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This purpose of this page is to describe how one would go about setting up laptops or workstations for a Freesurfer course. This purpose of this page is to describe how one would go about setting up laptops (or workstations) for a Freesurfer course.

FreeSurfer Course Setup

This purpose of this page is to describe how one would go about setting up laptops (or workstations) for a Freesurfer course.

Laptop Hardware

  • Laptop hardware should meet or exceed the recommended System Requirements for running freesurfer.

  • In addition to the listed System Requirements, laptops should have 17" screens to facilitate viewing of images on the screen.
  • Laptops should have internet access. (For following course tutorials and performing last minute updates of the data set)

Laptop Software

  • Laptops should have the Development Version of freesurfer installed either locally, or via a central server.

  • Laptops should have a recent versions of FSL installed either locally, or via a central server. FSL is required for the Diffusion and TRACULA tutorials.

  • Optional: If the course is doing the FSFAST tutorial, than laptops should have the Matlab runtime installed (version 8.3, no license required). However, the commands requiring Matlab have been marked and can be skipped because the output data has already been provided. So Matlab is not an absolute requirement.

Tutorial Data

  • Laptops should have access to the "Lightweight" version of freesurfer tutorial data either downloaded locally, or via a central server, or external storage device (thumb drive, external hard drive, etc). Note that it is important for each laptop to have access its own sandboxed version of the data, with read/write access, because course participants will be creating files within their workspace.

Startup Script

  • The following lines should be added to a .bashrc file in the users home directory so that freesurfer is automatically sourced (and other environment variables set) whenever a terminal window is opened.

## Set location of tutorial location
export TUTORIAL_DATA=<location_of_tutorial_data>

## Set location of FSL (Required for Diffusion and TRACULA tutorials only)
export FSLDIR=<location_of_fsl_installation>

## Set location of Matlab and other variable (Required for FSFAST tutorial only)
export FS_MCRROOT=<location_of_matlab_installation>
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/runtime/glnxa64"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/bin/glnxa64"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/sys/os/glnxa64" 
export FS_SPMREG_USE_BIN=1
export FS_MKCON_USE_BIN=1
export FS_SXA3_USE_BIN=1

## Source freesurfer
export FREESURFER_HOME=<location_of_freesurfer_installation>
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Testing

  • Once the steps above have been taken, the best an most reliable way to test your setup is simply to run thru one or more of the tutorials.

  • A more automated way to test your setup is to run the test_tutorials.sh script. This script comes with freesurfer and can be run in the following ways:

  $> <source_freesurfer>

  ## Run a quick test.  
  $> test_tutorials.sh -quick
  
  ## If this above command runs to completion without crashing than your probably all set.

  ## Run the Multi-Modal Integration tutorial
  $> test_tutorials.sh -multimodal

  ## Run the TRACULA tutorial
  $> test_tutorials.sh -tracula

  ## Display help and other options
  $> test_tutorials.sh -help

FsTutorial/CourseLaptopSetup (last edited 2017-03-30 11:01:12 by ZekeKaufman)