2008 Summer Project Week

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Summer 2008

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
• Next Project Week in Utah -- January 5-9, 2009

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)
  • 5:30pm adjourn for day
• Thursday
  • 8:30am breakfast
  • noon lunch
  • 2:30-3:30pm Project Week 2008 Special topic breakout: GWE (Stata 32 D-451) (Marco Ruiz)
  • 5:30pm adjourn for day
• Friday
  • 8:30am breakfast
  • 10am-noon: Project Progress using update Project Wiki pages
  • Noon: Lunch boxes and adjourn. (Next one in Utah the week of Jan 5, 2009)

Projects

DBP II

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
17. IGT_Projects_Discussion

Non-Medical Collaborations

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

Preparation

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
112. Nicu Archip BWH
113. Florin Talos BWH
114. Stephen Aylward Kitware

Pictures

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  Lunch

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  Day 1

PICTURES! taken by Jeffrey Hawley