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.

Hardware

• Laptops/workstations should have an Operating System and hardware which meet or exceed the recommended System Requirements for running freesurfer.

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

Software

• Laptops/workstations should have Freesurfer v6 installed.

• Laptops/workstations should have a recent version of FSL installed. (FSL is required for the Diffusion and TRACULA tutorials)

• Laptops/workstations should have Matlab runtime version 8.3 installed (no license required). (Matlab is required for the FSFAST only, and 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.)

• A tarball has been created which contains Freesurfer v6, FSL, and the Matlab runtime, (along with a custom .bashrc file), so that all these packages can be installed in one step. This tarball can be downloaded from the following link:

Tutorial Data

• Laptops/workstations 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

• A .basrch file comes with the Freesurfer/FSL/Matlab runtime package from above. The course administrator should link either link the users .bashrc to the one in the freesurfer installation:

  cd ~
  ln -s freesurfer/.bashrc

  or copy its contents into the users already existing .bashrc file:

  ## set deflaut location of freesurfer
  FSHOME=~/freesurfer
  
  ## Set location of tutorial data
  export TUTORIAL_DATA=~/tutorial_data
  
  ## Set location of FSL (Required for Diffusion and TRACULA tutorials only)
  export FSLDIR=$FSHOME/fsl_507
  
  ## Set location of Matlab and other Matlab/FSFAST related variables (Required for FSFAST tutorial only)
  export FS_MCRROOT=$FSHOME/MCRv83
  export LD_LIBRARY_PATH="$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=$FSHOME
  source $FREESURFER_HOME/SetUpFreeSurfer.sh

Testing

• Make sure the TUTORIAL_DATA environment variable is set correctly by typing ls $TUTORIAL_DATA in a terminal window. You should see the output below:

$> ls $TUTORIAL_DATA
buckner_data                    fsfast-functional
diffusion_recons                fsfast-tutorial.subjects
diffusion_tutorial              long-tutorial

• Once you verify freesurfer is sourced correctly and the TUTORIAL_DATA environment variable is set correctly, the best and 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. The script can be run in the following ways (after sourcing freesurfer and properly setting TUTORIAL_DATA):

## Run a quick test
$> test_tutorials.sh -quick

## If the above command runs to completion without crashing then you're probably
## all set. But the following commands can be used to test specific tutorials.

## 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