2005 AHM: 3D Slicer/Freesurfer Workshop

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Home < 2005 AHM: 3D Slicer < Freesurfer Workshop

Who should attend

Clinical and basic biomedical science researchers interested in introductory training in 3DSlicer, an open-source medical imaging data visualization and analysis software tool and Freesurfer, a quantitative morphometric analysis software suite optimized for working with brain imaging data.

Workshop Goals

Introduction in how to use Freesurfer and Slicer to analyze, view and make figures from structural MRI data of the brain.

Orientation to the wealth of supporting documentation available so participants can continue to advance their 3D Slicer/Freesurfer skills after the Workshop ends.

Tool experts (users and developers) from the Biomedical Informatics Research Network (BIRN) and the National Alliance for Medical Image Computing (NA-MIC) will also be available to participants for consultation.

Please provide us feedback on this training event on the workshop testimonials page.

Workshop Logistics

  • The day-long workshop will be held on Thursday, Oct. 20 in the Cal IT Building on the UC San Diego campus. Directions and the room designated for the workshop will be posted in the near future.
  • To sign-up for this event, send an e-mail to Sonia Pujol (spujol at bwh.harvard.edu) with your contact information and any specific training requests.
  • The maximum enrollment for this workshop is 200, first come, first served.
  • All participants must come with their own PC, LINUX or MacOS 10.4 laptop computer with the Slicer software and demonstration data sets loaded (see below). If you also want to have Freesurfer loaded, you will need to have either a LINUX or MacOS 10.4 laptop, PCs are not supported.
  • The Workshop room does not permit food. Participants will be provided on site lunch and an afternoon coffee break by the BIRN.

Workshop Participants

Support Personnel who will assist Workshop particpants

(We will have one of these folks for each 10-15 participants- they will float around the auditorium helping individuals who get stuck or have questions or need tech support)

  1. Nicole Aucoin (BWH)
  2. Katie Hayes (BWH)
  3. Wendy Plesniak (BWH)
  4. Amanda Grethe (UCSD)
  5. Christine Fennema-Notestine (UCSD)
  6. Nick Schmansky (MGH)
  7. Thang Nguyen (UCI)
  8. Heidi Schmidt (MGH)

Preparation for Workshop -- Important Information for all attendees

Please do these installations now. All attendees are required to complete the following items prior to the workshop. Support will be provided as requested.

  1. Software Installation: Please install the newest version of the Slicer program Slicer2.5 MGH appropriate to the computer you will be bringing to the workshop.
  1. Data to Download: Get the tutorial data tutorial-with-dicom.zip, and the FreeSurfer example datasets FreeSurferSubjects.zip.

Freesurfer Installation for LINUX and Mac OS 10.4 users: If you would like to process your own data (pre-processed data is already provided for the Slicer tutorial) then please download the newest version of FreeSurfer. Please visit the FreeSurfer Wiki page for download information, documentation and help with installation.

We will be happy to assist anybody who may encounter difficulties in the installation process. As first point of contact for Slicer instation problems, send an email to the NAMIC-developers mailing list which will be closely monitored by NAMIC Tookit experts. For Freesurfer problems, the contact information for help is on their Wiki pages. Because we will focus on how to use the application(s) during the workshop not on how to install them, please do the installations before you arrive.


9:00 AM - 4:00 PM

9:00 - 9:15 AM Goals of Workshop, Introduction to the Workshop, and People-Introductions (Randy Gollub)

9:15 - 11:45 Hands-on Session 1- Freesurfer training (Doug Greve)

11:45 - 12:45 Lunch (provided)

12:45- 2:00 Hands-on Session 2- (Sonia Pujol)

2:00- 2:15 Coffee Break (provided)

2:15- 3:30 Hands-on Session 3- Freesurfer integration with Slicer (Randy Gollub)

  • Slicer Training 6
    • Viewing segmentation results
    • Model Making from segmentation results
    • Viewing surface data
    • Making figures

3:30 - 4:00 Brief overview of other Freesurfer and Slicer modules and how to learn to use them