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

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