Slicer3:Slicer3 Workshop UNC Chapel Hill 2008

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Syllabus

This workshop provides an introduction to the Slicer3 software platform, part of the National Alliance for Medical Imaging Computing open-source toolkit. Participants will learn how to use Slicer3 for image analysis and 3D visualization, and how to integrate external programs with the open-source software.

Course Faculty

  • Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School
  • Randy Gollub, M.D., Ph.D., Athinoula A. Martinos Center for Biomedical Imaging, Harvard Medical School
  • Steve Piper, Ph.D., Isomics
  • Kathryn Hayes, M.S.E., Surgical Planning Laboratory, Brigham and Women's Hospital

Logistics

  • Participants are required to come with their own computer (PC, Linux or MacOS) with a built-in version of Slicer3.
  • Attendance is limited to 40 participants. To sign-up for this event, please send an e-mail with the subject line 'NA-MIC Workshop Registration - April 14' to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu) with your contact information (Name, Title, Affiliation and Address) and the characteristics of your laptop computer (OS, RAM, Processor).

Goals of the Workshop

  • The goal of the workshop is to provide participants a practical experience with the image processing and 3D visualization capabilities of Slicer3.
  • The morning session is user-oriented, and provides the basics for loading and visualizing data.
  • The afternoon session is intended for participants who want to to learn how to program and integrate external executables with Slicer3, using the new Execution Model

Agenda 9:00 AM - 5:00 PM

  • 9:00 am - 9:10 am Preliminary session: Software and data installation trouble shooting
  • 9:10 am - 9:20 am Welcome and introduction to the Workshop (Randy Gollub)
  • 9:20 am - 10:00 am Slicer3 Overview and Applications (Steve Pieper) Slides
  • 10:00 am - 10:45 am Hands-on Session 1: Data Loading and Visualization (Sonia Pujol)
  • 10:45 am - 11:00 am Coffee-break
  • 11:00 am - 11:45 am Hands-on Session 2: Data Saving (Sonia Pujol)
  • 11:45 am - 12:00 pm Slicer3 Execution Model Introduction (Steve Pieper) Slides
  • 12:00 pm - 1:45 pm Lunch on Your Own
  • 1:45 pm - 3:15 pm Hands-on Session 3: Slicer3 Plug-ins Part 1(Sonia Pujol)
  • 3:15 pm - 3:30 pm Coffee-break
  • 3:30 pm - 4:30 pm Hands-on Session 3: Slicer3 Plug-ins Part 2 (Sonia Pujol)
  • 4:30 pm - 4:45 pm Going Further with Command Line Modules (Steve Pieper) Slides
  • 4:45 pm - 5:00 pm Feedback from participants and Conclusion (Randy Gollub)

Workshop feedback survey

Preparation for the Workshop

Please complete the following items prior to the course. Support will be provided as requested.

  • Software Installation: Please build Slicer3 on the computer you will be bringing to the workshop.

The instructions for installing the pre-requisite development packages and for building Slicer3 are posted on the Slicer website.

Please note To fully participate in the afternoon session you must have built the software on your machine. Pre-built binaries of slicer3 are available and can be used for the morning session only.

Note: The process of building Slicer3 takes 2 hours and requires 2 GB of RAM.

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