Events:Slicer Workshop August 2009

Course Syllabus

The purpose of this tutorial is to provide the members of the research community with a practical experience of the image processing, 3D visualization, and Image-Guided Therapy capabilities of the Open Source 3D Slicer software platform. The curriculum is hands-on which means that participants are required to attend the workshop with a suitable laptop, preloaded with the software and sample data as specified below. Attendance is limited in order to ensure quality interactions between the faculty and participants.

Course Faculty

• Sonia Pujol, Ph.D., Instructor in Radiology, Harvard Medical School

Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

• Noby Hata, Ph.D, Assistant Professor in Radiology, Harvard Medical School

Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

• Kathryn Hayes, M.S.E.

Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

Logistics

• Date: Tuesday, August 25, 2009
• Time: 9am - 4pm
• Location: 1249 Boylston Street, Boston MA
• Participants are required to come with their own computer (PC, Linux or MacOS).

Agenda

Morning: Introduction to Slicer

• 9:00 am - 9:10 am Preliminary session: Software and data installation trouble shooting
• 9:10 am - 9:30 am Slicer3 Overview and Applications (Sonia Pujol)
• 9:30 am - 10:30 am Hands-on Session 1: Data Loading and 3D Visualization (Sonia Pujol)
• 10:30 am - 10:45 am Coffee-break
• 10:45 am - 11:30 am Hands-on Session 2: Data Saving (Sonia Pujol)
• 11:30 am - 12:00 pm Discussion and Conclusion
• 12:00pm-1pm Lunch Break

Afternoon: Introduction to Slicer IGT

• 1:00-1:30pm Introduction: Why Slicer 3 for your IGT research? An example from BWH BrainLab collaboration (15 min. Hata)
• 1:30 - 4:00 Neurosurgical Planning and Guidance by Slicer"
  • Module 1-3 (1:30-2:45)

1. Loading and visualizing anatomical MRI data
2. Incorporating fMRI data using image registration and thresholding
3. Creating a 3D model of the tumour volume

• 2:45 pm - 3:00 pm Coffee-break
  • Module 4-6 (3:00-4:00)

1. Predicting the locations of brain structures using image registration and a brain atlas
2. Incorporating brain fiber tractography from diffusion weighted images
3. Annotating the preoperative plan and saving the scene

Preparation for the Workshop

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

• Software Installation: Please install the newest Slicer3 release appropriate to the computer you will be bringing to the workshop:
  • Windows: Slicer3-3.2.2008-08-08-win32.exe
  • Mac OSX Darwin PPC: Slicer3-3.2.2008-08-08-darwin-ppc.tar.gz
  • Mac OSX Darwin Intel: Slicer3-3.2.2008-08-08-darwin-x86.tar.gz
  • Linux x86 Slicer3-3.2.2008-08-08-linux-x86.tar.gz
  • Linux x86-64 Slicer3-3.2.2008-08-08-linux-x86_64.tar.gz

The instructions for installing the Slicer3 program describe the different steps of the procedure on Mac OS, Linux and Windows.

Recommended 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.

• Data to download: Please install the tutorial dataset SlicerSampleVisualization.tar.gz.

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