If you have downloaded a container release there is no need to install FSL - please follow the usage instructions for the container.


FSL is normally installed by the installer script,, downloaded via the Download page. Selecting some Debian/Ubuntu versions on that page will take you to the Neurodebian site instead. As distributed, both these methods require no additional software to run. See the FAQ for help with running FSL on other Linux platforms (e.g. SuSE).

The script is written in Python 2 for maximum compatibility with supported operating systems. Some of the latest OSes (e.g. Ubuntu 18.04) do not have Python 2 available in the default install and this will need to be installed. On Ubuntu 18.04 this is achieved with sudo apt install python

FSL Install Script

The script carries out the installation of FSL, configuring your environment to enable you to run FSL from a terminal window (e.g. (/Applications/Utilities/ on macOS).

Running the installer (on macOS or Linux)

Administrative privileges may be required

Installation into certain folders on your computer (e.g. the default, /usr/local) may require administrative privileges. If this is the case, the installer will attempt to gain these privileges through the use of the sudo command, which will require you to enter your password for verification. If you don't have permission to use sudo (an administration account on macOS) then the installer will fail and will need to either install into a folder belonging to your user or to run the installer as the root user. Should you install as root see the configuring your account for FSL section for details on how to use the installer to setup your user account for FSL.

The installer requires access to the internet to be able to download the FSL software appropriate for your platform and runs from within a terminal session, so you need to open a terminal:

  • Linux (Centos 7)
    • The Terminal application can be found in Applications > Utilities > Terminal menu

  • macOS
    • The Terminal application can be found in /Applications/Utilities

In the terminal change to the folder containing the file and run it with python; assuming that you wish to install into /usr/local (the default) then just press the Return key when the installer asks where to install to. For example if you downloaded to your Downloads folder:

cd ~/Downloads

The installer requires python 2.x to run which is the default on macOS and Centos 6 & 7, if you have installed python version 3 and made it the default when you run python then you will need to run it with a python 2 version, you can often find this as:

  • /usr/bin/python
  • python27
  • python2.7
  • python26
  • python2.6

Once the install completes Linux users should log out (System (top right icon) > Log out) and log back in to complete the FSL setup. If you are accessing the Linux computer via a remote SSH session then close the SSH session and re-login. Apple macOS users should open a new terminal window to begin using FSL.

if you use Mathworks' MATLAB it will configure your startup.m file to allow you to use the FSL MATLAB functions and on macOS platforms it will also install FSLEyes and FSLView into /Applications.

Advanced Options

The installer has some advanced options which, amongst other things, allows you to:

  • customise the FSL installation location.
  • automate the FSL installation - this is useful if you would like to call the installer from an automated script.

Type python -h for a list of all available options.

Checking the installation

Test that the environment and command line tools are set up correctly by doing the following:

  • Start a new Terminal session (File > Open Terminal under Linux/Gnome, Shell > New Window on macOS)

  • Check that your environment is correct by typing:
    echo $FSLDIR
    This should display the name of the directory that you installed FSL in.
  • Check that your path is correct by typing:
    flirt -version
    which should display a line like:
    FLIRT version 6.0
    (although the version number might be different).
  • Check that the miniconda environment installation completed successfully:
    which imcp
    • which should display a line like:

    If the imcp command cannot be found, this suggests that the FSL miniconda environment was not installed correctly - see the section titled Commands missing after installation on the main FSL installation page.

In general, to run the FSL tools from the command line (within a terminal) you need to enter the program name in lower case (e.g. bet). Typing a command on its own (without any arguments or options) gives you a help message for that command.

A more complete test of the FSL installation can be run, if desired, by using the testing and evaluation suite FEEDS.

Running the programs

The FSL command line tools are located in $FSLDIR/bin. In general command-line programs are lower case (e.g. bet); the GUI version capitalised (e.g. Bet).

To bring up a simple GUI which is just a menu of the main individual FSL GUI tools, just type fsl. You are now ready to run FSL

Advanced usage

System-wide configuration

The script is capable of configuring Centos computers such that all user accounts can automatically use FSL without having to configure their accounts themselves. See Shell Setup for details.

Installing as root user on Linux

If you need to install as the root user, you can do this using these commands (again assuming you downloaded to the your Desktop folder):

cd ~/Desktop
su -c "python"

and entering the root account password. You should now configure your user account to enable FSL use.

Using FSL from MATLAB

On macOS, the fslinstaller script will usually set this up for you so you should not need to do this. However, if the installer cannot configure MATLAB for some reason you may need to do this by hand.

FSL ships with several MATLAB scripts for loading NIFTI files. These libraries are dependent on FSL environment variables which may not be set when you start up MATLAB from your desktop environment. You can configure MATLAB to be FSL-aware by adding the following to your ~/Documents/MATLAB/startup.m file (create it if it doesn't already exist):

% If you have installed FSL somewhere
% other than  /usr/local/fsl/, change
% this first line accordingly.
fsldir = '/usr/local/fsl/'; 
fsldirmpath = sprintf('%s/etc/matlab',fsldir);
setenv('FSLDIR', fsldir);
path(path, fsldirmpath);
clear fsldir fsldirmpath;

FslInstallation/Linux (last edited 14:16:37 22-09-2020 by PaulMcCarthy)