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 Ibanez)
  • 3-5pm: 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

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 Hybrid Navigation (Isaiah Norton, Dan Marcus, Noby Hata)
• Dynamic Image Fusion for Guidance of Cardiac Therapies (Feng Li)
• PerkStation Module (Tamas Ungi)
• Co-registration of PET and DWI Images for the targeting of Glioma Biopsies (Gareth Smith)
• Implementing Open IGT Link to Virtual Place for research support (Nicholas Herlambang, Noby Hata)

Radiotherapy

• Dicom RT plugin (Greg Sharp, Tamas Ungi)
• Adaptive Radiation Therapy for H&N cancer (Marta Peroni,Polina Golland,Greg Sharp)
• Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

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, Badri Roysam, Sean Megason)
• ITK Multiphase and GPAC level sets (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
• JPEG2000 and HDF5 Image Readers in ITK (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
• Median binary pattern texture measures for cell nuclei segmentation (Adel Hafiane, Lucas Menand, K. Palaniappan, 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)
• Particle Based Shape Regression (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)

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)
• Implementing Two-tensor tractography in Slicer (Python) (Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
• Application of the DTI pipeline to the teenage substance abuse study (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)

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