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 80-120 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. Polina Golland, MIT
2. Ron Kikinis, BWH
3. Nicole Aucoin, BWH/SPL
4. Peter Anderson
5. Daniel Blezek, Isomics, Inc.
6. Lucia Cevidanes, University of Michigan
7. Adrian Dalca, MIT
8. Simon Drouin, Montreal Neurological Institute
9. Janek Groehl, German Cancer Research Center
10. Tina Kapur, BWH/HMS
11. Thomas Kirchner, German Cancer Research Center
12. Hans Meine, University of Bremen/MEVIS
13. Vivek Narayan, Dana Farber Cancer Institute
14. Danielle Pace, MIT
15. Laura Pascal, University of Michigan
16. Steve Pieper, Isomics, Inc.
17. Csaba Pinter, Queen's University
18. Gregory Sharp, MGH
19. James Miller, GE Research
20. Kyle Sunderland, Queen's University
21. Ethan Ulrich, University of Iowa
22. Jean-Baptiste Vimort, University of Michigan
23. Miaomiao Zhang, MIT
24. Beatriz Paniagua, University of North Carolina at Chapel Hill
25. Sonia Pujol, BWH
26. Junichi Tokuda, BWH
27. Katie Mastrogiacomo, BWH
28. Niravkumar Patel, Worcester Polytechnic Institute
29. Michael Onken, Open Connections (Germany)
30. Erich Bremer, Stony Brook University
31. Xiao Da, MGH
32. Tobias Frank, Leibniz Universität Hannover
33. Kirby Vosburgh, BWH
34. P. Jason White, BWH
35. Lauren O'Donnell, BWH
36. Pegah Kahali, BWH
37. Fan Zhang, BWH
38. Adam Rankin, Robarts Research Institute
39. Simon Leoard, Johns Hopkins University
40. David Gering, HealthMyne
41. Johan Andruejol, Kitware
42. Jean-Christophe Fillion-Robin, Kitware
43. Kelli Xu, MIT
44. Christian Askeland, SINTEF
45. Katharine Carter, BWH
46. Nick Todd, BWH
47. Ye Cheng, BWH
48. Andriy Fedorov, BWH/HMS
49. Sudhanshu Semwal, UCCS Professor
50. Michael Halle, BWH
51. Kallirroi Retzepi, MGH
52. Jayender Jagadeesan, BWH
53. Nathalie Agar, BWH
54. Curtis Lisle, KnowledgeVis, LLC
55. Andras Lasso, PerkLab, Queen's University
56. Sarah Frisken, BWH
57. Yi Gao, Stony Brook University
58. Christian Herz, BWH
59. Prashin Unadkat, SPL/BWH
60. Jorge Onieva, BWH
61. James Ross, BWH
62. Raul SanJose, BWH
63. Jayashree Kalpathy-Cramer, MGH/HMS
64. Daniel Glazer, BWH
65. Valentin Demeusy, SPL Intern
66. Ameet Jain, Phillips Research
67. Utsav Soni, BWH
68. Matthew Toews, Ecole de Technologie Superieure
69. Isaiah Norton, BWH
70. Sean Doyle, MGH
71. Stuart Pomerantz, MGH
72. Randy Gollub, MGH
73. Melissa Mallory, BWH
74. Axel Krieger, Children's National Medical Center
75. Nobuhiko Hata, BWH
76. Carl-Fredrik Westin, BWH/HMS
77. Terry Yoo, NLM-NIH/Harvard IACS