top | previous | next

FreeSurfer Setup and Configuration

Basic setup

Usage of C shell (csh) or enhanced C shell (tcsh) is recommended, although bash/sh scripts are also provided for the setup scripts. The shell type on your system can be checked by typing ps at the command line in a terminal window. To explicitly launch csh or tcsh (tcsh is recommended), simply enter the following command in a terminal window:

tcsh

The prompt may change, and some login files may not be run in the new shell environment. See the man pages for tcsh for details.

If you do not have a preference for a particular shell, the default shell can be permanently switched to tcsh by typing the following:

chsh -s /bin/tcsh

The file <freesurfer_installation_directory>/SetUpFreeSurfer.csh is a csh (C-shell) script that will configure the environment so that FreeSurfer can be used. It sets a few environment variables, sources other csh scripts to set up support libraries, and performs some checks that need to be passed before FreeSurfer can start. This file needs to be 'sourced' before running any FreeSurfer binaries.

To setup the tools to run, from a tcsh or csh, type:

setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

Where <freesurfer_installation_directory> is replaced with the path of whereever you installed the distribution.

If using bash or sh, type:

export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Alternately, the resource file for the shell can be configured to source the file automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file .cshrc if C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for Bash, and .profile for sh, to include the previous two lines (which setenv FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script).

Upon 'sourcing' the SetUpFreeSurfer.csh(sh) script, you should see output like this (assuming an installation path of /usr/local):

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME     /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR    /usr/local/freesurfer/subjects
MNI_DIR         /usr/local/freesurfer/mni

If any warnings appear, it's usually safe to ignore them, but make sure that they are not stating that a file or directory that should exist cannot be found.

If any error messages appear, check that the installation process was successfully completed.

License

If you haven't done so already, obtain a license, and copy the .license file to your $FREESURFER_HOME.

Optional configuration settings

The defaults declared in the SetUpFreeSurfer.csh script should work for most installations. However, users should free to edit this file to customize certain environment variables:

1. Your declaration of the FREESURFER_HOME variable could be moved within the SetUpFreeSurfer.csh script.

2. The default SUBJECTS_DIR, which is $FREESURFER_HOME/subjects, is most likely the first variable that you will want to customize, as you may keep different groups of subjects in different directories. You may include the following either directly in the SetUpFreeSurfer.csh script, or prior to calling it:

• setenv SUBJECTS_DIR <full path to subject dir>

3. If you do NOT intend to use the functional tools, then add the following line to the additional configuration section:

• setenv NO_FSFAST

If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file:

• fsfasthome = getenv('FSFAST_HOME');
  fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
  path(path,fsfasttoolbox);
  

4. You may also wish to declare a path to an FSL installation you might have:

• setenv FSL_DIR /usr/local/fsl

5. Save the file. You will need to source this file (SetUpFreeSurfer.csh) every time you want to use Freesurfer.

Optional removal of third-party packages

Freesurfer includes in its distribution several third-party open-sourced packages which are required for Freesurfer to fully function. The distributed packages have not been modified from their source origins, so it is possible to delete the distributed package if an equivalent package is already installed on your system. Please be aware that the packages distributed with Freesurfer have been tested for compatibility with its tools.

The distributed packages, their version, and location are listed here:

*refers to MINC version **refers to Tcl/Tk version

To use a prior installed package, just move or delete the Freesurfer directory containing the package, and replace with a symbolic link to your own package. For instance, assuming an MNI toolkit is already installed in /usr/local/mni:

cd $FREESURFER_HOME
mv mni mni-backup
ln -s /usr/local/mni mni

The FreeSurferEnv.csh setup script will now point to those tools.

Testing FreeSurfer

Next: testing your FreeSurfer installation.