Slicer:User Workshop Jan26

Using 3D Slicer for Medical Image Analysis & Visualization

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Logistics

January 26, 2005

8am to 3.45pm

1249 Boylston St. Boston, Room 245, 2nd Fl. conference room (SPL) Directions

(Lunch and refreshments provided)

Registration

• Registration is required, deadline is January 21st.*
  • *Fee is $50 for all registrants.*

To register visit: www.hcnr.med.harvard.edu/courses.php [1]

Overview:

This workshop offers day-long instruction on using 3D Slicer software, hands-on overview of its basic use, and demonstrations of advanced features. Participants will become familiar with the 3D Slicer's extensive functionality, and should depart with the ability to apply its suite of tools in their own work.

• Background

3D Slicer is a freely-available and open source package for medical imaging analysis; its development began at the MIT Artificial Intelligence Laboratory and the Surgical Planning Laboratory at Brigham and Women's Hospital. 3D Slicer (or simply "Slicer") uniquely integrates several facets of image-guided medicine into a single environment. It provides capabilities for automatic registration (aligning data sets), semi-automatic segmentation (extracting structures such as vessels and tumors from the data), generation of 3D surface models, 3D visualization, and quantitative analysis (measuring distances, angles, surface areas, and volumes) of various medical scans. Slicer is available for download both in source code format for developers who wish to add custom features, and in pre-compiled binaries for Linux, Windows, and Sun Solaris platforms (for users familiar with a point-and-click menu environment). Slicer has a broad base of users and developers (with over 4000 downloads worldwide as of early 2004) and is actively used as a research tool in diagnostic and interventional clinical settings worldwide.

Participants should be comfortable with the use of GUI-based software tools, familiar with medical imaging applications, and have an interest in applying image analysis or visualization in their work.

Schedule

8:00 - 9:00 Verify Slicer Installations, Coffee

9:00 - 9:30 Introduction (Sandy Wells)

9:30 - 10:30 Slicer Basics - Loading Data, Viewing, UI Overview (Steve Pieper)

10:30 - 10:45 Break

10:45 - 12:00 Manual and Semi-Automatic Segmentation (Steve Pieper)

12:00 - 1:00 Lunch

1:00 - 1:35 DTI Processing (Sandy Wells and Steve Pieper)

1:35 - 2:10 Statistical Segmentation (Sandy Wells and Steve Pieper)

2:10 - 2:25 Break

2:25 - 3:00 Registration (Sandy Wells and Steve Pieper)

3:00 - 3:45 fMRI Processing (Sandy Wells and Wendy Plesniak)

Computer Requirements

Participants must bring their own laptop, configured as noted below, and must have Slicer preinstalled. The simplest installation involves downloading precompiled binaries appropriate for your platform. To get the software, visit: www.slicer.org http://www.slicer.org

• speed: at least 500 MHz
• memory: at least 500 MB
• graphics: ATI, nVIDIA, or other 3D acceleration hardware
• OpenGL (typically pre-installed with system)
• platform: Windows or Red Hat Linux 7.3
• Disk Space: 11.5 MB for installer, which expands to 45 MB
• + 37 MB for tutorial data set

Last-minute Updates

For participants bringing a Windows laptop, please download an updated Slicer2.4 binary from: https://share.spl.harvard.edu/share/birn/public/software/slicer2.4/slicer2.4-win32-2005-01-24.zip

In addition to the standard tutorial dataset you've already downloaded, please also download and unzip the following two additional tutorial datasets containing structural and functional MRI volumes (together, they will require about 200MB): ftp://ftp.fil.ion.ucl.ac.uk/spm/data/MoAEpilot/MoAEpilot.tgz ftp://ftp.fil.ion.ucl.ac.uk/spm/data/MoAEpilot/MoAEpilot_snrf.tgz

• Additional data for registration examples is available here: MRT Data