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 Updates
    • 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, Noby)
4. SLicer3, BioImage Suite 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. Fluid mechanics tractography and visualization (Nathan Hageman UCLA)
11. DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman UCLA)
12. Cortical Thickness Pipeline (Clement Vachet)
13. Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)
14. Skull Stripping (Xiaodong, Snehashis Roy, Nicole Aucoin)
15. HAMMER Registration (Guorong Wu, Xiaodong Tao, Jim Miller)
16. White Matter Lesion segmentation (Minjeong Kim, Xiaodong Tao, Jim Miller)
17. FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)
18. Meningioma growth simulation (Fedorov, Marcel, Ron)
19. Automatic brain MRI processing pipeline (Marcel, Hans)
20. XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
21. Spherical Mesh Diffeomorphic Demons Registration (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
22. MRSI Module (Bjoern Menze, Jeff Yager, Vince Magnotta)
23. Measuring Alcohol Stress Interaction (Vidya Rajgopalan, Andrey Fedorov)
24. DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)

IGT Projects:

1. Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
2. Gated 4D ultrasound reconstruction for Slicer3 (Danielle Pace)
3. integration of stereo video into Slicer (Mehdi)
4. multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego Cantor, 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 de Siebenthal, Sylvain Bouix)
4. Deferring heavy computational tasks with python (Julien de Siebenthal, Sylvain Bouix)
5. Developing realtime feedback using CUDA (Julien de Siebenthal, Sylvain Bouix)
6. VTK 3d Widgets in Slicer3 (Nicole, Karthik, Sebastien, Wendy)
7. Updates to Slicer3 Colors module (Nicole)
8. EM Segmenter (Sylvain Jaume, Nicolas Rannou)
9. Plug-in 3D Viewer based on XIP (Lining)
10. IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
11. Slicer3 Informatics Workflow Design & XNAT updates for Slicer (Wen, Steve, Dan M, Dan B)
12. BSpline Registration in Slicer3 (Samuel Gerber,Jim Miller, Ross Whitaker)
13. EPI Correction in Slicer3 (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
14. Registration reproducibility in Slicer3 (Andriy, Luis, Bill, Jim, Steve)
15. 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. Randy Gollub, MGH
9. Nicole Aucoin, BWH (NA-MIC)
10. Dan Marcus, WUSTL
11. Junichi Tokuda, BWH (NCIGT)
12. Alex Gouaillard, Harvard Systems Biology
13. Arnaud Gelas, Harvard Systems Biology
14. Kishore Mosanliganti, Harvard Systems Biology
15. Lydie Souhait, Harvard Systems Biology
16. Luis Ibanez, Kitware Inc
17. Vincent Magnotta, UIowa
18. Hans Johnson, UIowa
19. Xenios Papademetris, Yale
20. Gregory S. Fischer, WPI (Mon, Tue, Wed)
21. Daniel Blezek, Mayo (Tue-Fri)
22. Danielle Pace, Robarts Research Institute / UWO
23. Clement Vachet, UNC-Chapel Hill
24. Dave Welch, UIowa
25. Demian Wassermann, Odyssée lab, INRIA, France
26. Manasi Ramachandran, UIowa
27. Greg Sharp, MGH
28. Rui Li, MGH
29. Mehdi Esteghamatian, Robarts Research Institute / UWO
30. Misha Milchenko, WUSTL
31. Kevin Archie, WUSTL
32. Tim Olsen, WUSTL
33. Wendy Plesniak BWH (NAC)
34. Haiying Liu BWH (NCIGT)
35. Curtis Lisle, KnowledgeVis / Isomics
36. Diego Cantor, Robarts Research Institute / UWO
37. Daniel Haehn, BWH
38. Nicolas Rannou, BWH
39. Sylvain Jaume, MIT
40. Alex Yarmarkovich, Isomics
41. Marco Ruiz, UCSD
42. Andriy Fedorov, BWH (NA-MIC)
43. Harish Doddi, Stanford University
44. Saikat Pal, Stanford University
45. Scott Hoge, BWH (NCIGT)
46. Vandana Mohan, Georgia Tech
47. Ivan Kolosev, Georgia Tech
48. Behnood Gholami, Georgia Tech
49. James Balter, U Michigan
50. Dan McShan, U Michigan
51. Zhou Shen, U Michigan
52. Maria Francesca Spadea, Italy
53. Lining Yang, Siemens Corporate Research
54. Beatriz Paniagua, UNC-Chapel Hill
55. Bennett Landman, Johns Hopkins University
56. Snehashis Roy, Johns Hopkins University
57. Marta Peroni, Politecnico di Milano
58. Sebastien Barre, Kitware, Inc.
59. Samuel Gerber, SCI University of Utah
60. Ran Tao, SCI University of Utah
61. Marcel Prastawa, SCI University of Utah
62. Katie Hayes, BWH (NA-MIC)
63. Sonia Pujol, BWH (NA-MIC)
64. Andras Lasso, Queen's University
65. Yong Gao, MGH
66. Minjeong Kim, UNC-Chapel Hill
67. Guorong Wu, UNC-Chapel Hill
68. Jeffrey Yager, UIowa
69. Yanling Liu, SAIC/NCI-Frederick
70. Ziv Yaniv, Georgetown
71. Bjoern Menze, MIT
72. Vidya Rajagopalan, Virginia Tech
73. Sandy Wells, BWH (NAC, NCIGT)
74. Lilla Zollei, MGH (NAC)
75. Lauren O'Donnell, BWH
76. Florin Talos, BWH (NAC)
77. Nobuhiko Hata, BWH (NCIGT)
78. Alark Joshi, Yale
79. Yogesh Rathi, BWH
80. Jimi Malcolm, BWH
81. Dustin Scheinost, Yale
82. Dominique Belhachemi, Yale
83. Sam Song, JHU
84. Nathan Cho, JHU
85. Julien de Siebenthal, BWH
86. Peter Savadjiev, BWH
87. Carl-Fredrik Westin, BWH
88. John Melonakos, AccelerEyes (Wed & Thu morning)
89. Yi Gao, Georgia Tech
90. Sylvain Bouix, BWH
91. Zhexing Liu, UNC-CH
92. Eric Melonakos, BWH
93. Lei Qin, BWH
94. Giovanna Danagoulian, BWH
95. Andrew Rausch, BWH (1st day only)
96. Haytham Elhawary, BWH
97. Jayender Jagadeesan, BWH
98. Marek Kubicki, BWH
99. Doug Terry, BWH
100. Nathan Hageman, LONI (UCLA)

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