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

Software

Tutorial Data

Startup Script

## Set location of tutorial data
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 Matlab/FSFAST related variables (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

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

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

## If the above command runs to completion without crashing then you're 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