2013 Summer Project Week

From NAMIC Wiki
Jump to: navigation, search
Home < 2013 Summer Project Week

Back to Events


Welcome to the web page for the 17th Project Week!


The 17th PROJECT EVENT was held on June 17-21, 2013 at MIT. It recorded 104 registered attendees, who worked on 75 projects. These attendees represented 22 academic sites (Brigham and Women’s Hospital, Massachusetts General Hospital, Boston Children’s Hospital, MIT, WPI, WIT, University of Alabama, Rochester Institute of Technology, University of Utah, University of Iowa, University of Michigan, UCLA, Rutgers University, University del Estado de Mexico, Ecole Polytechnique Federale de Lausanne, Zhejiang University of Technology, Queen’s University, University of Sydney, University of Western Australia, University Sao Paulo, Leibniz University, Hannover, University Magna Graecia of Catanzaro) and 13 companies (NIRAL-UNC, Radnostics, GE Healthcare, GE Global Research, Kitware, zSpace, AZE Technology Inc, IEEE, Medical Science & Computing Inc, Fraunhofer MEVIS, Isomics Inc, IGI Technologies, KUKA Laboratories). The agenda and projects are detailed below.

A summary of all past Project Events.


  • Dates: June 17-21, 2013.
  • Location: MIT, Cambridge, MA.


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)


9:30-10:30am Tutorial Contest Presentations
Grier Rooms
10am-12pm: Breakout Session:
Image-Guided Therapy (Tina Kapur) 32-D407

10am-12pm: Project Progress Updates

12pm Tutorial Contest Winner Announcement Grier Rooms

12pm-1pm Lunch Lunch Lunch Lunch in Outdoor Amphitheather! 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
Closed Door Session with Ron


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


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


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

Some Stats

75 Projects, 104 Attendees. First time attendees 25.

Huntington's Disease

7 projects

Traumatic Brain Injury

5 projects

Atrial Fibrillation and Cardiac Image Analysis

8 projects

Radiation Therapy

10 projects

IGT and Device Integration with Slicer

11 projects

Chronic Obstructive Pulmonary Disease

3 projects

Additional Collaborations

20 projects


12 projects


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 Women's 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.

Please make sure that you are on the NA-MIC Project Week mailing list.


  • 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


  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.


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