2005 AHM Planning: Slicer/Freesurfer

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Who should attend

Researchers interested in introductory training in 3DSlicer, a neuroimaging data visualization and analysis software tool and Freesurfer, a quantitative morphometric analysis software suite.

Topics to be covered

How to use and integrate 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 advance their 3D Slicer/Freesurfer skills.

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.

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@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 LINUX or MacOS 10.4 laptop computer with both the Freesurfer and Slicer software and demonstration data sets loaded (see below). If you use a PC laptop, you should come with the Slicer software and demonstration data sets loaded and have the ability to connect your computer to the internet (via an Ethernet connection or wireless- which one Mark James?) so you can follow along on the Freesurfer Wiki during the first session. (There is no Freesurfer buiild for the PC, it is assumed you will return to your laboratory and now know how to begin using it on your LINUX or MAC workstation).

  • 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 need to plan on having 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 Acuion
  2. Marianna Jakab
  3. Michele Perry
  4. Steve Pieper
  5. Amanda Grethe (?)
  6. Christine Fennema Notestine (?)
  7. Thang Nyguen

Preparation for Workshop -- Important Information for all attendees

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.
  2. Data to Download: Get the tutorial data pointed to at Slicer User Training 101 page tutorial-with-dicom.zip, and the FreeSurfer example datasets subjects.zip that are necessary for the second half of the Workshop.

We will be happy to assist anybody who may encounter difficulties in the installation process. As first point of contact, send an email to the NAMIC-developers mailing list which will be closely monitored by NAMIC Tookit experts. Because we will focus on how to use the application(s) during the workshop not on how to install it, please do the install before you arrive.

Optional Freesurfer Installation: 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.

Tentative Agenda

8:30 AM - 4 PM

8:30 - 8:45 AM Goals of Workshop, Introduction to the Workshop, and People-Introductions (Randy Gollub)

8:45 - 11:30 Hands-on Session 1- Freesurfer training (Doug Greve)

11:30 - 12:30 Lunch (provided)

12:30- 1:45 Hands-on Session 2- Slicer Training (Sonia Pujol)

  • Loading Data (Volumes, Models, Scenes)
  • Interacting with Images and Models
  • Saving data

1:45- 2:00 Coffee Break (provided)

2:00- 3:15 Hands-on Session 3- Freesurfer integration with Slicer (Randy Gollub)

  • Viewing segmentation results
  • Model Making from segmentation results
  • Viewing surface data
  • Making figures

3:15 - 4:00 Brief overview of other Freesurfer and Slicer modules and how to learn to use them