2008 Summer Project Week

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Summer 2008


Dates: June 23-27, 2008

Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.

Registration Fee: $260 (this will cover 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

Registration Method Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

If you are attending for one day only, the registration fee is not required.

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.

(This is a checklist for the onsite planning items)

Introduction to NA-MIC Project Week

NA-MIC Project Week is a hands on activity -- programming using the NA-MIC Kit, algorithm design, and clinical application -- that has become one of the major events in the NA-MIC Kit calendar. This event is the seventh of the series. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

  • NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
  • Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
  • This is not an introduction to the components of the NA-MIC Kit.
  • NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
  • NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the NA-MIC Kit capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
  • NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
  • External Collaborators - if you are working on a project that uses the NA-MIC kit, and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
  • Everyone should bring a laptop. We will have four projectors.
  • About half the time will be spent working on projects and the other half in project related discussions.
  • You do need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.



  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...

A History in Wiki Links

A history of all the programming/project events in NA-MIC is available by following this link.



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. EPI-DWI Distortion correction (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. Finsler method (John Melonakos GATech, Marek Kubicki BWH)
    5. Group Analysis on 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. DTI tools for a) DWI preparation and b) DTI atlas building (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. Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)

Structural Analysis

Diffusion Image Analysis

  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)


NA-MIC Kit - Slicer 3

  1. CVS / SVN auto synchronization
  2. 3D Widgets in Slicer
    1. Issues with existing widgets
    2. Design of new widgets
  3. Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
  4. Module Chaining (Marco, Jim, Steve, Dan B., Luca)
  5. Nonlinear transforms (Jim, Steve, Luis)
    1. TransformToWorld/TransformFromWorld, integration with slice viewing
  6. Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien)
    1. Review and enrich use cases

External Collaborations

  1. NA-MIC/Projects/Collaboration/UWA-Perth (Adam Wittek)
  2. NA-MIC/Projects/Collaboration/MRSI Module for Slicer (Bjoern Menze)
  3. NIREP: Non-rigid Image Registration Evaluation (Gary Christensen Group)
  4. Lung Atlas (Gary Christensen Group)
  5. 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)

Non-Medical Collaborations

Attendee List

  1. Ron Kikinis, BWH
  2. Carl-Fredrik Westin, BWH
  3. Gary Christensen, The University of Iowa
  4. Jeffrey Hawley, Gary Christensen's student
  5. Kate Raising, Gary Christensen's student
  6. Nathan Fritze, Gary Christensen's student
  7. Paul Song, Gary Christensen's student
  8. Cheng Zhang, Gary Christensen's student
  9. Ying Wei, Gary Christensen's student
  10. Nathan Burnette, The University of Iowa
  11. Hans Johnson, The University of Iowa
  12. Vincent Magnotta, The University of Iowa
  13. Keith Gunderson, The University of Iowa
  14. Steve Pieper, Isomics, Core 2/6
  15. Dana C. Peters, BIDMC Harvard Medical
  16. Jason Taclas, BIDMC Harvard Medical
  17. Nicole Aucoin, BWH, Core 2
  18. Will Schroeder, Kitware, Cores 2/4
  19. Sebastien Barre, Kitware, Core 2
  20. Julien Jomier, Kitware, Core 2
  21. Luis Ibanez, Kitware, Core 2
  22. Curtis Lisle, KnowledgeVis, Core 2
  23. Katie Hayes, BWH, Core 2
  24. Randy Gollub, MGH, Core 5
  25. Clement Vachet, UNC, Core 3
  26. Zhexing Liu, UNC, Core 1/3
  27. Casey Goodlett, Utah, Core 1
  28. Marcel Prastawa, Utah, Core 1
  29. Jeffrey Grethe, UCSD, Core 2
  30. Marco Ruiz, UCSD, Core 2
  31. Zhen Qian, Rutgers University
  32. Jinghao Zhou, Rutgers University
  33. Luca Antiga, Mario Negri Institute
  34. Adam Wittek, The University of Western Australia
  35. Grand Joldes, The University of Western Australia
  36. Jamie Berger, The University of Western Australia
  37. Serdar Balci, MIT, Core 1
  38. Bryce Kim, MIT, Core1
  39. Tina Kapur, BWH, Core 6
  40. Carling Cheung, Robarts Research Institute / The University of Western Ontario
  41. Danielle Pace, Robarts Research Institute / The University of Western Ontario
  42. Sean Megason, Dept of Systems Biology, Harvard Medical School
  43. Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
  44. Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
  45. Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
  46. Sonia Pujol, Surgical Planning Laboratory, BWH
  47. Bjoern Menze, (then) Surgical Planning Laboratory, BWH
  48. Alex Yarmarkovich, Isomics, Core 2
  49. Sylvain Bouix, BWH, Core 3
  50. Priya Srinivasan, BWH, Core 3
  51. Chris Churas, UCSD, Core 2
  52. John Melonakos, Georgia Tech, Core 1
  53. Yi Gao, Georgia Tech, Core 1
  54. Tauseef Rehman, Georgia Tech, Core 1
  55. Clare Poynton, MIT, Core 1
  56. H. Jeremy Bockholt, MRN Lupus DBP Core 3
  57. Mark Scully, MRN Lupus DBP Core 3
  58. Gabor Fichtinger, Queen's, Core 2
  59. David Gobbi, Queen's, Core 2
  60. Purang Abolmaesumi, Queen's, Core 2
  61. Siddharth Vikal, Queen's, Core 2
  62. Daniel Blezek, Mayo
  63. Csaba Csoma, JHU, Core 2
  64. Ran Tao, University of Utah, Core 1
  65. Jim Miller, GE Research, Core 2
  66. Xiaodong Tao, GE Research, Core 2
  67. Dirk Padfield, GE Research, Core 2
  68. Viswanath Avasarala, GE Research, NAC
  69. Dan Marcus, Washington University
  70. Tim Olsen, Washington University
  71. Kevin Archie, Washington University
  72. Misha Milchenko, Washington University
  73. Wendy Plesniak, BWH, Core 2
  74. Demian Wasserman, INRIA, LMI-collaborator
  75. Xenophon Papademetris, Yale, Collaborator
  76. Xenophon P's postdoc, Yale, Collaborator
  77. Xenophon P's student, Yale, Collaborator
  78. Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
  79. Greg Sharp, MGH, External Collaborator
  80. Marta Peroni, MGH, External Collaborator
  81. Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
  82. Jacek Kukluk, BWH,
  83. Nobuhiko Hata, BWH
  84. Junichi Tokuda, BWH
  85. Haying Liu, BWH
  86. Ragini Verma, UPenn (June 24)
  87. Luke Bloy, UPenn (Ragini Verma's student) (June 24)
  88. Yang Li, UPenn (Ragini's postdoc) (June 24)
  89. Jack Blevins, Acoustic Med, Collaborator