The FSL software suite requires the X11 windowing system - please install XQuartz before continuing with the FSL installation. The FSL install script will warn you if it is unable to find X11 on your computer.
We have created an installation video which gives an overview of the installation procedure on a Mac.
FSL Install Script
The fslinstaller.py script carries out the installation of FSL, configuring your environment to enable you to run FSL from a terminal window (e.g. (/Applications/Utilities/Terminal.app 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
The Terminal application can be found in /Applications/Utilities
In the terminal change to the folder containing the fslinstaller.py 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 python fslinstaller.py
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:
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.
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 fslinstaller.py -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: This should display the name of the directory that you installed FSL in.
- Check that your path is correct by typing: 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 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.
Migrating to zsh
Recent versions of macOS use zsh as the default terminal shell, whereas older versions used bash. If you installed FSL, and then upgraded macOS or changed your default shell to zsh, you will need to migrate your FSL configuration commands. See the Shell Setup page for more details.
Running the GUIs
To run a GUI version of a program you can either type its capitalised name with an additional '_gui' appended in the terminal (e.g. Bet_gui), or you can start the main FSL GUI by just typing fsl.
If this doesn't work the see the FAQ for how to go about fixing this, otherwise you are ready to run FSL.
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); setenv('FSLOUTPUTTYPE', 'NIFTI_GZ'); path(path, fsldirmpath); clear fsldir fsldirmpath;