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) |
| 1:00-3:00l | 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
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)
TBI
Stroke
Cardiac
Lung
- Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Jim Miller)
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)
Head and Neck Cancer / Radiotherapy
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)
Additional Brain Image Analysis
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.
- Nicole Aucoin ; Brigham and Women's Hospital
- Bamshad Azizi Koutenaei ; Children's National Health System
- Christian Bauer ; University of Iowa
- Peter Behringer ; Brigham and Women's Hospital
- Francois Budin ; UNC
- Byunghyun Cho; Koh Young Technology Inc.
- Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
- Andriy Fedorov ; Brigham and Women's Hospital
- JC Fillion-Robin; Kitware, Inc.
- James Fishbaugh; University of Utah
- Yang Gao ; Brigham and Women's Hospital
- German Gonzalez ; Brigham and Women's Hospital
- Rola Harmouche ; Brigham and Women's Hospital
- Hans Johnson ; University of Iowa
- Tina Kapur ; Brigham and Women's Hospital
- Ron Kikinis ; Brigham and Women's Hospital
- Eun Young Regina Kim ; University of Iowa
- Sangyong Kim, Kohyoung Techonology
- Franklin King, Queen's University and Brigham and Women's Hospital
- Ming Li ; Brigham and Women's Hospital
- Ye Li ; Brigham and Women's Hospital
- Ruizhi Liao; Brigham and Women's Hospital
- Julia Lopinto ; The University of Michigan
- Bill Lorensen; Noware
- Bradley Lowenkamp; Medical Science Computing
- Lucie Macron ; The University of Michigan
- Artem Mamonov ; MGH Martinos
- Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
- Alireza Mehrtash ; Brigham and Women's Hospital
- James Miller ; GE Global Research
- Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
- Jorge Onieva ; Brigham and Women's Hospital
- Guillaume Pernelle; Imperial College London
- Steve Pieper ; Isomics Inc.
- Csaba Pinter ; Queens University
- Adam Rankin ; Robarts Research Institute
- James Ross ; Brigham and Women's Hospital
- Raul San Jose ; Brigham and Women's Hospital
- Anuja Sharma; University of Utah
- Matthew Toews; Brigham and Women's Hospital
- Junichi Tokuda ; Brigham and Women's Hospital
- Bo Wang ; SCI Institute University of Utah
- William Wells; Brigham and Women's Hospital
- Alexander Yarmarkovich; Brigham and Women's Hospital
