2012 Summer Project Week

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Summary: The 15th PROJECT EVENT was held June 18-22,2012 at MIT. It recorded 88 registered attendees, who worked on 62 projects. These attendees represented 20 academic sites (Brigham and Women's Hospital, University of Utah, UNC Chapel Hill, UCLA, MIT, Georgia Tech, Boston University, UIowa, Queen University, Massachusetts General Hospital, WUSTL, Robarts, Princess Margaret Hospital, Childrens Hospital Boston, Northwestern University, Rutgers, Erasmus, NLM/NIH, University of Cork, UBC) and 8 companies (Kitware, Isomics, GE Research, Radnostics, AZE, InnerOptic, A*Star, Fraunhofer Mevis). The projects are detailed below.

Agenda

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: What's new in Slicer4 (Charts - Jim, DICOM - Steve, Multivolume - Andrey) Grier Room (Left) ---------------------------------------- 10-11am Slicer4 Python Q&A Grier Room (Left)	9am-11pm: Breakout Session: Slicer and SimpleITK (Hans) Kiva Room ---------------------------------------- 10am-12pm: Computation Core PIs: closed meeting with Ron: Star Room	9am-12pm: Breakout Session: Slicer in Networked Environment (Junichi) Grier 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 ---------------------------------------- 3:30-4:30pm Slicer4 Extensions (JC) Grier Room (Left)	3-4pm: Tutorial Contest Presentations Grier Rooms ---------------------------------------- 4-5pm: Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre) Star Room	12:45-1pm: Tutorial Contest Winner Announcement Grier Rooms ---------------------------------------- 3-30pm: Breakout Session: QtTesting (JC)	1-3pm: Breakout Session: Ultrasound (Tamas) Grier Room ---------------------------------------- 3:00-4:00pm Lean Slicer (Andras) Grier Room
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 project pages for this event.

Neurosurgery, Brain and Spine, Traumatic Brain Injury

1. Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Danielle Pace, Stephen Aylward, Jack van Horn, Guido Gerig)
2. Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
3. An Ultrasound-based Method for Aberration Correction in TCFUS (Jason White, Greg Clement)
4. Early Dementia Diagnostic Tools (Marcel Koek, Sonia Pujol)
5. Spine Segmentation & Osteoporosis Detection In CT Imaging Studies (Anthony Blumfield, Ron Kikinis)

Radiation Therapy

1. Atlas-based segmentation for head and neck (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
2. First class structure set support in Slicer (Greg Sharp, Steve Pieper, Jim Miller, Andras Lasso)
3. Plastimatch loadable module (James Shackleford, Greg Sharp)
4. Deformable Registration for Head and Neck (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
5. Radiotherapy extensions for Slicer 4 (Andras Lasso, Csaba Pinter, Kevin Wang)
6. SUV Threshold Computation (Nadya Shusharina, Greg Sharp)

Huntington's Disease

1. Slicer/Nipype Integration (Hans Johnson)
2. DicomToNrrdConverter Integration (Kent Williams, Hans Johnson)
3. QA Evaluation Module (Dave Welch, Hans Johnson, Steve Pieper, JC Fillion-Robin)
4. 4D Shape Analysis: Software Tools (James Fishbaugh, Marcel Prastawa, Guido Gerig)
5. DTI atlas based fiber analysis (Francois Budin)

Atrial Fibrillation

1. Cardiac MRI Registration Module (Alan Morris, Danny Perry, Josh Cates, Rob MacLeod)
2. Automatic Left Atrial Scar Detection (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
3. MRI Inhomogeneity Correction Filter (Alan Morris, Eugene Kholmovski, Josh Cates, Greg Gardner, Danny Perry, Rob MacLeod)
4. Vector-Valued Cardiac MRI Registration (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
5. Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI (Arie Nakhmani, Allen Tannenbaum)

Device Integration with Slicer and Image Guided Therapy

1. Web Interface to Slicer 4 (Steve Pieper)
2. Improvement of OpenIGTLink IF for Slicer 4 (Junichi Tokuda, Laurent Chauvin)
3. Lean Slicer to facilitate regulatory approval (Andras Lasso, Chris Wedlake)
4. Live Ultrasound (Tamas Ungi, Simrin Nagpal, Andinet Enquobahrie, Junichi Tokuda)
5. Integration of BK ProFocus US with Slicer via PLUS library (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
6. Transform Recorder and other IGT modules (Simrin Nagpal, Tamas Ungi)
7. Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
8. iGyne for Gynecological Cancer Brachytherapy (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
9. Interactive Needle Segmentation for Gynecological Cancer Brachytherapy (Nabgha Farhat, Yi Gao, Xiaojun Chen, Neha Agrawal, Jan Egger, Tina Kapur, Steve Pieper)
10. User Driven Bladder Segmentation in Female Pelvis (Scott Tyler Blevins, Nabgha Farhat, Jan Egger, Tobias Penzkofer, Tina Kapur)
11. Single Vertebra CT-US Registration (Saman Nouranian, Samira Sojoudi, Simrin Nagpal, Tamas Ungi, David Welch)
12. Fast Fiducial Registration Module (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
13. Steered Registration for Image Guided Therapy (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
14. 4D Ultrasound on Slicer4 (Laurent Chauvin, Nobuhiko Hata)
15. Kinect4Slicer (Laurent Chauvin, Nobuhiko Hata)
16. Needle Tip Tracking for complex MR images (Atsushi Yamada, Nobuhiko Hata)

General Segmentation

1. Semi-automated airway segmentation from 0.64mm lung CT datasets (Pietro Nardelli, Padraig Cantillon-Murphy, Raul San Jose Estepar)
2. Loading and segmentation of histopathology imaging for radiological-pathological correlation (Tobias Penzkofer, Andrey Fedorov)
3. Porting ABC extension to Slicer 4 (Marcel Prastawa, Bo Wang, Guido Gerig)
4. Quantitative PET Image Analysis Module (Markus Van Tol)

General Registration

1. NiftyReg integration (Marc Modat, Sonia Pujol)
2. Elastix integration (Stefan Klein, Sonia Pujol)
3. Highly Deformable DTI Registration for cases with large pathological variations (Aditya Gupta, Martin Styner, Matthew Toews)
4. Registration of Difficult Images (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, Petter Risholm, Dominik Meier, William Wells)

Informatics

1. Applicability of AIM to QIN use cases (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)
2. Reporting module (Andrey, Nicole, Steve, Ron, Pat)
3. CMake-fying AIM API (Pat Mongklowat, Vlad Kleper, Andrey Fedorov)

Infrastructure

1. Built-In Self-Testing (BIST) for Slicer (Steve, Julien, Jc, Sonia)
2. Annotation module redesign for Slicer (Nicole)
3. Multivolume support (Andrey, Jim, Brendan Moloney)
4. Python CLI modules (Demian, JC, Julien, Steve).
5. Charting (Jim)
6. Editor Effects (Steve, Jim, Brad, Ivan, Yi)
7. XTK/WebGL Exporter (Daniel, Nicolas - Boston Children's Hospital)
8. Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
9. XNAT/Slicer Integration (Sunil, Dan, Steve,...)
10. ITKv4 Integration (Hans Johnson, Julien Finet, Jim). See #2007
11. SimpleITK Integration (Hans Johnson, Bradley Lowekamp)
12. Slicer Module for longitudinal analysis of PET-CT (Paul, Andriy, Ron, Markus,...)
13. Threat Modeling (JC, J2, Anthony, Steve)
14. CUDA Volume Rendering as Extension (J2, Elvis)

Background

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.

Logistics

• 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: No room blocks have been reserved in any area hotel. Please select a hotel of your choice and make reservations as early as possible. Some area hotels are:
  • marriott cambridge center
  • marriott residence inn kendall square
  • le meridien central square
  • hotel marlowe cambridge
  • royal sonesta hotel cambridge

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 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.

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. Anderson, Peter, retired, traneus@verizon.net
2. Arbisser, Amelia, MIT, arbisser@mit.edu
3. Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
4. Aylward, Stephen, Kitware, stephen.aylward@kitware.com
5. Blevins, Scott, BWH, stblevins@gmail.com
6. Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
7. Budin, Francis, NIRAL-UNC, fbudin@unc.edu
8. Cao, Kunlin, GE Research, cao@ge.com
9. Chambers, Micah, UCLA, micahcc@ucla.edu
10. Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
11. Chen, Elvis, Robarts, chene@robarts.ca
12. Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
13. Datar, Manasi, Utah SCI, datar@sci.utah.edu
14. Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
15. Egger, Jan, BWH, egger@bwh.harvard.edu
16. Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
17. Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
18. Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
19. Finet, Julien, Kitware, julien.finet@kitware.com
20. Fishbaugh, James, SCI, jfishbau@sci.utah.edu
21. Gao, Yi, BWH, gaoyi@bwh.harvard.edu
22. Gardner, Greg, SCI, ggardner@sci.utah.edu
23. Golland, Polina, MIT CSAIL, polina@csail.mit.edu
24. Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
25. Gupta, Aditya, NIRAL UNC, aditya_gupta@med.unc.edu
26. Irimia, Andrei, UCLA, andrei.irimia@loni.ucla.edu
27. Jagadeesan, Jayender, SPL, jayender@bwh.harvard.edu
28. Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
29. Kalpathy-Cramer, Jayashree, MGH, kalpathy@nmr.mgh.harvard.edu
30. Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
31. Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
32. Klein, Stefan, (cancelled registration) Erasmus MC, s.klein@erasmusmc.nl
33. Kleper, Vladimir, Northwestern Univ, vkleper@northwestern.edu
34. Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
35. Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
36. Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
37. Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
38. Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
39. Macule, Raul, AZE R&D, raul.macule@azeresearch.com
40. Mastrogiacomo, Katie, SPL, BWH, kmast@bwh.harvard.edu
41. Meier, Dominik, BWH, meier@bwh.harvard.edu
42. Mercea, Paul, SPL, pmercea@bwh.harvard.edu
43. Miller, Jim, GE Research, millerjv@ge.com
44. Mizutani, Tatsushi, Nagoya Univ, tatsushi0207@me.com
45. Modat, Marc, Univ College London, m.modat@ucl.ac.uk
46. Moloney, Brendan, AIRC, moloney.brendan@gmail.com
47. Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
48. Montillo, Albert, GE Research, montillo@ge.com
49. Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
50. Nakhmani, Arie, BU, nakhmani@gmail.com
51. Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
52. Norton, Isaiah, BWH, inorton@partners.org
53. Nouranian, Saman, Univ BC, samann@ece.ubc.ca
54. O'Donnell, Lauren, BWH, odonnell@bwh.harvard.edu
55. Oyama, Rie, BWH, royama@bwh.harvard.edu
56. Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
57. Penzkofer, Tobias, SPL, pt@bwh.harvard.edu
58. Pernelle, Guillaume, BWH, gpernelle@gmail.com
59. Pieper, Steve, Isomics, pieper@bwh.harvard.edu
60. Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
61. Pujol, Sonia, BWH, spujol@bwh.harvard.edu
62. Rannou, Nicolas, Childrens Hospital, nicolas.rannou@childrens.harvard.edu
63. Razzaque, Sharif, InnerOptic Technology, sharif@inneroptic.com
64. Risholm, Petter, Harvard, pettri@bwh.harvard.edu
65. San Jose, Raul, BWH, rjosest@bwh.harvard.edu
66. Schroeder, William, Kitware, will.schroeder@kitware.com
67. Shackleford, James, MGH, jshackleford@partners.org
68. Sharp, Greg, MGH, gcsharp@partners.org
69. Shusharina, Nadya, MGH, nshusharina@partners.org
70. Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
71. Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
72. Sridharan, Ramesh, MIT CSAIL, rameshvs@MIT.EDU
73. State, Andrei, InnerOptic Technology, andrei@inneroptic.com
74. Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
75. Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
76. Tokuda, Junichi, BWH, tokuda@bwh.harvard.edu
77. Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
78. Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
79. Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
80. Wang, Bo, SCI, bowang@sci.utah.edu
81. Wang, Kevin, Princess Margaret Hospital, kevin.wang@rmp.uhn.on.ca
82. Wedlake, Chris, Robarts, cwedlake@robarts.ca
83. Welch, David, Univ Iowa, david-welch@uiowa.edu
84. Wells, William, HMS BWH, sw@bwh.harvard.edu
85. Whitaker, Ross, SCI, whitaker@cs.utah.edu
86. White, Phillip, BWH HMS, white@bwh.harvard.edu
87. Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
88. Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu