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

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

Registration

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

IGT

1. MR to CT Registration for Prostate Brachytherapy Dose Calculation (Andriy Fedorov, Dominik Meier, Hans Johnson)
2. Intraoperative Brain Shift Monitoring Using Shear Model Transcranial Ultrasound (Jason White, Steve Pieper?, Pratik Patel?)
3. Prostate Intervention(Junichi, Sam Song, Tamas Ungi)
4. Liver Ablation (Haiying Liu)
5. BrainLab-Aurora Hybrid Navigation (Isaiah Norton, Dan Marcus, Noby Hata)
6. Dynamic Image Fusion for Guidance of Cardiac Therapies (Feng Li)
7. PerkStation Module (Tamas Ungi, Xiaodong Tao)
8. Co-registration of PET and DWI Images for the targeting of Glioma Biopsies (Gareth Smith, Dominik Meir, Vince Magnotta)
9. Implementing Open IGT Link to Virtual Place for research support (Nicholas Herlambang, Noby Hata)

Radiotherapy

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

Analysis

1. Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
2. Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
3. MRSI module and SIVIC interface (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
4. Automatic SPHARM Shape Analysis in 3D Slicer (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
5. Computer_Aided_Photodynamic_Therapy (E Pietka, D Spinczyk, P Szabelak)

Microscopy Image Analysis

1. DICOM supplement 145  : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
2. Microscopy Extensions for ITK : convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
3. Flow Cytometry (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
4. Import/Export Farsight-GoFigure results (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
5. Farsight nuclear segmentation as GoFigure plugin (Arnaud Gelas, Sean Megason, Badri Roysam)
6. ITK Spherical Harmonics filter for shape analysis of cell nuclei (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
7. ITK Analysis of Large Histology Datasets (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
8. CTK Transfer function widget (Nicolas Rannou, Julien Finet, Stever Pieper)
9. Seedings results comparison (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
10. ITK Multiphase and GPAC level sets (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
11. JPEG2000 and HDF5 Image Readers in ITK (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
12. Median binary pattern texture measures for cell nuclei segmentation (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)

Shape Analysis

1. Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)
2. Shape Analysis projects, integration with Slicer3 (Beatriz Paniagua, Martin Styner)
3. Particle Based Shape Regression (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)

Diffusion

1. Fluid Mechanics Based Tractography (Nathan Hageman)
2. Efficient Diffusion Connectivity via Multi­directional F­star (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
3. Implementing Two-tensor tractography in Slicer (Python) (Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
4. Application of the DTI pipeline to the teenage substance abuse study (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
5. NAMIC Tools Suite for DTI analysis (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
6. QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data (Sudhir Pathak)

NA-MIC Kit Internals

1. Module Inventory (Steve, Jim)
2. Viewer Manager Factory (Alex Yarmarkovich, Kilian, Steve, Nicole)
3. Programmatic use of Volume Rendering module (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
4. Consistent visual language for Slicer4: icon rework marathon (Wendy Plesniak)
5. Slicer Wizard for PET/CT workflow (Wendy Plesniak, Ron Kikinis)
6. PythonQt and console widget (Steve Pieper, Jean-Christophe Fillion-Robin)
7. VTKWidgets (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
8. Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
9. 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. Anderson Peter , GE Navigation (Retired)
2. Aucoin Nicole , BWH
3. Audette Michel , Kitware
4. Aylward Stephen , Kitware, Inc
5. Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
6. Bouix Sylvain , BWH
7. Bowers Michael , Johns Hopkins University
8. Budin Francois , UNC
9. Burdette Everette , Acoustic MedSystems, Inc.
10. CHAUVIN Laurent , Brigham and Women's Hospital
11. Chen Min , Johns Hopkins University
12. Crane Jason , UCSF
13. Datar Manasi , SCI Institute
14. Ding Liya , The Ohio State University
15. Eckbo Ryan , BWH
16. Ersoy Ilker , University of Missouri Columbia
17. Fedorov Andriy , Surgical Planning Lab
18. Fillion-Robin Jean-Christophe , Kitware Inc.
19. Finet Julien , Kitware Inc
20. Fishbaugh James , SCI Institute
21. Fritscher Karl , UMIT
22. Gao Yi , Gerogia Tech
23. GELAS Arnaud , Harvard Medical School
24. Gorgolewski Chris , SPL
25. gouaillard alexandre , CoSMo Software
26. Gouttard Sylvain , SCI Institute
27. Grama Kedar , Rensselaer Polytechnic Institute
28. Haehn Daniel , University of Pennsylvania
29. Hafiane Adel , ENSI-Bourges
30. Hageman Nathan , UCLA
31. Hahn Dieter , University Erlangen
32. Halle Michael , BWH/SPL
33. Hamel Corentin , UNC Chapel Hill
34. Hata Nobuhiko , Brigham and Women's Hospital
35. Hayes Kathryn , Brigham and Women's Hospital
36. Herlambang Nicholas , AZE, Ltd.
37. Holton Leslie , Medtronic Navigation
38. Ibanez Luis , KITWARE Inc.
39. Jagadeesan Jayender , SPL
40. Johnson Hans , University of Iowa
41. Kapur Tina , Brigham and Women's Hospital
42. Kikinis Ron , Brigham and Women's Hospital
43. Kim Minjeong , UNC-Chapel Hill
44. Kolesov Ivan , Georgia Institute of Technology
45. Larson Garrett , UNC-CH
46. Lee Joohwi , UNC Chapel Hill
47. Li Rui , MGH
48. Lienhard Stefan , LMI
49. Lisle Curtis , KnowledgeVis, LLC
50. Liu Felix , Beth Israel Deaconess Medical Center
51. Liu Yanling , SAIC-Frederick, Inc.
52. Liu Haiying , Brigham and Women's Hospital
53. Lowekamp Bradley , Lockheed Martin
54. machiraju raghu , The Ohio State University
55. Magnotta Vincent , The University of Iowa
56. malaterre mathieu , CoSMo Software
57. Marcus Daniel , Washington University
58. Marks William , Focused Ultrasound Lab, BWH, HMS
59. Mastrogiacomo Katie , Brigham and Women's Hospital
60. Matsui Joy , University of Iowa
61. Megason Sean , Harvard Medical School
62. Meier Dominik , BWH, Boston MA
63. menze bjoern , CSAIL MIT
64. menze bjoern , CSAIL MIT
65. Milchenko Mikhail , WUSTL
66. Miller James , GE Research
67. Mosaliganti Kishore , Harvard Medical School
68. Niethammer Marc , UNC Chapel Hill
69. Norton Isaiah , BWH Neurosurgery
70. Olson Beck , UCSF
71. Onofrey John , Yale University
72. Padmanabhan Raghav , RPI
73. Palaniappan Kannappan , university of Missouri
74. Paniagua Beatriz , University of North Caolina at Chapel Hill
75. Papademetris Xenophon , Yale University
76. Partyka David , Kitware Inc
77. Patel Pratik , Brainlab Inc
78. Pathak Sudhir , Univeristy Of Pittsburgh
79. PECOT Thierry , Ohio State University
80. Peroni Marta , Politecnico di Milano, MIT, MGH
81. Perrot-Audet Antonin , Harvard Medical School
82. Pieper Steve , Isomics, Inc.
83. Plesniak Wendy , BWH
84. Pohl Kilian , IBM
85. Pujol Sonia , Brigham and Women's Hospital
86. Rannou Nicolas , Harvard Medical School
87. Riklin Raviv Tammy , MIT, CSAIL
88. Ruiz Marco , UCSD
89. Schroeder William , Kitware
90. Scully Mark , The Mind Research Network
91. Sharp Greg , MGH
92. Shi Yundi , UNC Chapel Hill
93. Shusharina Nadya , MGH
94. Singh Shantanu , The Ohio State University
95. Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
96. Souhait Lydie , Harvard Medical School
97. Spinczyk Dominik , Silesian University of Technology
98. Srinivasan Padmapriya , BWH
99. Tao Xiaodong , GE Research
100. Tokuda Junichi , Brigham and Women's Hospital
101. Ungi Tamas , Queen's University
102. Vachet Clement , UNC Chapel Hill
103. Veni Gopalkrishna , SCI Institute
104. Wassermann Demian , SPL/LMI/PNL
105. Weinrich Adam , Nokia
106. Wells Sandy , BWH
107. White Phillip , BWH/HMS
108. Wu Guorong , University of North Carolina at Chapel Hill
109. Yamada Atsushi , Nagoya Institute of Technology
110. Yarmarkovich Alexander , ISOMICS
111. Zaitsev Alexander , Brigham and Womens Hospital