2015 Winter Project Week

Welcome to the 20th Project week page!

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. The next events in this ongoing series will occur in Salt Lake City, Utah in January of 2015, followed by one in Boston, MA in June of 2015.

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

Logistics

• Dates: January 5-9, 2015.
• Location: Salt Lake City, Utah
• REGISTRATION: Please click here to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
• Venue: The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking here. The room rate for the meeting is 149 USD per night.

Agenda

Time	Monday, January 5	Tuesday, January 6	Wednesday, January 7	Thursday, January 8	Friday, January 9
	Project Activities (Olympus B)	Project Activities (Olympus B)	Project Activities (Olympus B)	Project Activities (Olympus B)	Project Activities (Olympus B)
7:30-8:00		Breakfast (Olympus A)	Breakfast (Olympus A)	Breakfast (Olympus A)	Breakfast (Olympus A)
8:00-10:00		9-10am: Breakout Session:COPD (Raul San Jose) (Amethyst 1)	9-10am: Breakout Session:QIICR and DICOM (Andrey Fedorov, Steve Pieper) (Amethyst 1)	Project Activities (Olympus B)	9am: Project Presentations (Olympus B)
10:00-10:30		Coffee (General area)	Coffee (General area)	Coffee (General area)	Coffee (General area)
10:30-12:00				Project Activities (Olympus B)
12:00-1:00	Lunch (Olympus A)	Lunch (Olympus A)	Lunch (Olympus A)	Lunch (Olympus A)	Boxed Lunch and Adjourn (Olympus A)
1:00-3:00	A tribute to Ferenc Jolesz Project Presentations (Olympus B)		(Olympus B)
3:00-3:30	Coffee (General area)	Coffee (General area)	Coffee (General area)	Coffee (General area)
3:00-5:00		3:15-4pm: Breakout Session: Segmentations (Amethyst 1)		Project Activities (Olympus B)
05:00-07:00				6:00 Optional: Beer at Murphy's (like last year)

Projects

• Template for project pages

Image-Guided Therapy

• Image-based Needle Detection from MRI (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
• Review of data from recent AMIGO US/MR neurosurgery (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
• Tracked ultrasound benchtop experimental system for neurosurgery (Steve Pieper, Jim Miller)
• Workflow for percutaneous needle place (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
• Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
• Prostate segmentation and biopsy (Peter Behringer, Andriy Fedorov)
• Needle Finder Tutorial (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
• A new modified Frechet distance for measuring the similarity between fiber tracts (Ruizhi Liao, Lauren O'Donnell)
• Performance of UKF tractography in edema (Ruizhi Liao, Lauren O'Donnell)

Huntington's Disease

• PREDICT-HD Longitudinal Shape Analysis (Regina EY Kim, James Fishbaugh, Hans Johnson)

COPD

• SlicerCIP Extension (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
• Lung nodule sizing tool (Raul San Jose)
• Density Inspector (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
• Pulmonary Artery/Aorta measuring tool (Jorge Onieva, Rola Harmouche, German Gonzalez)
• Picasa Snap: tagging your favorite slicer snapshots (Jorge Onieva)
• Feature Extraction on ROIs based on Particles (Raul San Jose, James Ross)
• CIP analysis pipelines in Nipype (Rola Harmouche, James Ross, Alex Yarmakovich)
• Supervised fissure enhancement (James Ross, German Gonzalez, Rola Harmouche)
• Organ detection with OpenCV (German Gonzalez, James Ross, Raul San Jose)

QIICR

• Segmentation object and enhanced multiframe object IO in DCMTK and Slicer (Steve, Andrey, Michael)
• T1 mapping for variable flip angle (Artem, Xiao, Andrey)
• Representation of Iowa QIN data using DICOM (Andrey, Christian Bauer, Steve Pieper)
• Whole Body PET/CT Reference Region segmentation (Christian Bauer)
• Bolus Arrival Time (BAT) Estimation in PK Modelling (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
• DICOM Module Improvements (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
• Slice View Annotations (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

Feature Extraction

• 3D SIFT Feature Visualization in Slicer (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)

Slicer4 Extensions

• PET Tumor Segmentation (Christian Bauer)

TMJOA RO1 - Collaboration with NAMIC

• Improved model display (Francois Boudin, Steve Pieper)

Infrastructure

• Micro and Macro Scale in Slicer (Nicole Aucoin, Bradley Lowenkamp)
• Markups (Nicole Aucoin)
• Segmentations (Csaba Pinter, ?)
• DICOM references (Andrey Fedorov, Csaba Pinter, Steve Pieper)
• Open Atlas (Bill Lorensen)
• automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the ctk-cli-indexer (JC, maybe Hans Meine remotely)

Registrants

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

1. Nicole Aucoin ; Brigham and Women's Hospital
2. Bamshad Azizi Koutenaei ; Children's National Health System
3. Christian Bauer ; University of Iowa
4. Peter Behringer ; Brigham and Women's Hospital
5. Francois Budin ; UNC
6. Byunghyun Cho; Koh Young Technology Inc.
7. Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
8. Andriy Fedorov ; Brigham and Women's Hospital
9. JC Fillion-Robin; Kitware, Inc.
10. James Fishbaugh; University of Utah
11. Yang Gao ; Brigham and Women's Hospital
12. German Gonzalez ; Brigham and Women's Hospital
13. Rola Harmouche ; Brigham and Women's Hospital
14. Hans Johnson ; University of Iowa
15. Tina Kapur ; Brigham and Women's Hospital
16. Ron Kikinis ; Brigham and Women's Hospital
17. Eun Young Regina Kim ; University of Iowa
18. Sangyong Kim, Kohyoung Techonology
19. Franklin King, Queen's University and Brigham and Women's Hospital
20. Ming Li ; Brigham and Women's Hospital
21. Ye Li ; Brigham and Women's Hospital
22. Ruizhi Liao; Brigham and Women's Hospital
23. Julia Lopinto ; The University of Michigan
24. Bill Lorensen; Noware
25. Bradley Lowenkamp; Medical Science Computing
26. Lucie Macron ; The University of Michigan
27. Artem Mamonov ; MGH Martinos
28. Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
29. Alireza Mehrtash ; Brigham and Women's Hospital
30. James Miller ; GE Global Research
31. Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
32. Jorge Onieva ; Brigham and Women's Hospital
33. Guillaume Pernelle; Imperial College London
34. Steve Pieper ; Isomics Inc.
35. Csaba Pinter ; Queens University
36. Adam Rankin ; Robarts Research Institute
37. James Ross ; Brigham and Women's Hospital
38. Raul San Jose ; Brigham and Women's Hospital
39. Anuja Sharma; University of Utah
40. Matthew Toews; Brigham and Women's Hospital
41. Junichi Tokuda ; Brigham and Women's Hospital
42. Bo Wang ; SCI Institute University of Utah
43. William Wells; Brigham and Women's Hospital
44. Alexander Yarmarkovich; Brigham and Women's Hospital