2009 Summer Project Week

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• Dates: June 22-26, 2009
• Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.

Introduction to the FIRST JOINT PROJECT WEEK

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the NA-MIC Kit, algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of NA-MIC, NCIGT, NAC, Harvard Catalyst, and CIMIT. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available 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
  • 9:30-10am: NA-MIC Kit Overview (Jim Miller)
  • 10-10:30am Slicer 3.4 Update (Steve Pieper)
  • 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
  • 11am-12:00pm Breakout Session: 2009 Project Week Breakout Session: Slicer-Python (Demian W)
  • noon lunch
  • 2:30pm-5pm: Data Clinic (Ron Kikinis)
  • 5:30pm adjourn for day
• Wednesday
  • 8:30am breakfast
  • 9am-12pm Breakout Session: 2009 Project Week Breakout Session: ITK (Luis Ibanez)
  • noon lunch
  • 2:30pm: Breakout Session: 2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation (Alex G.)
  • 5:30pm adjourn for day
• Thursday
  • 8:30am breakfast
  • 9-11pm Tutorial Contest Presentations
  • noon lunch
  • 2:30pm: Breakout Session: 2009 Project Week Breakout Session: XNAT (Dan M.)
  • 5:30pm adjourn for day
• Friday
  • 8:30am breakfast
  • 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update Project Wiki pages
    • 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 developer mailing lists
    • Next Project Week in Utah, January 4-8, 2010

Projects

The list of projects for this week will go here.

Collaboration Projects

1. 2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images
2. 4D Imaging (Perfusion, Cardiac, etc.) (Junichi, Dan Blezek?, Steve, Alex G?)
3. Liver Ablation in Slicer (Haiying, Ziv)
4. SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
5. Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
6. Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
7. Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
8. Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
9. xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
10. Grid Wizard+xnat clinic (Clement Vachet)
11. ?Fluid Mechanincs Module (Nathan Hageman)
12. ?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
13. Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
14. Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
15. Skull Stripping (Xiaodong, Snehashis Roy)
16. FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)
17. Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
18. Automatic brain MRI processing pipeline (Marcel, Hans)
19. XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
20. Spherical Mesh Diffeomorphic Demons Registration (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
21. MRSI Module (Bjoern Menze, Jeff Yager, Vince Magnotta)
22. Measuring Alcohol Stress Interaction (Vidya Rajgopalan, Andrey Fedorov)

IGT Projects:

1. Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
2. port 4d gated ultrasound code to Slicer - (Danielle)
3. integration of stereo video into Slicer (Mehdi)
4. multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
5. neuroendoscope workflow presentation (sebastien barre)
6. breakout session on Dynamic Patient Models (James Balter)
7. 2d/3d Registration (and GPGPU acceleration) for Radiation Therapy (Sandy Wells, Jim Balter, and others)

NA-MIC Engineering Projects

1. DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
2. Using ITK in python (Steve, Demian, Jim)
3. Taking advantage of multicore machines & clusters with python (Julien)
4. VTK 3d Widgets in Slicer3 (Nicole, Karthik, Sebastien, Wendy)
5. Updates to Slicer3 Colors module (Nicole)
6. EM Segmenter (Sylvain Jaume, Nicolas Rannou)
7. Plug-in 3D Viewer based on XIP (Lining)
8. IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
9. Slicer3 Informatics Workflow Design & XNAT updates for Slicer (Wen, Steve, Dan M, Dan B)
10. BSpline Registration in Slicer3 (Samuel Gerber,Jim Miller, Ross Whitaker)
11. EPI Correction in Slicer3 (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
12. Fix bug 416 in registration (Andriy, Luis, Bill, Jim, Steve)
13. The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn)

Preparation

1. Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
2. Join the kickoff TCON on April 16, 3pm ET.
3. June 18 TCON at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
4. By 3pm ET on June 11, 2009: 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.
5. By 3pm on June 18, 2009: 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)
6. 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...
7. People doing Slicer related projects should come to project week with slicer built on your laptop.
   1. Projects to develop extension modules should work with the Slicer-3-4 branch (new code should not be checked into the branch).
   2. Projects to modify core behavior of slicer should be done on the trunk.

Attendee List

If you plan to attend, please add your name here.

1. Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
2. Ferenc Jolesz, BWH (NCIGT, NAC)
3. Clare Tempany, BWH (NCIGT)
4. Tina Kapur, BWH (NA-MIC, NCIGT)
5. Steve Pieper, Isomics Inc
6. Jim Miller, GE Research
7. Xiaodong Tao, GE Research
8. Bill Lorensen, EAB
9. Randy Gollub, MGH
10. Nicole Aucoin, BWH (NA-MIC)
11. Dan Marcus, WUSTL
12. Junichi Tokuda, BWH (NCIGT)
13. Alex Gouaillard, Harvard Systems Biology
14. Arnaud Gelas, Harvard Systems Biology
15. Kishore Mosanliganti, Harvard Systems Biology
16. Lydie Souhait, Harvard Systems Biology
17. Luis Ibanez, Kitware Inc
18. Vincent Magnotta, UIowa
19. Hans Johnson, UIowa
20. Xenios Papademetris, Yale
21. Gregory S. Fischer, WPI (Mon, Tue, Wed)
22. Daniel Blezek, Mayo (Tue-Fri)
23. Danielle Pace, Robarts Research Institute / UWO
24. Clement Vachet, UNC-Chapel Hill
25. Dave Welch, UIowa
26. Demian Wassermann, Odyssée lab, INRIA, France
27. Manasi Ramachandran, UIowa
28. Greg Sharp, MGH
29. Rui Li, MGH
30. Mehdi Esteghamatian, Robarts Research Institute / UWO
31. Misha Milchenko, WUSTL
32. Kevin Archie, WUSTL
33. Tim Olsen, WUSTL
34. Wendy Plesniak BWH (NAC)
35. Haiying Liu BWH (NCIGT)
36. Curtis Lisle, KnowledgeVis / Isomics
37. Diego Cantor, Robarts Research Institute / UWO
38. Daniel Haehn, BWH
39. Nicolas Rannou, BWH
40. Sylvain Jaume, MIT
41. Alex Yarmarkovich, Isomics
42. Marco Ruiz, UCSD
43. Andriy Fedorov, BWH (NA-MIC)
44. Harish Doddi, Stanford University
45. Saikat Pal, Stanford University
46. Scott Hoge, BWH (NCIGT)
47. Vandana Mohan, Georgia Tech
48. Ivan Kolosev, Georgia Tech
49. Behnood Gholami, Georgia Tech
50. James Balter, U Michigan
51. Dan McShan, U Michigan
52. Zhou Shen, U Michigan
53. Maria Francesca Spadea, Italy
54. Lining Yang, Siemens Corporate Research
55. Beatriz Paniagua, UNC-Chapel Hill
56. Bennett Landman, Johns Hopkins University
57. Snehashis Roy, Johns Hopkins University
58. Marta Peroni, Politecnico di Milano
59. Sebastien Barre, Kitware, Inc.
60. Samuel Gerber, SCI University of Utah
61. Ran Tao, SCI University of Utah
62. Marcel Prastawa, SCI University of Utah
63. Katie Hayes, BWH (NA-MIC)
64. Sonia Pujol, BWH (NA-MIC)
65. Andras Lasso, Queen's University
66. Yong Gao, MGH
67. Minjeong Kim, UNC-Chapel Hill
68. Guorong Wu, UNC-Chapel Hill
69. Jeffrey Yager, UIowa
70. Yanling Liu, SAIC/NCI-Frederick
71. Ziv Yaniv, Georgetown
72. Bjoern Menze, MIT
73. Vidya Rajagopalan, Virginia Tech
74. Sandy Wells, BWH (NAC, NCIGT)
75. Lilla Zollei, MGH (NAC)
76. Lauren O'Donnell, BWH
77. Florin Talos, BWH (NAC)
78. Nobuhiko Hata, BWH (NCIGT)
79. Alark Joshi, Yale
80. Yogesh Rathi, BWH
81. Jimi Malcolm, BWH
82. Dustin Scheinost, Yale
83. Dominique Belhachemi, Yale
84. Sam Song, JHU
85. Nathan Cho, JHU
86. Julien de Siebenthal, BWH
87. Peter Savadjiev, BWH
88. Carl-Fredrik Westin, BWH
89. John Melonakos, AccelerEyes (Wed & Thu morning)
90. Yi Gao, Georgia Tech

Logistics

• Dates: June 22-26, 2009
• 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 12th, 2009. 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 this is your first event and you are attending for only one day, the registration fee is waived. Please let us know, so that we can cover the costs with one of our grants.
• Registration Method Add your name to the Attendee List section of this page
• Hotel: We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). 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.
• 2009 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