Robarts Training Session

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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.

Course Faculty

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

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

Registration

  • 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

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)
    • Overview of NA-MIC
  • 08:45-10:00 Engineering methodology (Steve, Nicole, Katie, Junichi?)
    • Extreme programming
    • What is a software engineering methodology, do I need one?
    • The components of the NA-MIC kit software engineering tools: CMAKE, CTEST, CPACK, Dashboards
  • 8:30 - 10:00 IGT workflows using neurosurgical planning as an example (Pace)
    • Segmentation, Model Making and Diffusion Tensor (Part 2)
Coffee Break Coffee Break (10:00-10:30) Coffee Break (10:00-10:30)
Morning Session 2
  • 10:30 - 11:00 ITK, VTK, XNAT and Batchmake (Steve, Nicole, Katie, Junichi?)
  • 11:00 - 12:30 Slicer3 (Pieper)
    • Overview and Features
    • Architecture and Implementation
  • 10:30 - 11:30 I/O to trackers, devices, and scanners: OpenIGTLink (Pace)
  • 11:30 - 12:00 Slicer interactive modules and programming resources (Pieper)
Lunch (12:30-1:30) Lunch (12:00-1:00)
Afternoon Session 1
  • 1:30 - 4:00 Slicer3 user training (Pujol)
    • 3D visualization
    • Automatic segmentation
  • Programming in Slicer3 (Pujol)
    • 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 (Hata)
    • The IGT Toolkit
    • Concept, Architecture, Design
    • Application specific modules: Neuro, MRIg Prostate, Cardiac 3D US
  • 4:45 - 5:15 Lego robot tutorial as an example of robot control (Pace)
  • 5:15 - 6:00 IGT Workflows using neurosurgical planning as an example (Pace)
    • Image registration (Part 1)
  • Programming in Slicer3 (Pujol)
    • 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. Please complete the Developer Prerequisites in advance of the workshop. This includes both building Slicer from source 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.
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