2010 Summer Project Week

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Background

We are pleased to announce the 11th 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.

Active preparation begins on Thursday, April 15th 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 30-50 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 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 21-25, 2010
• 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, or send a check.
• Registration Fee: $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
• Hotel: We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) Please click here to reserve. You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

   All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of
   $189/night/room (plus tax).
   This rate is good only through June 1.

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

• Here is some information about several other Boston area hotels that are convenient to NA-MIC events: Boston_Hotels. Summer is tourist season in Boston, so please book your rooms early.
• For hosting projects, we are planning to make use of the NITRC resources. See Information about NITRC Collaboration

Agenda

Monday, June 21, 2010

• • noon-1pm lunch
  • 1pm: Welcome (Ron Kikinis)
  • 1:05-3:30pm Introduce Projects using templated wiki pages (all Project Leads) (Wiki Template)
  • 3:30-5:30pm Tutorial: 2010 Summer Project Week Breakout: Getting Started with Qt (Adam Weinrich, Nokia)

Tuesday, June 22, 2010

• • 8:30am breakfast
  • 9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
  • 9:45-10:30am 3D Slicer Update (Steve Pieper)
  • 10:30-11am OpenIGTLink Update (Junichi Tokuda)
  • 11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
  • noon lunch
  • 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
  • 3pm: Tutorial Contest Presentations
  • 4-5pm 2010 Summer Project Week Breakout Session: Data Management (Dan Marcus, Stephen Aylward)
  • 5:30pm adjourn for day

Wednesday, June 23, 2010

• • 8:30am breakfast
  • 9am-12pm Breakout Session: 2010 Project Week Breakout Session: ITK (Luis Ibanez)
  • noon lunch
  • 12:45pm: Tutorial Contest Winner Announcement
  • 1-3pm: Breakout Session: Microscopy_Image_Analysis (Sean Megason)
  • 3-5pm: Breakout Session: 2010 Summer Project Week Breakout Session:QA Training (Luis Ibanesz)
  • 3-4pm: Breakout Session: 2010 Summer Project Week Breakout Session:VTK Widget (Nicole, Kilian, JC)
  • 5:30pm adjourn for day

Thursday, June 24, 2010

• • 8:30am breakfast

• • 9am-5pm: Breakout Session: OpenIGTLink
  • noon lunch
  • 1-2pm: 2010 Summer Project Week Breakout Session:GWE (Marco Ruiz)
  • 2-2:30pm: Simple Git (Steve Pieper)
  • 5:30pm adjourn for day

Friday, June 25, 2010

• • 8:30am breakfast
  • 10am-noon: Project Progress Updates
    • Noon: Lunch boxes and adjourn by 1:30pm.
    • We need to empty room by 1:30. You are welcome to use wireless in Stata.
    • Please sign up for the developer mailing lists
    • Next Project Week in Utah, Fill in Dates

Projects

Segmentation

• Robust Statistics Segmenter Slicer Module (Yi Gao, Allen Tannenbaum, Ron Kikinis)
• Multi-scale Shape Based Segmentation for the Hippocampus (Yi Gao, Allen Tannenbaum)
• Segmentation on Mesh Surfaces Using Geometric Information (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
• The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
• Prostate Segmentation from MRI (Andriy Fedorov, Yi Gao)
• SPECTRE: Skull Stripping integration with Slicer (Nicole Aucoin, Min Chen)
• White Matter Lesion segmentation (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
• LV scar segmentation display and fusion (Dana C. Peters, Felix Liu, BIDMC, Boston)
• EMSegmentation: Automatic Intensity Initialization using KMeans (Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

Registration

• The 3DSlicer Registration Case Library (Dominik Meier)
• Fiducial-based deformable image registration (Nadya Shusharina, Greg Sharp)
• HAMMER: Deformable Registration (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
• Best Regularization Term for Demons Registration Algorithm (Rui Li, Greg Sharp)
• Evaluation of Registration in Slicer (James Fishbaugh, Guido Gerig, Domink Meier)
• MR to Ultrasound Registration Methodology (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
• Groupwise Registration (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

IGT

• MR to CT Registration for Prostate Brachytherapy Planning (Andriy Fedorov, Dominik Meier, Hans Johnson)
• Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
• Liver Ablation (Haiying Liu)
• BrainLab-Aurora HybridNav (Isaiah Norton, Dan Marcus)
• Dynamic Image Fusion for Guidance of Cardiac Therapies (Feng Li)

Radiotherapy

• Dicom RT plugin (Greg Sharp)
• Adaptive Radiation Therapy for H&N cancer (Marta Peroni,Polina Golland,Greg Sharp)

Analysis

• Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
• Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
• MRSI module and SIVIC interface (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
• NAMIC Tools Suite for DTI analysis (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
• Automatic SPHARM Shape Analysis in 3D Slicer (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

Microscopy Image Analysis

• Malaterre, Gouaillard: DICOM supplement 145: Microscopy Image in the Dicom Standard
• Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
• Gouaillard: Flow Cytometry
• Import/Export Farsight-GoFigure results (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
• Farsight nuclear segmentation as GoFigure plugin (Arnaud Gelas, Sean Megason, Badri Roysam)
• ITK Spherical Harmonics filter for shape analysis of cell nuclei (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
• CTK Transfer function widget (Nicolas Rannou, Julien Finet, Stever Pieper)
• Seedings results comparison (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
• ITK GPAC level set (K. Palaniappan, Kishore Mosaliganti, Sean Megason)
• JPEG2000 and HDF5 Image Readers in ITK (Kishore Mosaliganti, Luis Ibanez, Sean Megason)

Shape Analysis

• Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)
• Shape Analysis projects, integration with Slicer3 (Beatriz Paniagua, Martin Styner)

Informatics

• Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

Diffusion

• Fluid Mechanics Based Tractography (Nathan Hageman)
• Efficient Diffusion Connectivity via Multi­directional F­star (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)

NA-MIC Kit Internals

• Module Inventory (Steve, Jim)
• Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
• Programmatic use of Volume Rendering module (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
• XNAT Enterprise webservices client for Slicer (Wendy, Mark)
• PythonQt and console widget (Steve Pieper, Jean-Christophe Fillion-Robin)

• VTKWidgets (JC, will, Schroeder, Nicole, Ron)
• Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
• Paraview Support for Computational Anatomy (Michel Audette, Mike Bowers)

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 15, 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 June 10, 2009: 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.
4. By 3pm on June 17, 2010: 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)
5. 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...
6. 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.

Attendee List

NOTE: THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD NOT EDIT THIS, BUT REGISTER BY CLICKING HERE.

1. Aucoin Nicole , BWH
2. Audette Michel , Kitware
3. Aylward Stephen , Kitware, Inc
4. Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
5. Bouix Sylvain , BWH
6. Budin Francois , UNC
7. Burdette Everette , Acoustic MedSystems, Inc.
8. CHAUVIN Laurent , Brigham and Women's Hospital
9. Chen Min , Johns Hopkins University
10. Crane Jason , UCSF
11. Datar Manasi , SCI Institute
12. Eckbo Ryan , BWH
13. Fedorov Andriy , Surgical Planning Lab
14. Fillion-Robin Jean-Christophe , Kitware Inc.
15. Finet Julien , Kitware Inc
16. Fishbaugh James , SCI Institute
17. Gao Yi , Gerogia Tech
18. GELAS Arnaud , Harvard Medical School
19. gouaillard alexandre , CoSMo Software
20. Gouttard Sylvain , SCI Institute
21. Haehn Daniel , University of Pennsylvania
22. Hageman Nathan , UCLA
23. Hahn Dieter , University Erlangen
24. Hamel Corentin , UNC Chapel Hill
25. Hata Nobuhiko , Brigham and Women's Hospital
26. Hayes Kathryn , Brigham and Women's Hospital
27. Herlambang Nicholas , AZE, Ltd.
28. Holton Leslie , Medtronic Navigation
29. Ibanez Luis , KITWARE Inc.
30. Johnson Hans , University of Iowa
31. Kapur Tina , Brigham and Women's Hospital
32. Kikinis Ron , Brigham and Women's Hospital
33. Kim Minjeong , UNC-Chapel Hill
34. Kolesov Ivan , Georgia Institute of Technology
35. Larson Garrett , UNC-CH
36. Li Rui , MGH
37. Lisle Curtis , KnowledgeVis, LLC
38. Liu Haiying , Brigham and Women's Hospital
39. Liu Yanling , SAIC-Frederick, Inc.
40. Magnotta Vincent , The University of Iowa
41. malaterre mathieu , CoSMo Software
42. Marcus Daniel , Washington University
43. Mastrogiacomo Katie , Brigham and Women's Hospital
44. Matsui Joy , University of Iowa
45. Megason Sean , Harvard Medical School
46. Meier Dominik , BWH, Boston MA
47. menze bjoern , CSAIL MIT
48. Milchenko Mikhail , WUSTL
49. Miller James , GE Research
50. Mosaliganti Kishore , Harvard Medical School
51. Niethammer Marc , UNC Chapel Hill
52. Norton Isaiah , BWH Neurosurgery
53. Paniagua Beatriz , University of North Caolina at Chapel Hill
54. Papademetris Xenophon , Yale University
55. Partyka David , Kitware Inc
56. Pathak Sudhir , Univeristy Of Pittsburgh
57. Peroni Marta , Politecnico di Milano, MIT, MGH
58. Perrot-Audet Antonin , Harvard Medical School
59. Pieper Steve , Isomics, Inc.
60. Plesniak Wendy , BWH
61. Pohl Kilian , IBM
62. Pujol Sonia , Brigham and Women's Hospital
63. Rannou Nicolas , Harvard Medical School
64. Riklin Raviv Tammy , MIT, CSAIL
65. Ruiz Marco , UCSD
66. Schroeder William , Kitware
67. Scully Mark , The Mind Research Network
68. Sharp Greg , MGH
69. Shi Yundi , UNC Chapel Hill
70. Shusharina Nadya , MGH
71. Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
72. Souhait Lydie , Harvard Medical School
73. Spinczyk Dominik , Silesian University of Technology
74. Srinivasan Padmapriya , Brigham and Women's Hospital
75. Tao Xiaodong , GE Research
76. Ungi Tamas , Queen's University
77. Vachet Clement , UNC Chapel Hill
78. Veni Gopalkrishna , SCI Institute
79. Wassermann Demian , SPL/LMI/PNL
80. Wells Sandy , BWH
81. Wu Guorong , University of North Carolina at Chapel Hill