2013 Summer Project Week

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Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.


Agenda

Time Monday, June 17 Tuesday, June 18 Wednesday, June 19 Thursday, June 20 Friday, June 21
Project Presentations NA-MIC Update Day IGT and RT Day Reporting Day
8:30am Breakfast Breakfast Breakfast Breakfast
9am-12pm 10-11am Slicer4 Python Modules, Testing, Q&A (Steve Pieper)

Grier Room (Left)

9:30-11pm: Breakout Session:
Slicer and SimpleITK (Hans Johnson, Brad Lowekamp)

32-D507

10am-12pm: Breakout Session:
Image-Guided Therapy (Tina Kapur)

32-D407

10am-12pm: Project Progress Updates

Grier Rooms

12pm-1pm Lunch Lunch Lunch Lunch Lunch boxes; Adjourn by 1:30pm
1pm-5:30pm 1-1:05pm: Ron Kikinis: Welcome

Grier Rooms
----------------------------------------
1:05-3:30pm: Project Introductions (all Project Leads) Grier Rooms
----------------------------------------
3:30-4:30pm Slicer4 Extensions (Jean-Christophe Fillion-Robin)
Grier Room (Left)

1-3pm: NA-MIC Renewal
PIs
Closed Door Session with Ron

32-262
----------------------------------------
3-4pm: Tutorial Contest Presentations
Grier Rooms

12:45-1pm: Tutorial Contest Winner Announcement

Grier Rooms


----------------------------------------
3-5:30pm: Breakout Session:
Radiation Therapy (Greg, Csaba)

32-D407

5:30pm Adjourn for the day Adjourn for the day Adjourn for the day Adjourn for the day

Projects

Please use this template to create wiki pages for your project. Then link the page here with a list of key personnel.


Some Stats

71 Projects, 97 Attendees. First time attendees 25.

Huntington's Disease

7 projects

Traumatic Brain Injury

5 projects

Atrial Fibrillation and Cardiac Image Analysis

7 projects

Radiation Therapy

8 projects

IGT and Device Integration with Slicer

12 projects

Chronic Obstructive Pulmonary Disease

3 projects

Additional Collaborations


16 projects

Infrastructure

13 projects

Background

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. 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. If you would like to learn more about this event, please click here to join our mailing list.


Active preparation begins on Thursday, April 25th 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 40-50 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, CIMIT, and OCAIRO. 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 is available here.


Logistics

  • Dates: June 17-21, 2013.
  • Location: Stata Center / RLE MIT.
  • REGISTRATION: http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
  • Registration Fee: $300.
  • Hotel: Similar to previous years, no rooms have been blocked in a particular hotel.
  • Room sharing: If interested, add your name to the list before May 27th. See here

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. The NA-MIC engineering team will be discussing projects in a their weekly teleconferences. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
  3. By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
  4. By 3pm ET on Thursday June 6, all project leads to complete 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 13: Create a directory for each project on the NAMIC Sandbox (Matt)
    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. XNAT/MIDAS). 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. Where possible, 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. (Matt)
  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. See the Developer Section of slicer.org for information.
    2. Projects to develop extension modules should be built against the latest Slicer4 trunk.

Registrants

Do not add your name to this list - it is maintained by the organizers based on your paid registration. (Please click here to register.)

  1. Parth Amin, WIT, aminp@wit.edu
  2. Charles Anderson, BWH, canderson26@partners.org
  3. Peter Anderson, retired, traneus@verizon.net
  4. Nicole Aucoin, BWH, nicole@bwh.harvard.edu
  5. Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
  6. Kayhan Batmanghelich, MIT, kayhan@csail.mit.edu
  7. Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
  8. Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
  9. Vinicius Boen, Univ Michigan, vboen@umich.edu
  10. Matthew Brennan, MIT, brennanm@mit.edu
  11. Francois Budin, NIRAL-UNC, fbudin@unc.edu
  12. Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
  13. Josh Cates, Univ UT, cates@sci.utah.edu
  14. Micah Chambers, UCLA, micahcc@ucla.edu
  15. Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
  16. Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
  17. Adrian Dalca, MIT, adalca@MIT.EDU
  18. Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
  19. Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
  20. Sneha Durgapal, BWH, durgapalsneha@gmail.com
  21. Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
  22. Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
  23. Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
  24. Gregory Fischer, WPI, gfischer@wpi.edu
  25. Barton Fiske, zSpace Inc, bfiske@zspace.com
  26. Matthew Flynn, WIT, flynnm3@wit.edu
  27. Karl Fritscher, MGH, kfritscher@gmail.com
  28. Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
  29. Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
  30. Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
  31. Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
  32. Rola Harmouche, BWH, rharmo@bwh.harvard.edu
  33. Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
  34. Nobuhiko Hata, BWH, hata@bwh.harvard.edu
  35. Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
  36. Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
  37. Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
  38. Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
  39. Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
  40. Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
  41. Alex Kikinis, BWH, alexkikinis@gmail.com
  42. Ron Kikinis, HMS, kikinis@bwh.harvard.edu
  43. Nils Klarlund, IEEE, klarlund@ieee.org
  44. Daniel Kostro, BWH, dkostro@bwh.harvard.edu
  45. Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
  46. Rui Li, GE Global Research, li.rui@ge.com
  47. Xu Li, BWH, lixu0103@gmail.com
  48. Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
  49. Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
  50. William Lorensen, Bill's Basement, bill.lorensen@gmail.com
  51. Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
  52. Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
  53. Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
  54. Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
  55. Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
  56. Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
  57. Jim Miller, GE Global Research, millerjv@ge.com
  58. Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
  59. Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
  60. Isaiah Norton, BWH, inorton@bwh.harvard.edu
  61. Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
  62. Dirk Padfield, GE Global Research, padfield@research.ge.com
  63. Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
  64. George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
  65. Nirav Patel, WPI, napatel@wpi.edu
  66. Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
  67. Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
  68. Steve Pieper, Isomics Inc, pieper@isomics.com
  69. Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
  70. Sonia Pujol, HMS, spujol@bwh.harvard.edu
  71. Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
  72. Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
  73. Raul San Jose, BWH, rjosest@bwh.harvard.edu
  74. Peter Savadjiev, BWH, petersv@bwh.harvard.edu
  75. Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
  76. Greg Sharp, MGH, gcsharp@partners.org
  77. Nadya Shusharina, MGH, nshusharina@partners.org
  78. Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
  79. Clare Tempany, BWH, ctempanyafdhal@partners.org
  80. Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
  81. Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
  82. Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
  83. Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
  84. Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
  85. Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
  86. Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
  87. Christian Wachinger, MIT, wachinge@mit.edu
  88. Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
  89. Demian Wassermann, BWH, demian@bwh.harvard.edu
  90. David Welch, Univ Iowa, david-welch@uiowa.edu
  91. William Wells, BWH/HMS, sw@bwh.harvard.edu
  92. Phillip White, BWH/HMS, white@bwh.harvard.edu
  93. Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
  94. Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
  95. Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
  96. Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
  97. Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu
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