2013 Summer Project Week

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Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

Agenda

Time	Monday, June 17	Tuesday, June 18	Wednesday, June 19	Thursday, June 20	Friday, June 21
	Project Presentations	NA-MIC Update Day		IGT and RT Day	Reporting Day
8:30am		Breakfast	Breakfast	Breakfast	Breakfast
9am-12pm		10-11am Slicer4 Python Modules, Testing, Q&A (Steve Pieper) Grier Room (Left)	9:30-11pm: Breakout Session: Slicer and SimpleITK (Hans Johnson, Brad Lowekamp) 32-D507	10am-12pm: Breakout Session: Image-Guided Therapy (Tina Kapur) 32-D407	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 ---------------------------------------- 3:30-4:30pm Slicer4 Extensions (Jean-Christophe Fillion-Robin) Grier Room (Left)	1-3pm: NA-MIC Renewal PIs Closed Door Session with Ron 32-D407 ---------------------------------------- 3-4pm: Tutorial Contest Presentations Grier Rooms	12:45-1pm: Tutorial Contest Winner Announcement Grier Rooms	---------------------------------------- 3-5:30pm: Breakout Session: Radiation Therapy (Greg, Csaba) 32-D407
5:30pm	Adjourn for the day	Adjourn for the day	Adjourn for the day	Adjourn for the day

Projects

Please use this template to create wiki pages for your project. Then link the page here with a list of key personnel.

Huntington's Disease

• Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend (Dave)
• DWIConvert (Dave, Kent Williams)
• Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data (Hans, Demian)
• Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation (Hans)
• Enhance and update SPL atlas (Dave, Hans)
• Linear Mixed-effects shape model to explore Huntington's Disease Data (Manasi, Dave, Hans, Ross)

Traumatic Brain Injury

• Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
• Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
• Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
• A Portable Ultrasound Device for Intracranial Hemorrhage Detection (Jason White, Vicki Noble, Kirby Vosburgh)

Atrial Fibrillation and Cardiac Image Analysis

• Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
• Cardiac MRI Toolkit Documentation Project (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
• LA model visualization (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
• Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
• Medical Volume Segmentation Using Sobolev Active Contours (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
• Fibrosis distribution analysis (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
• Left Ventricle Motion Analysis using Tagged MRI (Yang Yu, Shaoting Zhang, Dimitris Metaxas)

Radiation Therapy

• Landmark Registration (Steve, Nadya, Greg, Paolo, Erol)
• SlicerRT: Dicom-RT Export (Greg Sharp, Kevin Wang, Csaba Pinter)
• Proton dose calculation (Greg Sharp, Kevin Wang, Maxime Desplanques)
• Deformable registration validation toolkit (Greg Sharp, Kevin Wang, Andrey Fedorov, anyone else?)
• Analysis of different atlas-based segmentation techniques for parotid glands (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
• Deformable transform handling in Transforms module (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
• Cranio-Maxillofacial Registration (Vinicius Boen)

IGT and Device Integration with Slicer

• Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
• Interface for the integration of a KUKA robot using OpnIGTLink (Sebastian Tauscher, Nobuhiko Hata)

• SlicerIGT extension (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
• Ultrasound Calibration (Matthew Toews, Daniel Kostro, William Wells, Steven Aylward, Isaiah Norton, Tamas Ungi)
• Application of Statistical Shape Modeling to Robot Assisted Spine Surgery (Marine Clogenson)
• Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery (Luiz Murta)
• Is Neurosurgical Rigid Registration Really Rigid? (Athena)
• Liver Trajectory Management (Laurent Chauvin, Junichi Tokuda)
• 4D Ultrasound (Laurent Chauvin, Junichi Tokuda)
• Individualized Neuroimaging Content Analysis using 3D Slicer (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
• Computer Assisted Reconstruction of Complex Bone Fractures (Karl Fritscher, Peter Karasev, Ron Kikinis)
• Perk Tutor Extension (Matthew Holden, Tamas Ungi)
• Tract Atlas and Clustering (Lauren O'Donnell)

Informatics

• 3D Slicer based Biomedical image computing teaching modules (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
• Robot Control (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
• XNAT 3D Viewer (Amanda Hartung, Steve Pieper, Daniel Haehn)

Infrastructure

• Markups/Annotations rewrite (Nicole Aucoin, Ron Kikinis)
• Patient hierarchy (Csaba Pinter, Andras Lasso, Steve Pieper)
• CLI Improvements (hierarchy nodes, related nodes, roles) (Andras Lasso, Csaba Pinter, Jc, Steve, Jim, ?)
• Sample Data (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
• Plastimatch in NiPype (Paolo, Dave, Hans)
• Optimizing start time of slicer (Jc, Steve)
• Common resampling and conversion utility functions in Slicer (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
• Integrating CTK CLI modules into MeVisLab (Hans Meine, Steve, Jc)
• Web-based anatomical teaching framework (Daniel Haehn, Steve Pieper, Rudolph Pienaar, Lilla Zollei, Nathaniel Reynolds)

Brain & Spine Segmentation

• Multi-Atlas-Based Multi-Image Segmentation for Brain MR Images (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)
• Spine Segmentation & Osteoporosis Detection In CT Imaging Studies (Anthony Blumfield, Ron Kikinis)

Chronic Obstructive Pulmonary Disease

• Porting Airway Inspector to Slicer 4 (Raul San Jose, Demian Wassermann, Rola Harmouche)
• Airway Inspector: Slicer Extension and MRML Infrastructure (Demian Wassermann, Raul San Jose, Rola Harmouche)
• Integration of Nipype with CLI modules in the Chest Imaging Platform Library (Rola Harmouche,Demian Wassermann, Raul San Jose)

Background

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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 25th 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, CIMIT, and OCAIRO. 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 17-21, 2013.
• Location: Stata Center / RLE MIT.
• REGISTRATION: http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
• Registration Fee: $300.
• Hotel: Similar to previous years, no rooms have been blocked in a particular hotel.
• Room sharing: If interested, add your name to the list before May 27th. See here

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 projects in a their weekly teleconferences. 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 8, all participants to add a one line title of their project to #Projects
4. By 3pm ET on Thursday June 6, 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 13: Create a directory for each project on the NAMIC Sandbox (Matt)
   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. Where possible, 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. (Matt)
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. See the Developer Section of slicer.org for information.
   2. Projects to develop extension modules should be built against the latest Slicer4 trunk.

Registrants

Do not add your name to this list - it is maintained by the organizers based on your paid registration. (Please click here to register.)

1. Charles Anderson, BWH, canderson26@partners.org
2. Peter Anderson, retired, traneus@verizon.net
3. Nicole Aucoin, BWH, nicole@bwh.harvard.edu
4. Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
5. Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
6. Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
7. Vinicius Boen, Univ Michigan, vboen@umich.edu
8. Matthew Brennan, MIT, brennanm@mit.edu
9. Francois Budin, NIRAL-UNC, fbudin@unc.edu
10. Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
11. Josh Cates, Univ UT, cates@sci.utah.edu
12. Micah Chambers, UCLA, micahcc@ucla.edu
13. Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
14. Adrian Dalca, MIT, adalca@MIT.EDU
15. Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
16. Sneha Durgapal, BWH, durgapalsneha@gmail.com
17. Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
18. Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
19. Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
20. Gregory Fischer, WPI, gfischer@wpi.edu
21. Karl Fritscher, MGH, kfritscher@gmail.com
22. Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
23. Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
24. Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
25. Rola Harmouche, BWH, rharmo@bwh.harvard.edu
26. Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
27. Nobuhiko Hata, BWH, hata@bwh.harvard.edu
28. Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
29. Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
30. Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
31. Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
32. Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
33. Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
34. Alex Kikinis, BWH, alexkikinis@gmail.com
35. Ron Kikinis, HMS, kikinis@bwh.harvard.edu
36. Daniel Kostro, BWH, dkostro@bwh.harvard.edu
37. Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
38. Rui Li, GE Global Research, li.rui@ge.com
39. Xu Li, BWH, lixu0103@gmail.com
40. Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
41. William Lorensen, Bill's Basement, bill.lorensen@gmail.com
42. Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
43. Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
44. Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
45. Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
46. Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
47. Jim Miller, GE Global Research, millerjv@ge.com
48. Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
49. Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
50. Isaiah Norton, BWH, inorton@bwh.harvard.edu
51. Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
52. Dirk Padfield, GE Global Research, padfield@research.ge.com
53. Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
54. Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
55. Steve Pieper, Isomics Inc, pieper@isomics.com
56. Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
57. Sonia Pujol, HMS, spujol@bwh.harvard.edu
58. Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
59. Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
60. Raul San Jose, BWH, rjosest@bwh.harvard.edu
61. Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
62. Greg Sharp, MGH, gcsharp@partners.org
63. Nadya Shusharina, MGH, nshusharina@partners.org
64. Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
65. Clare Tempany, BWH, ctempanyafdhal@partners.org
66. Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
67. Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
68. Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
69. Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
70. Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
71. Christian Wachinger, MIT, wachinge@mit.edu
72. Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
73. Demian Wassermann, BWH, demian@bwh.harvard.edu
74. David Welch, Univ Iowa, david-welch@uiowa.edu
75. William Wells, BWH/HMS, sw@bwh.harvard.edu
76. Phillip White, BWH/HMS, white@bwh.harvard.edu
77. Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
78. Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
79. Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
80. Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu