FreeSurfer Course Setup

This page is meant to provide and brief write up on how one would go about setting up laptops or workstations for a Freesurfer course.

Laptop Hardware

Laptop Software

Tutorial Data

Startup Script

## 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

  $> <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