2011 Summer Project Week

From NAMIC Wiki
Jump to: navigation, search
Home < 2011 Summer Project Week

Back to Events


Welcome to the web page for the 13th Project Week!


The 13th Project Week was held on June 20-24, 2011 at MIT. It recorded 104 registered attendees, who worked on 61 projects. These attendees represented 17 academic sites and 8 companies. The projects, agenda, and affiliations of attendees are detailed below.

A summary of all past Project Events.


  • Dates: June 20-24, 2011
  • Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.
  • REGISTRATION: Please register here. Payment must be made by credit card.
  • Registration Fee: $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
  • Hotel: Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book here or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. All reservations must be made by May 29, 2011 to receive the discounted rate.


Neurosurgery, Brain and Spine, Traumatic Brain Injury

  1. Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Micah Chambers, Marcel Prastawa, Guido Gerig)
  2. Multimodality Image Registration for TBI (Yifei Lou, Danielle Pace, Jack Van Horn, Micah Chambers)
  3. White Matter Laterality in Python/Slicer4 (Lauren O'Donnell)
  4. Intraoperative Brain Shift Monitor (Jason White, Alex Golby, Steve Pieper, Junichi Tokuda)
  5. Obtaining and Evaluation of Glioblastoma Multiforme (GBM) Segmentation Masks (Jan Egger,Tina Kapur, Andriy Fedorov, Rivka Colen, Ron Kikinis, Alex Golby, Christopher Nimsky)
  6. Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
  7. Spine Segmentation & Osteoporosis Screening In CT Imaging Studies (Anthony Blumfield)
  8. Quantitative Magnetic Susceptibility Mapping (Clare Poynton)

Radiation Therapy

  1. Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, Xiaodong Tao, Nadya Shusharina, Allen Tannenbaum)
  2. Contouring of Anatomy Structures Like Tumor, Bladder, Rectum and Sigmoid for Gynecological Brachytherapy (Tina Kapur, Akila Viswanathan, Jan Egger)
  3. Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer (Firdaus Janoos, Jan Egger, Greg Sharp, Andriy Fedorov, Tina Kapur)
  4. Dose Volume Histograms in Slicer (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
  5. Synthetic Images, Vector Fields, RT Structures and RT Doses in Slicer and ITK. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)

Huntington's Disease

  1. Iowa Huntington's Disease Data Sharing (Hans Johnson, Mark Scully)
  2. Normal Consistency in Particle Correspondence Computation using Great Circles inPrincipal Spheres - Huntington's Disease, (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
  3. SPHARM & Particles Shape Analysis - Huntington's Disease (Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
  4. Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Marcel Prastawa, Guido Gerig, Hans Johnson)
  5. DTIPrep - "Study-specific Protocol" Based Automatic DWI/DTI Quality Control and Preparation - Huntington's Disease (Mahshid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
  6. DTI Pair-wise Registration Module - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)
  7. DTI Analysis for Huntington's Disease (Gopal Veni, Ross Whitaker)

Atrial Fibrillation

  1. Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy (Yi Gao, Kedar Patwardhan, Steve Pieper, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
  2. Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)

Device Integration with Slicer and General Image Guided Therapy

  1. Wireless Joystick Controlling Medical Devices and Software (e.g. Slicer4) in the Operating Room (Szymon Kostrzewski)
  2. Live Tracked Ultrasound with Slicer4 (Tamas Heffter)
  3. Surveying Research Teams Interested in Open IGT Link Support of Stealth Station (Nobuhiko Hata, Ron Kikinis)
  4. Needle Detection to Control Scanner for Prostate Biopsy (Atsushi Yamada, Loïc Cadour, Junichi Tokuda and Nobuhiko Hata)
  5. Segementation and Reconstruction of the Pericardial Sac (Mohsen Mahvash, Noby Hata, Ron Kikinis)
  6. 4D Ultrasound / Hybrid Probe / OsteoPlan (Laurent Chauvin, Noby Hata)
  7. AMIGO (Mallika Winsor, Vivian He, Dan Kacher, Tina Kapur)
  8. Patient-mounted Robot Control using OpenIGTLink (Conor James Walsh, Maryam Shokri, Faye Wu)
  9. Open-source Electromagnetic Trackers using OpenIGTLink (Peter Traneus Anderson)
  10. Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer (Petter Risholm, Jim Miller, Sandy Wells)
  11. Tractography Bundle/Cluster Interaction and Display in Slicer4 (Isaiah Norton, Lauren O'Donnell, Demian Wasserman)
  12. Integration of LANDWARP into Interactive Registration Module (Andrey Fedorov, Greg Sharp, Nadya Shusharina)

General Segmentation

  1. 2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3(Regina Kim, ... )
  2. EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
  3. Customizing EMSegmenter Pipelines for Brain Lesions (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
  4. Integrating Plastimatch into the EMSegmenter (Dominique Belhachemi, Kilian Pohl, Greg Sharp, Daniel Haehn)
  5. Slicer Extension for GLioma Image SegmenTation and Registration (GLISTR) (Andreas Schuh, Daniel Haehn, Kilian Pohl)

General Registration

  1. Integrate New Features into BRAINSFit (Andrey Fedorov, Hans Johnson, Mark Scully)
  2. Registration of Mouse Brains (Francois Budin, Ipek Oguz, Martin Styner, Dominik Meier)
  3. Integrate Fast Explicit Diffusion into Sliding Organ Registration Module (Danielle Pace)
  4. Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)

General Diffusion Tractography

  1. Re-parametrize Fiber Tracts for Fiber Statistics Analysis (Yundi Shi, Clement Vachet, Benjamin Yvernault, Anuja Sharma, Martin Styner)
  2. ODF Computation Through Fiber Counting (Yinpeng Li, Ipek Oguz, Martin Styner)
  3. Nifti Support for Diffusion Tensor Images (Demian)
  4. Finishing Details on the Workflows: DICOM to Full Brain Tractography / peritumoral (Demian)
  5. Adding Streamlined Tractography to the Finsler Front Propagation Tractography Toolkit (Antonio Tristán-Vega)
  6. DTI Volumetric Tractography (Steve Callahan, Mark Scully, Jim Miller)
  7. Slicer Module for Building an Average Population DWI Atlas (Ryan Eckbo, Sylvain Bouix)
  8. DTI Volumetric Segmentation for Group Studies (Gopal Veni, Ross Whitaker)


  1. The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper, Kilian Pohl, Ron Kikinis)
  2. Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)


  1. Annotation Module in Slicer4 (Nicole Aucoin, Daniel Haehn)
  2. RECIST Slicer4 module (Nicole Aucoin)
  3. DicomToNrrdConverter Refactoring ( Xiaodong Tao, Mark Scully)
  4. Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)
  5. DICOM Networking Interface for Slicer4 (Steve Pieper, Nicole Aucoin, Noby Hata)
  6. Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)
  7. FetchMI: Slicer Integration with XNAT 1.5 (Misha Milchenko, Wendy Plesniak)
  8. Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)


We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, 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 28th 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, 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 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.


  1. Please make sure that you are on the NA-MIC Project Week mailing list.
  2. The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old 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 12, all participants to add a one line title of their project to #Projects
  4. By 3pm ET on Thursday June 9, 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 16: 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. 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. 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-3-6 branch (new code should not be checked into the branch).
    2. Projects to modify core behavior of slicer should be done on the trunk.


Time Monday, June 20 Tuesday, June 21 Wednesday, June 22 Thursday, June 23 Friday, June 24
Project Presentations NA-MIC Update Day IGT Day Reporting Day
8:30am Breakfast Breakfast Breakfast Breakfast
9am-12pm 9am-10am: Slicer4 Extension (Writing Tutorial) (pdf, ppt) (Jean-Christophe Fillion-Robin)

10-11am Slicer 4 Core Modules Usability Review (Continued)
Grier Room (Left)
11-12pm: Breakout Session: Slicer4 Annotations (Nicole Aucoin)
Star Room

9am-12pm: Breakout Session:
ITK (Luis Ibanez)

Kiva Room

9am-4pm: Breakout Session:

Kiva Room
10:30am-12pm: Breakout Session:

Star Room

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
3:30-4:15pm Slicer4 Developers Guided Tour (Pieper) (Slides).
Grier Room (Left)
4:15-5:00pm Slicer 4 Core Modules Usability Review
Grier Room (Left)
4:15-5:00pm How to get DBP Data
Grier Room (Right)

1-3pm: Breakout Session:
Slicer4 MultiVolume Containers (Nicole Aucoin)

Star Room
3-4pm: Tutorial Contest Presentations
Grier Rooms
4-5pm: VTK Charts (Marcus Hanwell) (Slides)
Star Room

12:45-1pm: Tutorial Contest Winner Announcement

Grier Rooms
3-4pm: Breakout Session:
Inter-subject Registration for EM segmenter
Kiva Room

1-4pm: Breakout Session:

Kiva Room

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


Do not add your name to this list- it is maintained by the organizers based on your paid registration (see Logistics for link)

  1. Peter Anderson :: Retired
  2. Nicole Aucoin :: Brigham and Women's Hospital
  3. Dominique Belhachemi :: University of Pennsylvania
  4. Anthony Blumfiled :: Radnostics
  5. Lucile Bompard :: University of North Carolina
  6. Sylvain Bouix :: Brigham and Women's Hospital
  7. Francois Budin :: University of North Carolina
  8. Steve Callahan :: University of Utah
  9. Joshua Cates :: University of Utah
  10. Micah Chambers :: UCLA
  11. Laurent Chauvin :: Brigham and Women's Hospital
  12. Nikos Chrisochoides :: Old Dominion University
  13. Rivka Colen :: Brigham and Women's Hospital
  14. Adrian Dalca :: Massachusetts Institute of Technology
  15. Manasi Datar :: University of Utah
  16. Colin Davey :: Electrical Geodesics Inc.
  17. Ryan Eckbo :: Brigham and Women's Hospital
  18. Jan Egger :: University Hospital of Marburg
  19. Mahshid Farzinfar :: University of North Carolina
  20. Andriy Fedorov :: Brigham and Women's Hospital
  21. Jean-Christophe Fillion-Robin :: Kitware, Inc.
  22. Julien Finet :: Kitware, Inc.
  23. James Fishbaugh :: University of Utah
  24. Yi Gao :: Georgia Institute of Technology
  25. Greg Gardner :: University of Utah
  26. Ronen Globinsky :: Yale University
  27. Randy Gollub :: Massachusetts General Hospital
  28. Maged Goubran :: Robarts Research Institute
  29. Daniel Haehn :: University of Pennsylvania
  30. Michael Halle :: Brigham and Women's Hospital
  31. Marcus Hanwell :: Kitware, Inc.
  32. Nobuhiko Hata :: Brigham and Women's Hospital
  33. Vivian He :: Brigham and Women's Hospital
  34. Tamas Heffter :: Queen's University
  35. Nicholas Herlambang :: AZE Technology, Inc.
  36. Luis Ibanez :: Kitware, Inc.
  37. Andrei Irimia :: UCLA
  38. Firdaus Janoos :: Brigham and Women's Hospital
  39. Hans Johnson :: University of Iowa
  40. Ilknur Kabul :: Kitware, Inc.
  41. Tina Kapur :: Brigham and Women's Hospital
  42. Peter Karasev :: Georgia Institute of Technology
  43. Ron Kikinis :: Brigham and Women's Hospital
  44. Eun Young Regina Kim :: University of Iowa
  45. Ivan Kolesov :: Georgia Institute of Technology
  46. Szymon Kostrzewski :: Ecole Polytechnique Federale de Lausanne
  47. Dillon Lee :: University of Utah
  48. Yinpeng Li :: University of North Carolina
  49. Yifei Lou :: Georgia Institute of Technology
  50. Mohsen Mahvash :: Harvard Medical School
  51. Nikos Makris :: Massachusetts General Hospital
  52. Katie Mastrogiacomo :: Brigham and Women's Hospital
  53. Joy Matsui :: University of Iowa
  54. Dominik Meier :: Brigham and Women's Hospital
  55. Mikhail Milchenko :: Washington University in St. Louis
  56. James Miller :: General Electric
  57. Zach Mullen :: Kitware, Inc.
  58. Isaiah Norton :: Brigham and Women's Hospital
  59. Lauren O'Donnell :: Brigham and Women's Hospital
  60. Danielle Pace :: Kitware, Inc.
  61. Beatriz Paniagua :: University of North Carolina
  62. Xenophon Papademetris :: Yale University
  63. Pratik Patel :: Brainlab
  64. Kedar Patwardhan :: General Electric
  65. Steve Pieper :: Isomics, Inc.
  66. Csaba Pinter :: Queen's University
  67. Wendy Plesniak :: Brigham and Women's Hospital
  68. Kilian Pohl :: University of Pennsylvania
  69. Clare Poynton :: Massachusetts Institute of Technology
  70. Marcel Prastawa :: University of Utah
  71. Sonia Pujol :: Brigham and Women's Hospital
  72. Martin Rajchl :: Robarts Research Institute
  73. Petter Risholm :: Brigham and Women's Hospital
  74. Peter Savadjiev :: Brigham and Women's Hospital
  75. William Schroeder :: Kitware, Inc.
  76. Andreas Schuh :: University of Pennsylvania
  77. Mark Scully :: University of Iowa
  78. Gregory Sharp :: Massachusetts General Hospital
  79. Yundi Shi :: University of North Carolina
  80. Maryam Shokri :: Massachusetts General Hospital
  81. Nadya Shusharina :: Massachusetts General Hospital
  82. Ramesh Sridharan :: Massachusetts Institute of Technology
  83. Hao Su :: Worcester Polytechnic Institute
  84. Suares Tamekue Tatuebu :: Brigham and Women's Hospital
  85. Xiaodong Tao :: General Electric
  86. Matthew Toews :: Brigham and Women's Hospital
  87. Junichi Tokuda :: Brigham and Women's Hospital
  88. Clement Vachet :: University of North Carolina
  89. Antonio Vega :: Brigham and Women's Hospital
  90. Gopalkrishna Veni :: University of Utah
  91. Bo Wang :: University of Utah
  92. Andrew Wasam :: CoSMo Software
  93. Demian Wassermann :: Brigham and Women's Hospital
  94. Sandy Wells :: Brigham and Women's Hospital
  95. Jason White :: Brigham and Women's Hospital
  96. Mallika Winsor :: Brigham and Women's Hospital
  97. Faye Wu :: Massachusetts Institute of Technology
  98. Atsushi Yamada :: Brigham and Women's Hospital
  99. Alexander Yarmarkovich :: Isomics, Inc.
  100. Alexander Zaitsev :: Brigham and Women's Hospital
  101. Luping Fang Zhejiang :: University of Technology, China