kishore Mosaliganti :: Ohio State University
  70. Timothy Olsen :: Washington University in St. Louis
  71. John Onofrey :: Yale University
  72. Danielle Pace :: University of Western Ontario
  73. Dirk Padfield :: General Electric
  74. Xenophon Papademetris :: Yale University
  75. Pratik Patel :: Brainlab
  76. Marta Peroni :: Massachusetts General Hospital
  77. Dana Peters :: Harvard Medical School
  78. Steve Pieper :: Isomics, Inc.
  79. Wendy Plesniak :: Brigham and Women's Hospital
  80. Kilian Pohl :: Brigham and Women's Hospital
  81. Cody Pollet :: University of Tulsa
  82. Clare Poynton :: Massachusetts Institute of Technology
  83. Marcel Prastawa :: University of Utah
  84. Sonia Pujol :: Brigham and Women's Hospital
  85. Zhen Qian :: Rutgers University
  86. Kate Raising :: University of Iowa
  87. Vidya Rajagopalan :: Virginia Tech
  88. Tauseef Rehman :: Georgia Institute of Technology
  89. Tammy Riklin Raviv :: Massachusetts Institute of Technology
  90. Marco Ruiz :: UCSD
  91. Dustin Scheinost :: Yale University
  92. Nikeisha Schimke :: University of Tulsa
  93. William Schroeder :: Kitware, Inc.
  94. Mark Scully :: The MIND Institute
  95. Gregory Sharp :: Massachusetts General Hospital
  96. Paul Song :: University of Iowa
  97. Priya Srinivasan :: Brigham and Women's Hospital
  98. Jason Taclas :: Harvard Medical School
  99. Florin Talos :: Brigham and Women's Hospital
  100. Ran Tao :: University of Utah
  101. Xiaodong Tao :: General Electric
  102. Junichi Tokuda :: Brigham and Women's Hospital
  103. Clement Vachet :: University of North Carolina
  104. Ragini Verma :: University of Pennsylvania
  105. Siddharth Vikal :: Queen's University
  106. Demian Wassermann :: Brigham and Women's Hospital
  107. Ying Wei :: University of Iowa
  108. Carl-Fredrik Westin :: Brigham and Women's Hospital
  109. Ross Whitaker :: University of Utah
  110. Adam Wittek :: University of Western Australia
  111. Alexander Yarmarkovich :: Isomics, Inc.
  112. Cheng Zhang :: University of Iowa
  113. Jinghao Zhou :: Rutgers University


  • 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