2011 Summer Project Week

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• Dates: June 20-24, 2011
• Location: MIT

Agenda

Time	Monday, June 20	Tuesday, June 21	Wednesday, June 22	Thursday, June 23	Friday, June 24
	Project Presentations	NA-MIC Update Day		IGT Day	Reporting Day
8:30am		Breakfast	Breakfast	Breakfast	Breakfast
9am-12pm		9am-11am: Slicer 4 Core Modules Usability Review Star Room ---------------------------------------- 11-12pm: Breakout Session: Slicer4 Annotations (Nicole Aucoin) Star Room	9am-12pm: Breakout Session: ITK (Luis Ibanez) Kiva Room	9am-4pm: Breakout Session: OpenIGTLink Kiva 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 ---------------------------------------- 3:30-5:00pm: NA-MIC Kit Update Slicer4 Developers Guided Tour (Pieper) (Draft Slides), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin) Grier Rooms	1-3pm: Breakout Session: Slicer4 MultiVolume Containers (Nicole Aucoin) Star Room ---------------------------------------- 3-4pm: Tutorial Contest Presentations Grier Rooms ---------------------------------------- 4-5pm: VTK Charts (Marcus Hanwell) Star Room	12:45-1pm: Tutorial Contest Winner Announcement Grier Rooms ---------------------------------------- 3-4pm: Breakout Session: Inter-subject Registration for EM segmenter Kiva Room	1-4pm: Breakout Session: OpenIGTLink Kiva Room
5:30pm	Adjourn for the day	Adjourn for the day	Adjourn for the day	Adjourn for the day

Projects

• Please make a link for your project to a new page based on the 2011 Summer Project Page Template

Neurosurgery: Brain and Spine, Traumatic Brain Injury

1. Obtaining and Evaluation of Glioblastoma Multiforme (GBM) Segmentation Masks (Jan Egger,Tina Kapur, Andriy Fedorov, Rivka Colen, Ron Kikinis, Alex Golby, Christopher Nimsky)
2. Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
3. Spine Segmentation & Osteoporosis Screening In CT Imaging Studies (Anthony Blumfield)
4. Multimodality Image Registration for TBI (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
5. Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
6. Tractography Bundle/Cluster Interaction and Display in Slicer4 (Lauren, Isaiah, Demian)
7. White Matter Laterality in Python/Slicer4 (Lauren)
8. Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio Tristán-Vega)
9. Intraoperative Brain Shift Monitor (Jason White, Alex Golby, Steve Pieper)

Radiation Therapy

1. Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
2. Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer (Tina Kapur, Greg Sharp, Jan Egger, Firdaus Janoos, Andriy Fedorov)
3. Contouring of Anatomy Structures like Tumor, Bladder, Rectum and Sigmoid for Gynecological Brachytherapy (Tina Kapur, Akila Viswanathan, Jan Egger)
4. Dose volume histograms in Slicer (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
5. Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
6. Integrating Plastimatch into the EMSegmenter (Dominique Belhachemi, Kilian Pohl, Greg Sharp, Daniel Haehn)

Huntington's Disease

1. Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease, (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
2. SPHARM & particles shape analysis - Huntington's Disease - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
3. Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
4. DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
5. DTI pair-wise registration module - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)
6. DTI analysis for Huntington's disease (Gopal Veni, Ross Whitaker)

Atrial Fibrillation

1. Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
2. Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)

Vessels

1. The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper, Kilian Pohl, Ron Kikinis)
2. Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)

Device Integration with Slicer

1. Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room (Szymon Kostrzewski)
2. Live Tracked Ultrasound with Slicer4 (Tamas Heffter)
3. Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)
4. Needle Detection to Control Scanner for Prostate Biopsy (Atsushi Yamada, Loïc Cadour, Junichi Tokuda and Nobuhiko Hata)
5. 4D Ultrasound / Hybrid Probe / OsteoPlan (Laurent Chauvin, Noby Hata)

General Segmentation

1. 2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3(Regina Kim, ... )
2. EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
3. Customizing EMSegmenter pipelines for brain lesions (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
4. Slicer extension for GLiome Image SegmenTation and Registration (GLISTR) (Andreas Schuh, Daniel Haehn, Kilian Pohl)
5. DTI Volumetric Segmentation for Group studies (Gopal Veni, Ross Whitaker)
6. 2011_Summer_Project_Week_Segementation_Reconstruction_Pericardial_Sac (Mohasen)

General Registration

1. Integrate new features into BRAINSFit (Andrey Fedorov, Hans Johnson, Mark Scully)
2. Integration of LANDWARP into interactive registration module (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
3. Registration of mouse brains (Francois Budin)
4. Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer (Petter Risholm, Sandy Wells)

General Atlas

1. Slicer module for building an average population DWI Atlas (Ryan Eckbo, Sylvain Bouix)
2. Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)

General Diffusion Tractography'

1. White matter geometry measures in Slicer 4 (Peter Savadjiev)
2. Re-parameterize fiber tracts for fiber statistics analysis
3. ODF computation through fiber counting (Yinpeng Li, Ipek Oguz, Martin Styner)
4. Nifti Support for Diffusion Tensor Images (Demian)
5. Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
6. Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)

Infrastructure

1. Annotation Module in Slicer4 (Nicole Aucoin, Daniel Haehn)
2. RECIST Slicer4 module (Nicole Aucoin)
3. DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
4. Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
5. DICOM Networking interface for Slicer4 (Steve Pieper, Nicole Aucoin, Noby Hata)
6. Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)
7. FetchMI: Slicer integration with XNAT 1.5 (Misha Milchenko, Wendy Plesniak)

Background

We are pleased to announce the 13th 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. If you would like to learn more about this event, please click here to join our mailing list.

Active preparation begins on Thursday, April 28th 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, 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 20-24, 2011
• Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.
• REGISTRATION: Please register here. Payment must be made by credit card.
• Registration Fee: $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
• Hotel: Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book here or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. All reservations must be made by May 29, 2011 to receive the discounted rate.

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 28, 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 12, all participants to add a one line title of their project to #Projects
4. By 3pm ET on Thursday June 9, 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 16: 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)
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. 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.

Registrants

Do not add your name to this list- it is maintained by the organizers based on your paid registration (see Logistics for link)

1. Peter Anderson , retired
2. Nicole Aucoin , Brigham and Women's Hospital
3. Dominique Belhachemi , University of Pennsylvania
4. Anthony Blumfiled , Radnostics
5. Lucile Bompard , UNC NIRAL
6. Sylvain Bouix , Brigham and Women's Hospital
7. Francois Budin , UNC NIRAL
8. Steve Callahan , University of Utah
9. Joshua Cates , University of Utah
10. Micah Chambers , Laboratory of NeuroImaging
11. Laurent Chauvin , Brigham and Women's Hospital
12. Rivka Colen, Brigham and Women's Hospital
13. Adrian Dalca, MIT
14. Manasi Datar , University of Utah
15. Colin Davey ,
16. Ryan Eckbo , Brigham and Women's Hospital
17. Jan Egger , University Hospital of Marburg
18. Luping Fang , Zhejiang University of Technology, China
19. mahshid farzinfar , UNC
20. Andriy Fedorov , Brigham and Women's Hospital
21. Jean-Christophe Fillion-Robin , Kitware, Inc.
22. Julien Finet , Kitware, Inc.
23. James Fishbaugh , University of Utah
24. Yi Gao , Georgia Tech
25. Greg Gardner , University of Utah
26. Ronen Globinsky , Yale University
27. Maged Goubran , Robarts Research Institute
28. Daniel Haehn , University of Pennsylvania
29. Mike Halle , Brigham and Women's Hospital
30. Marcus Hanwell , Kitware, Inc.
31. Noby Hata , Brigham and Women's Hospital
32. Tamas Heffter , Queen's University
33. Nicholas Herlambang , AZE, Ltd.
34. Vivian Hu, Brigham and Women's Hospital
35. Luis Ibanez , Kitware, Inc.
36. Andrei Irimia , University of California, Los Angeles
37. Firdaus Janoos, Brigham and Women's Hospital
38. Hans Johnson , University of Iowa
39. Ilknur Kabul , Kitware, Inc.
40. Tina Kapur , Brigham and Women's Hospital
41. Peter Karasev , Georgia Institute of Technology
42. Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School
43. Regina Kim , University of Iowa
44. Ivan Kolesov , Ga Tech
45. Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL
46. Dillon Lee , University of Utah
47. Yinpeng Li , UNC-NIRAL
48. Yifei Lou , Georgia Institute of Technology
49. mohsen mahvash , Harvard Medical School (BWH and VA)
50. Katie Mastrogiacomo , Brigham and Women's Hospital
51. Joy Matsui , University of Iowa
52. Dominik Meier , BWH
53. Mikhail Milchenko , Washington University in St. Louis
54. James Miller , GE Research
55. Zach Mullen , Kitware, Inc.
56. Isaiah Norton , Brigham and Women's Hospital
57. Danielle Pace , Kitware, Inc.
58. Beatriz Paniagua , University of North Carolina at Chapel Hill
59. Xenophon Papademetris , Yale University
60. Kedar Patwardhan , GE Global Research
61. Steve Pieper , Isomics, Inc.
62. Csaba Pinter , Queen's University
63. Wendy Plesniak , Brigham and Women's Hospital
64. Kilian Pohl , UPenn
65. Marcel Prastawa , University of Utah
66. Sonia Pujol , Brigham and Women's Hospital
67. Martin Rajchl , Robarts Research Institute
68. Petter Risholm , Brigham and Women's Hospital
69. Peter Savadjiev , Brigham and Women's Hospital
70. Andreas Schuh , University of Pennsylvania
71. Mark Scully , University of Iowa
72. Gregory Sharp , MGH
73. Yundi Shi , UNC-Chapel Hill
74. Nadya Shusharina , MGH
75. Ramesh Sridharan, MIT
76. Hao Su , WPI
77. Suarez Tamekue , Brigham and Women's Hospital
78. Xiaodong Tao , GE Research
79. Junichi Tokuda, Brigham and Women's Hospital
80. Matthew Toews, Brigham and Women's Hospital
81. Clement Vachet , UNC Chapel Hill
82. Antonio Vega , Brigham and Women's Hospital
83. Gopal Veni , University of Utah
84. Bo Wang , University of Utah
85. Demian Wasserman , Brigham and Women's Hospital
86. Sandy Wells , Brigham and Women's Hospital
87. Jason White , Brigham and Women's Hospital
88. Mallika Winsor , Brigham and Women's Hospital
89. Atsushi Yamada , Brigham and Women's Hospital
90. Alexander Yarmarkovich , Isomics
91. Alexander Zaitsev , Brigham and Women's Hospital