Robarts Training Session

Course Description

The NA-MIC Kit is a free open-source software platform for biomedical researchers and algorithm developers working in the fields of medical image analysis, visualization and image-guided therapy. This NA-MIC Kit Software Workshop is a two-day interactive course allowing scientists and trainees to learn about the NA-MIC Kit, including 3D Slicer, The Visualization Toolkit (VTK), The Insight Toolkit (ITK) and CMake. Participants will receive hands-on training in the end-user applications and software libraries, making this course applicable to both clinical users interested in using the software for their image analysis and visualization tasks, and software developers considering using the NA-MIC Kit as their software platform.

Pictures from the Event

• 

  Introduction by Terry

• 

  Steve teaching

• 

  Guitar anyone?

• 

  Hard at work

• 

  Some unexpected visitors

• 

  The group

Course Faculty

• Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
• Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
• Kathryn Hayes, M.S.E., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
• Danielle Pace, B.CmpH, Robarts Research Institute and The University of Western Ontario
• Steve Pieper, Ph.D., Isomics Inc.
• Junichi Tokuda, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School

Local Hosts

• Aaron Fenster, Ph.D., Director, Ontario Institute for Cancer Research Imaging Pipeline Platform
• Terry Peters, Ph.D., Robarts Research Institute and The University of Western Ontario

Logistics

• Dates: Wednesday, October 15 - Thursday, October 16, 2008
• Venue: Room 100, London Hall, 1421 Western Road, The University of Western Ontario, London, Ontario, Canada
• The University of Western Ontario on Google Maps
• Driving directions to The University of Western Ontario
• Map of campus
• Parking map
  • Parking is available in either the "Huron Flats Lot" or "Althouse Lot" and is $4.00 (coin) per entry. Please note that the front desk of London Hall does not have change available for parking.
  • There is a pathway leading from the Huron Flats parking lot to London Hall. Althouse Lot is located behind Perth Hall on the opposite side of Western Road to London Hall.

Registration

Registration for this event is now closed.

List of participants

• In order to maintain a close participant-faculty ratio, space is extremely limited.
• Please register with Sandra Noble-Topham via email (snt [at] imaging.robarts.ca) by Friday, September 26, 2008. Please include your:
  • Full Name
  • Email address
  • Telephone number
  • Lab supervisor
  • University Name
  • Current status (Masters Candidate, PhD candidate, undergraduate, staff member or principal investigator)
  • Any dietary restrictions

Course Requirements

• To participate in this interactive workshop, attendees are required to bring their own laptop with the tutorial software and sample datasets pre-installed.

Sponsors

• 

  National Alliance for Medical Image Computing

• 

  Ontario Institute for Cancer Research

• 

  Imaging Research Laboratories, Robarts Research Institute

• 

  Neuroimage Analysis Center

• 

  National Center for Image Guided therapy

• 

  CIMIT

Agenda

Arrival: Tuesday, October 14

Time	Wednesday, October 15	Thursday, October 16
Breakfast	Breakfast (8:00-8:30)	Breakfast (8:00-8:30)
Morning Session 1	08:30-08:45 Welcome (Fenster, Peters, Pieper) 08:45-9:00 Overview of NA-MIC (Slides by Kikinis) (Hata) 09:00-10:00 Engineering methodology (Hata) Extreme programming What is a software engineering methodology, do I need one? The components of the NA-MIC kit software engineering tools: ITK, VTK, CMAKE, CTEST, CPACK, Dashboards Extreme Programming, CMake, CPack (Slides by Barre) CTest and Dashboard (Slides by Jomier) ITK (Jomier) (Slides by Jomier) VTK (Slides by Barre) KWWidgets (Slides by Barre) Batchmake (Slides by Jomier)	8:30 - 9:15 IGT Workflows using neurosurgical planning as an example (Pace) Diffusion Tensor (Part 2) 9:15 - 10:00 MR-Guided Prostate Interventions (Pace)
Coffee Break	Coffee Break (10:00-10:30)	Coffee Break (10:00-10:30)
Morning Session 2	10:30 - 11:00 XNAT (Pieper) (Slides) 11:00 - 12:30 Slicer3 (Pieper) Overview and Features (Slides) Architecture and Implementation (Slides)	10:30 - 11:30 I/O to trackers, devices, and scanners: OpenIGTLink (Pace) 11:30 - 12:00 Slicer interactive modules and programming resources (Pieper) (Slides)
	Lunch (12:30-1:30)	Lunch (12:00-1:00)
Afternoon Session 1	1:30 - 4:00 Slicer3 user training (SPujol) 3D Visualization (SPujol) Automatic Segmentation (SPujol)	Programming in Slicer3 (SPujol) 1:00 - 1:30 Introduction to the new execution model 1:30 - 2:30 Programming into Slicer3 (Part 1)
Coffee Break	Coffee Break (4:00-4:30)	Coffee Break (2:30-3:00)
Afternoon Session 2	4:30 - 4:45 Slicer 3 IGT capabilities (15 min. Hata) The IGT Toolkit Concept, Architecture, Design Application specific modules: Neuro, MRIg Prostate, Cardiac 3D US 4:45 - 6:00 IGT Workflows using neurosurgical planning as an example (Pace) Image registration and segmentation (Part 1)	Programming in Slicer3 (SPujol) 3:00-5:00 Programming into Slicer3 (Part 2) 5:00-6:00 Migrating to the NA-MIC Kit: Discussion and Conclusion

Pre-workshop Preparation List

The workshop is a series of hands-on sessions. All participants should complete the Developer Prerequisites in advance of the workshop. This includes both building Slicer from source, building the additional software and downloading the datasets.

• Note: Building Slicer can take up to 2 hours.
• We recommended the following configuration: Windows XP, Linux (x86 or x86_64), Mac OS (ppc or Intel), 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory.
• Please contact the Slicer Users mailing list for support and questions related to the software.