2010 Summer Project Week

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Agenda

Time	Monday, June 21	Tuesday, June 22	Wednesday, June 23	Thursday, June 24	Friday, June 25
	Project Presentations	NA-MIC Update Day		IGT Day	Reporting Day
8:30am		Breakfast	Breakfast	Breakfast	Breakfast
9am-12pm		9am: NA-MIC Kit Update (Jim Miller) ---------------------------------------- 9:45am: 3D Slicer Update (Steve Pieper) ---------------------------------------- 10:30-11am: OpenIGTLink Update (Junichi Tokuda) ---------------------------------------- 11am-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)	9am-12pm: Breakout Session: ITK (Luis Ibanez)	9am-5pm: Breakout Session: OpenIGTLink	10am-12pm: Project Progress Updates
12pm-1pm	Lunch	Lunch	Lunch	Lunch	Lunch boxes; Adjourn by 1:30pm
1pm-5:30pm	1-1:05pm: Ron Kikinis: Welcome ---------------------------------------- 1:05-3:30pm: Project Introductions (all Project Leads) ---------------------------------------- 3:30-5:30pm: Tutorial: Getting Started with Qt (Adam Weinrich, Nokia)	1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) ---------------------------------------- 3-4pm: Tutorial Contest Presentations ---------------------------------------- 4-5pm: Breakout Session: Data Management (Dan Marcus, Stephen Aylward)	12:45-1pm: Tutorial Contest Winner Announcement ---------------------------------------- 1-3pm: Breakout Session: Microscopy Image Analysis (Sean Megason) ---------------------------------------- 3-5pm: Breakout Session: QA Training (Luis Ibanez) ---------------------------------------- 3-4pm: Breakout Session: VTK Widgets (Nicole, Kilian, JC)	1-2pm: Breakout Session: GWE (Marco Ruiz) ---------------------------------------- 2-3pm: Build Instructions: Simple Git (Steve Pieper) ---------------------------------------- 3-4pm: Breakout Session: Volume Rendering Demos and Discussion (Yin Wu, Steve Pieper)
5:30pm	Adjourn for the day	Adjourn for the day	Adjourn for the day	Adjourn for the day

Please note:

• We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
• Please sign up for the developer mailing lists
• Next Project Week January 3-7, 2011, Salt Lake City, 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, Andriy Fedorov)
7. Groupwise Registration (Ryan Eckbo, Sylvain Bouix, 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. Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
3. Prostate Intervention(Junichi, Sam Song, Tamas Ungi)
4. Liver Ablation (Haiying Liu, Noby Hata)
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)
10. Tracking Neuroendoscope Using EM Tracker and OpenIGTLink (Laurent Chauvin, Junichi Tokuda, Noby Hata)
11. Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery (Atsushi Yamada, Junichi Tokuda, 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 Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis)
2. Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
3. Mouse brain cortical thickness analysis (Joohwi Lee, Ipek Oguz, Martin Styner)
4. Primate image analysis using the standard Slicer pipeline (Yundi Shi, Martin Styner)
5. MRSI module and SIVIC interface (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
6. Computer_Aided_Photodynamic_Therapy (E Pietka, D Spinczyk, P Szabelak)
7. IA-FEMesh Slicer3 Finite Meshing Module (N Grosland, V Magnotta, C Lisle, S Pieper)

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)
13. Standards and Interfaces for Microscopy Image Analysis in ITK (whoever has an opinion, 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)
4. Automatic SPHARM Shape Analysis in 3D Slicer (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
5. Shape Test Bench (Marc Niethammer, Sylvain Bouix)

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, Jim Barabas)
4. Inventory of Volume Rendering Functionality (Jim Barabas)
5. Consistent visual language for Slicer4: icon rework marathon (Wendy Plesniak)
6. Slicer Wizard for PET/CT workflow (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
7. PythonQt and console widget (Steve Pieper, Jean-Christophe Fillion-Robin)
8. VTKWidgets (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
9. Superbuild (David Partyka, Steve Pieper, Katie Hayes)
10. Paraview Support for Computational Anatomy (Michel Audette, Mike Bowers)

Workflows and Integration

1. Workflows and Service Oriented Architecture Solutions for Slicer3 Modules (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

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

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