2012 Summer Project Week

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  • Dates: June 18-22, 2012
  • Location: MIT


Time Monday, June 18 Tuesday, June 19 Wednesday, June 20 Thursday, June 21 Friday, June 22
Project Presentations NA-MIC Update Day IGT Day Reporting Day
8:30am Breakfast Breakfast Breakfast Breakfast
9am-12pm 9am-10am: Slicer4 (Jean-Christophe Fillion-Robin)

10-11am Slicer4 Breakout (Continued)
Grier Room (Left)
11-12pm: Breakout Session: )
Star Room

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

Kiva Room
10am-12pm: Core and Site PIs meeting with Ron:

Star 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 Session (Pieper)
Grier Room (Left)
4:15-5:00pm Slicer4 Developer Session Continued
Grier Room (Left)
4:15-5:00pm Breakout Session: TBD
Grier Room (Right)

1-3pm: Breakout Session:

Star Room
3-4pm: Tutorial Contest Presentations
Grier Rooms
4-5pm: Breakout Session:TBD
Star Room

12:45-1pm: Tutorial Contest Winner Announcement

Grier Rooms

1-4pm: Breakout Session:

Kiva Room

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


This is where the list of projects goes...

Please use THIS TEMPLATE to create project pages for this event.

Neurosurgery, Brain and Spine, Traumatic Brain Injury

  1. Early Dementia Diagnostic Tools (Marcel Koek, Sonia Pujol)
  2. Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
  3. Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
  4. Spine Segmentation & Osteoporosis Detection In CT Imaging Studies (Anthony Blumfield)

Radiation Therapy

  1. Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
  2. Overlapping structures (Greg Sharp, Steve Pieper)
  3. Atlas-based segmentation for head and neck (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)

Huntington's Disease

Atrial Fibrillation

  1. Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
  2. Cardiac MRI Registration Module (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
  3. Vector-Valued Cardiac MRI Registration (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
  4. Automatic Left Atrial Scar Detection (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
  5. MRI Inhomogeneity Correction Filter (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
  6. OpenIGT for realtime MRI-guided RF ablation (Rob MacLeod, Junichi Tokuda)

Device Integration with Slicer and General Image Guided Therapy

  1. iGyne for Gyne Brachytherapy (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
  2. Open-source electromagnetic trackers using OpenIGTLink
  3. Live Ultrasound (Tamas Ungi, Junichi Tokuda)
  4. Transform Recorder (Simrin Nagpal, Tamas Ungi)
  5. Single Vertebra CT-US Registration (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi)

General Segmentation

  1. Semi-automated airway segmentation from 0.64mm lung CT datasets (Padraig Cantillon-Murphy, Pietro Nardelli)
  2. Quantitative PET Image Analysis Module (Markus Van Tol)
  3. Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)

General Registration

  1. Interactive registration (Kunlin)
  2. NiftyReg integration (Marc Modat, Sonia Pujol)
  3. Elastix integration (Stefan Klein, Sonia Pujol)

General Diffusion Tractography



  1. Built-In Self-Testing (BIST) for Slicer (Steve, Julien, Jc, Sonia)
  2. Annotation module redesign (Nicole)
  3. Multivolume, nrrd, .... (Andriy, Jim)
  4. Python CLI modules (Demian, JC, Julien)
  5. Charting (Jim)
  6. ITKv4
  7. SimpleITK
  8. GPU Editor Effects
  9. XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
  10. General Usability issues (e.g. LM,FG,BG blending)
  11. Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
  12. XNAT/Slicer implementation (Sunil, Dan, Steve,...)
  13. Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)


We are pleased to announce the 15th 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 26th 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.


  • Dates: June 18-22, 2012.
  • Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.
  • REGISTRATION: Please click HERE to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
  • Registration Fee: $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
  • Hotel: TBD.


  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 infrastructure projects in a kickoff TCON on April 26, 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 10, all participants to add a one line title of their project to #Projects
  4. By 3pm ET on Thursday June 7, 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 14: 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.