2008 Summer Project Week

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

Summary

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.

• 

  Welcome

• 

  Opening Session

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  Lively Discussions

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  Hard at Work

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  Breakout Session

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  Modern Architecture

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  IGT Breakout

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  Lunchtime

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  Say no more...

More pictures (taken by Jeffrey Hawley).

Introduction to NA-MIC Project Week

Please read an introduction about these events here.

Agenda

• Monday
  • noon-1pm lunch
  • 1pm: Welcome (Ron Kikinis)
  • 1:05-3:30pm Introduce Projects using templated wiki pages (all Project Leads) (Wiki Template)
  • 3:30-5:30pm Start project work
• Tuesday
  • 8:30am breakfast
  • 10-10:30am Slicer 3.2 Update (Jim Miller, Steve Pieper)
  • 11-12noon Performance tuning for Slicer 3.2 (Jackson Room 38-466) (Ron Kikinis)
  • noon lunch
  • 1pm: Cut over to a new version of the NA-MIC SVN.
  • 1:00-4:00pm: Project Week 2008 Special topic breakout: XNAT Database (Stata 32-D451) (Daniel Marcus)
  • 5:30pm adjourn for day
• Wednesday
  • 8:30am breakfast
  • 9:00-12pm Project Week 2008 Special topic breakout: ITK (Stata Kiva Conference Room) (Luis Ibanez)
  • noon lunch
  • 2:30-3:30pm: Project Week 2008 Special topic breakout: Non-rigid Registration (Stata Kiva Conference Room) (Stephen Aylward)
  • 4:00-5:30pm: Project Week 2008 Special topic breakout: CMake/CPack/CTest/CDash, KWWidgets (Stata Kiva Conference Room) (Julien Jomier, Sebastien Barre)
  • 5:30pm adjourn for day
• Thursday
  • 8:30am breakfast
  • noon lunch
  • 2:30-3:30pm Project Week 2008 Special topic breakout: GWE (Stata Kiva Conference Room) (Marco Ruiz)
  • 5:30pm adjourn for day
• Friday
  • 8:30am breakfast
  • 10am-noon: Project Progress using update Project Wiki pages
  • Misc:
    • Noon: Lunch boxes and adjourn by 1:30pm.
    • We need to empty room by 1:30. You are welcome to use wireless in Stata.
    • Please sign up for the Slicer developer mailing list.
    • Collaborator RFA has been renewed
    • Events:TutorialContestJan2009
    • Next Project Week in Utah, January 5-9, 2009)

Projects

DBP II

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)

Preparation

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

Logistics

• 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