2016 Winter Project Week

Summary

The 22nd PROJECT EVENT was held January 4-8, 2016 at MIT. It recorded 77 registered attendees, who worked on 47 projects. These attendees represented 17 academic sites (MIT, Brigham and Women’s Hospital, , École de Technologie Supérieure, (Canada), Massachusetts General Hospital, Queen’s University (Canada), Robarts Research Institute (Canada), University of Michigan, Montreal Neurosurgical Institute, Dana Farber Cancer Institute Boston, DKFZ - Heidelberg Cancer Research Center, JHU, University of Iowa, UNC Chapel Hill, WPI, Childrens National Medical Center Washington DC, Harvard IAIC, University of Colorado at Colorado Springs (UCCS), and 8 companies (Kitware, Isomics Inc, GE, Philips Research, MEVIS, HealthMyne, KnowledgeVis, SINTEF).

Dates: January 4-8, 2016

Location: MIT CSAIL, Cambridge, MA. (Rooms: Kiva, R&D)

REGISTRATION: Register here.

Introduction

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded NCBC program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform 3D Slicer, built using VTK, ITK, CMake, and CDash, and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

Project Week is a semi-annual event which draws 60-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include NAC, NCIGT, QIICR, and OCAIRO.

A summary of all previous Project Events is available here.

This project week is an event endorsed by the MICCAI society.

Please make sure that you are on the na-mic-project-week mailing list

Agenda

Time	Monday, January 4	Tuesday, January 5	Wednesday, January 6	Thursday, January 7	Friday, January 8
	Project Presentations	Work on Projects	Work on Projects	IGT Day	Reporting Day
8:30am		Breakfast	Breakfast	Breakfast	Breakfast
9:00am-12:00pm	10:30am-12pm: [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi) Room: 32-D507.	10:00-11:30am: Breakout Session: Slicer Extensions Birds of a Feather	10:00-11:30am: Breakout Session: Slicer for Medical Robotics Research	8:30-9:30am MR, US, Mass Spect guided Breast Surgery (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) 9:30-10:30am Clinical perspective on Image Guided Neurosurgery (Alexandra Golby) 10:30-11:30am Clinical perspective on Multiparametric MRI (Fiona Fennessy) 11:30am-12pm Drug Delivery to Brain (Jason White)	10:00am-12:00pm: Project Progress Updates Kiva ----------------- 12pm: Tutorial Contest Winner Announcement Kiva
12:00pm-1:00pm	Lunch	Lunch	Lunch	Lunch	Lunch boxes; Adjourn by 1:30pm
1:00-5:30pm	1:00pm-1:05pm: Welcome Kiva ----------------- 1:05-2:30pm: Project Introductions (all Project Leads) Kiva ----------------- 2:45-4:00pm: Breakout Session: Ultrasound Kiva ----------------- 4:00-5:30pm: [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) Room: 32-D507.		1:00-2:30pm: Breakout Session: Diffusion MRI Kiva 3:00-4:30pm: Breakout Session: QIICR Tools	1:00-3:00pm: Breakout Session:What's Planned for Slicer Core Kiva 3:30-5:00pm: Breakout Session: 2016 Tutorial Contest Review (Kiva)	AMIGO Tour
5:30pm	Adjourn for the day	Adjourn for the day	Adjourn for the day	Adjourn for the day (Optional) Dinner on Thursday Night

Calendar

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

Projects

• Use this Updated Template for project pages

IGT

• 3D Slicer + ROS Integration (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
• External Beam Radiotherapy Planning (Greg Sharp, others)
• CryoPlanning Module in Slicer (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
• Tracked Ultrasound Standardization (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin, Thomas Kirchner, Janek Groehl)
• Integration of CustusX with PLUS on BK System (Christian A, Andras Lasso, Adam Rankin)
• Integration of Plus and MITK (Thomas Kirchner, Janek Groehl)
• Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
• Improvement of PLUS communication with Slicer (skip, see US standardization) (Adam Rankin)
• Prostate motion tracking and navigation in Slicer (Christian Herz, Andrey Fedorov, Andras Lasso)
• Measuring Anatomic Factors for Extraventricular Drain Placement (Kirby Vosburgh, P. Jason White)
• Localized GABA delivery via BBB disruption (Nick Todd)
• Sequences extension support for 3D+t NRRD (Adam Rankin)

Tractography

• Tractography Format Interoperability (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
• Slicer Diffusion MR / tractography workflow documentation (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
• Tractography Analysis Module Development and Testing (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

Image Analysis

• Interactive patch-based segmentation for congenital heart disease (Danielle Pace, Adrian Dalca, Polina Golland)
• Image Restoration via Patch GMMs (Adrian Dalca, Katie Bouman, Polina Golland)
• Patch Based Discrete Registration for Difficult Images (Adrian Dalca, Andreea Bobu, Polina Golland)
• Spherical Wavelet Shape Analysis (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
• Digital Pathology Nuclear Segmentation (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
• Moving beyond SlicerCMF and Future Projects (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
• Chest Imaging Platform: COPD and Other Pulmonary Diseases (Raúl San José, Jorge Onieva, James Ross)
• Nipype Workflows for the Chest Imaging Platform (James Ross, Raúl San José)
• Cluster-Driven Segmentation of Lung Nodules (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
• Batch Clinical Image Analysis (Sandy Wells, Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Randy Gollub)
• Slicer OpenCV Extension (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
• Interactive 4D Segmentation Module (Ethan Ulrich, Andrey Fedorov, Andras Lasso)
• Dynamic Susceptibility Contrast (DSC) MRI Analysis (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

• Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms (Miaomiao Zhang, Polina Golland)

Infrastructure

• Upgrade the NAMIC + Slicer Web Infrastructure (Mike Halle, JC)
• Common Data Structure for CMF modules in Slicer (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
• Statistical Shape Modeling in Slicer: OA Index (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
• CommonGL (Steve Pieper, Jim Miller)
• Running CLI Modules in MeVisLab Asynchronously (Hans Meine)
• Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab (Hans Meine, Steve Pieper)
• Kibana Dashboard for Browsing All Available CLI Modules (Hans Meine, JC?)
• Editor Widget using Segmentations (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper)
• Terminology Editor (Nicole Aucoin, Csaba Pinter, Andrey Fedorov)
• Integration of DICOM Segmentation Image Storage with Segmentations Module (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
• Integration of Anaconda Python in Slicer (JC, Raúl San José, Jorge Onieva, Slicer Community?)
• Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines (Raúl San José, Jorge Onieva)
• Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow (Raúl San José, Jorge Onieva)
• Integration of Anaconda Python in Slicer (JC, Raúl San José, Jorge Onieva, Slicer Community?)
• AIM for Interoperability (Hans Meine, Andrey Fedorov, ??)
• Developing support for Enhanced MR in Slicer (Michael Onken, Andrey Fedorov)
• Improve CLI robustness and testing (Johan Andruejol)
• Exploring a collaboration in visualization (SK Semwal)

Logistics

• Dates: January 4-8, 2016
• Location: MIT, Kiva Conference room; 4th floor of Building 32.
• REGISTRATION: Register here. 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 here

Registrants

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this registration site.

1. Nathalie Agar Brigham and Women's Hospital
2. Peter Anderson Retired
3. Johan Andruejol Kitware, Inc.
4. Christian Askeland SINTEF
5. Nicole Aucoin Brigham and Women's Hospital
6. Daniel Blezek Isomics, Inc.
7. Erich Bremer Stony Brook University
8. Katharine Carter Brigham and Women's Hospital
9. Lucia Cevidanes University of Michigan
10. Ye Cheng Brigham and Women's Hospital
11. Xiao Da Massachusetts General Hospital
12. Adrian Dalca Massachusetts Institute of Technology
13. Valentin Demeusy Brigham and Women's Hospital
14. Sean Doyle Massachusetts General Hospital
15. Simon Drouin Montreal Neurological Institute
16. Andriy Fedorov Brigham and Women's Hospital
17. Jean-Christophe Fillion-Robin Kitware, Inc.
18. Tobias Frank Leibniz Universität Hannover
19. Sarah Frisken Brigham and Women's Hospital
20. Yi Gao Stony Brook University
21. David Gering HealthMyne
22. Daniel Glazer Brigham and Women's Hospital
23. Polina Golland Massachusetts Institute of Technology
24. Randy Gollub Massachusetts General Hospital
25. Janek Groehl German Cancer Research Center
26. Michael Halle Brigham and Women's Hospital
27. Nobuhiko Hata Brigham and Women's Hospital
28. Christian Herz Brigham and Women's Hospital
29. Jayender Jagadeesan Brigham and Women's Hospital
30. Ameet Jain Phillips Research
31. Pegah Kahali Brigham and Women's Hospital
32. Jayashree Kalpathy-Cramer Massachusetts General Hospital
33. Tina Kapur Brigham and Women's Hospital
34. Ron Kikinis Brigham and Women's Hospital
35. Thomas Kirchner German Cancer Research Center
36. Axel Krieger Children's National Medical Center
37. Andras Lasso Queen's University
38. Simon Leoard Johns Hopkins University
39. Curtis Lisle KnowledgeVis, LLC
40. Melissa Mallory Brigham and Women's Hospital
41. Katie Mastrogiacomo Brigham and Women's Hospital
42. Hans Meine Fraunhofer MEVIS, Bremen
43. James Miller General Electric
44. Vivek Narayan Dana Farber Cancer Institute
45. Isaiah Norton Brigham and Women's Hospital
46. Lauren O'Donnell Brigham and Women's Hospital
47. Jorge Onieva Brigham and Women's Hospital
48. Michael Onken Open Connections
49. Danielle Pace Massachusetts Institute of Technology
50. Beatriz Paniagua University of North Carolina
51. Laura Pascal University of Michigan
52. Nirav Patel Worcester Polytechnic Institute
53. Steve Pieper Isomics, Inc.
54. Csaba Pinter Queen's University
55. Stuart Pomerantz Massachusetts General Hospital
56. Sonia Pujol Brigham and Women's Hospital
57. Adam Rankin Robarts Research Institute
58. Kallirroi Retzepi Massachusetts General Hospital
59. James Ross Brigham and Women's Hospital
60. Raul San Jose Estepar Brigham and Women's Hospital
61. Sudhanshu Semwal University of Colorado, Colorado Springs
62. Gregory Sharp Massachusetts General Hospital
63. Utsav Soni Brigham and Women's Hospital
64. Kyle Sunderland Queen's University
65. Nick Todd Brigham and Women's Hospital
66. Matthew Toews Ecole de Technologie Superieure
67. Junichi Tokuda Brigham and Women's Hospital
68. Ethan Ulrich University of Iowa
69. Prashin Unadkat Brigham and Women's Hospital
70. Jean-Baptiste Vimort University of Michigan
71. Kirby Vosburgh Brigham and Women's Hospital
72. Carl-Fredrik Westin Brigham and Women's Hospital
73. Jason White Brigham and Women's Hospital
74. Kelli Xu Massachusetts Institute of Technology
75. Terry Yoo National Library of Medicine
76. Fan Zhang Brigham and Women's Hospital
77. Miaomiao Zhang Massachusetts Institute of Technology# Nathalie Agar :: Brigham and Women's Hospital
78. Peter Anderson :: Retired
79. Johan Andruejol :: Kitware, Inc.
80. Christian Askeland :: SINTEF
81. Nicole Aucoin :: Brigham and Women's Hospital
82. Daniel Blezek :: Isomics, Inc.
83. Erich Bremer :: Stony Brook University
84. Katharine Carter :: Brigham and Women's Hospital
85. Lucia Cevidanes :: University of Michigan
86. Ye Cheng :: Brigham and Women's Hospital
87. Xiao Da :: Massachusetts General Hospital
88. Adrian Dalca :: Massachusetts Institute of Technology
89. Valentin Demeusy :: Brigham and Women's Hospital
90. Sean Doyle :: Massachusetts General Hospital
91. Simon Drouin :: Montreal Neurological Institute
92. Andriy Fedorov :: Brigham and Women's Hospital
93. Jean-Christophe Fillion-Robin :: Kitware, Inc.
94. Tobias Frank :: Leibniz Universität Hannover
95. Sarah Frisken :: Brigham and Women's Hospital
96. Yi Gao :: Stony Brook University
97. David Gering :: HealthMyne
98. Daniel Glazer :: Brigham and Women's Hospital
99. Polina Golland :: Massachusetts Institute of Technology
100. Randy Gollub :: Massachusetts General Hospital
101. Janek Groehl :: German Cancer Research Center
102. Michael Halle :: Brigham and Women's Hospital
103. Nobuhiko Hata :: Brigham and Women's Hospital
104. Christian Herz :: Brigham and Women's Hospital
105. Jayender Jagadeesan :: Brigham and Women's Hospital
106. Ameet Jain :: Phillips Research
107. Pegah Kahali :: Brigham and Women's Hospital
108. Jayashree Kalpathy-Cramer :: Massachusetts General Hospital
109. Tina Kapur :: Brigham and Women's Hospital
110. Ron Kikinis :: Brigham and Women's Hospital
111. Thomas Kirchner :: German Cancer Research Center
112. Axel Krieger :: Children's National Medical Center
113. Andras Lasso :: Queen's University
114. Simon Leoard :: Johns Hopkins University
115. Curtis Lisle :: KnowledgeVis, LLC
116. Melissa Mallory :: Brigham and Women's Hospital
117. Katie Mastrogiacomo :: Brigham and Women's Hospital
118. Hans Meine :: Fraunhofer MEVIS, Bremen
119. James Miller :: General Electric
120. Vivek Narayan :: Dana Farber Cancer Institute
121. Isaiah Norton :: Brigham and Women's Hospital
122. Lauren O'Donnell :: Brigham and Women's Hospital
123. Jorge Onieva :: Brigham and Women's Hospital
124. Michael Onken :: Open Connections
125. Danielle Pace :: Massachusetts Institute of Technology
126. Beatriz Paniagua :: University of North Carolina
127. Laura Pascal :: University of Michigan
128. Nirav Patel :: Worcester Polytechnic Institute
129. Steve Pieper :: Isomics, Inc.
130. Csaba Pinter :: Queen's University
131. Stuart Pomerantz :: Massachusetts General Hospital
132. Sonia Pujol :: Brigham and Women's Hospital
133. Adam Rankin :: Robarts Research Institute
134. Kallirroi Retzepi :: Massachusetts General Hospital
135. James Ross :: Brigham and Women's Hospital
136. Raul San Jose Estepar :: Brigham and Women's Hospital
137. Sudhanshu Semwal :: University of Colorado, Colorado Springs
138. Gregory Sharp :: Massachusetts General Hospital
139. Utsav Soni :: Brigham and Women's Hospital
140. Kyle Sunderland :: Queen's University
141. Nick Todd :: Brigham and Women's Hospital
142. Matthew Toews :: Ecole de Technologie Superieure
143. Junichi Tokuda :: Brigham and Women's Hospital
144. Ethan Ulrich :: University of Iowa
145. Prashin Unadkat :: Brigham and Women's Hospital
146. Jean-Baptiste Vimort :: University of Michigan
147. Kirby Vosburgh :: Brigham and Women's Hospital
148. Carl-Fredrik Westin :: Brigham and Women's Hospital
149. Jason White :: Brigham and Women's Hospital
150. Kelli Xu :: Massachusetts Institute of Technology
151. Terry Yoo :: National Library of Medicine
152. Fan Zhang :: Brigham and Women's Hospital
153. Miaomiao Zhang :: Massachusetts Institute of Technology