Training:User Workshop Fall HCNR 2006

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HCNR logo cbd.jpg


HCNR Lead:

  • Sandy Wells, Ph.D. - Andrew Lowe, MPA

NA-MIC Lead:

  • Sonia Pujol, Ph.D.

spujol at

Training Workshop Participants

Clinicians and biomedical science researchers interested in training in 3DSlicer, an open-source software for visualization and analysis of medical image data, for the specific purpose of analyzing Diffusion Weighted Imaging data. survey

Training Workshop Logistics

  • The workshop will be held on 'Wednesday November 1st, 2006' in the Demo room at the Surgical Planning Laboratory facility on Boylston Street, Boston MA. Please check 1249 Boylston Street, Boston, MA for directions.
  • To sign-up for this event, please complete the registration form and return it to the Harvard Center for Neurodegeneration and Repair (HCNR). (Fax Number: 617 432 3364)

Preparation for the Training Workshop -- Important Information for all attendees

This is hands-on training. All participants must come with their own computer and install our software and data. PC, Linux or MacOS 10.4 computers will work. A minimum of 512MB of RAM and a dedicated graphic accelerator with 64mb of on board graphic memory are recommended.

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

  • Software Installation: Please install the newest release of the Slicer program Slicer2.6 appropriate to the computer you will be bringing to the workshop.

NOTE: Intel based Macs will be supported on an experimental basis. Mac users please be sure to install the X11 application (available from the Mac OS X install disks).

  • Data to download: Please install the tutorial datasets,[/Wiki/images/2/2d/] and [/Wiki/images/f/f0/].


Agenda 9:00 AM - 4:15 PM

  • 9:00 am - 9:15 am Goals of Workshop, Introduction to the NAMIC Kit
  • 9:15 am - 9:30 am Preliminary session: checking for software and data installation.


  • 9:30 am - 10:45 am Slicer Basics - Hands-on Session 1 (Sonia Pujol)
    • Slicer Interface Overview
    • Loading Data: Volumes, Models, Scenes
    • Interacting with Images and Models
  • 10:45 am - 11:00 am Coffee-break
  • 11:00 pm - 12:30 pm Slicer Advanced - Hands-on Session 2 (Sonia Pujol)
    • Diffusion Weighted Imaging tools within Slicer: Nrrd file format

DWI parameters

  • 12:30 pm - 2:00 pm Lunch Break
  • 2:00 pm - 4:00 pm Slicer Advanced - Hands-on Session 3 (Sonia Pujol)
    • Diffusion Weighted Imaging tools within Slicer: DTI processing and visualization
  • 4:00 pm - 4:15 pm Feedback by participants and Conclusion

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