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Installation on macOS

FSL can be installed on all recent versiions of macOS, on both Intel and Apple Silicon (M1, M2, M3, etc) architectures.

Install FSL

For new users, we recommend using the getfsl.sh script to install FSL:

  1. Open a terminal.
  2. On Linux, you should be able to find a Terminal application in your system/application menu.
  3. On macOS, you can find the Terminal app via Finder, by navigating to Applications > Utilities.

  4. On Windows, open the WSL distribution, (e.g. the Ubuntu app, if you chose to install Ubuntu).

  5. Copy and paste the following command into the terminal, and push enter:

curl -Ls https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/getfsl.sh | sh -s

Or download the getfsl.sh script, and run sh ~/Downloads/getfsl.sh in your terminal.

  1. Wait for the installation to complete - if you have a fast internet connection, installation should take around 10-15 minutes. If your internet connection is slower, please be patient.

  2. Once the installation has finished, close and re-open your terminal window.

The installation script will print out a number of messages, reporting its progress, and any errors that may arise.

Please read the output carefully - the following message will be printed when the installation has completed successfully: 

FSL successfully installed

If you do not see this message: - Save a copy of all of the text that the installer printed to the terminal - Search in your home directory for a file called fsl_installation_<date>.log (where <date> is a series of numbers representing the current date. - Check the troubleshooting page for some potential solutions. - Send us a message with the above information, and we will try our best to help.

Otherwise, you can verify your installation to make sure that the installation has succeeded.

Installing optional components

FSL 6.0.7.13 and newer may contain additional optional components - for example, - the TRUENET deep learning segmentation tool - the osl-dynamics dynamic functional connectivity toolbox

If you wish to install these components, use the --extra option when running the getfsl.sh script. You also need to specify the FSL installation location (e.g. ~/fsl/), for example:

curl -Ls https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/getfsl.sh | sh -s -- ~/fsl/ --extra truenet

or

curl -Ls https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/getfsl.sh | sh -s -- ~/fsl/ --extra osl-dynamics

Custom/advanced installations

If you need to customise any aspects of the installation, instead of using getfsl.sh, we recommend downloading and running the fslinstaller.py script. This is a Python script which can be executed with any verison of Python 2.7 or newer. You can run the fslinstaller.py script like so:

python fslinstaller.py

And you can read about the available options by running:

python fslinstaller.py --help

Python is required

Your system must have a Python interpreter installed before you can run the fslinstaller.py script. Some systems do not have a command called python, and will print errors like python: command not found. If this happens try calling python3 fslinstaller.py or python2 fslinstaller.py.

Some versions of macOS do not have Python installed by default - if you do not have any Python command available, you can download an installer from https://www.python.org. Alternately, Python will be installed as part of Xcode, which you can install by running sudo xcode-select --install.

If you experience SSL certificate errors on macOS, try running the installer with /usr/bin/python fslinstaller.py or /usr/bin/python3 fslinstaller.py. If you have installed Python separately from https://www.python.org, make sure you have run the Install certificates script, as described here.

Do not install FSL onto a USB drive

FSL can only be installed onto file systems which support symbolic links and hard links - this does not include the FAT32 file system, which is used on many USB drives, so you are likely to encounter issues if you try to install FSL onto a USB drive.

By default, FSL is installed into your user account home directory (at ~/fsl/), and so does not require administrative privileges. You can specify a different location (e.g. /usr/local/fsl/) when running the fslinstaller.py script like so:

python fslinstaller.py -d /usr/local/fsl/

If you choose to install FSL to a different location, or are installing FSL on a multi-user system, you may need to enter your administrator password before the installation can proceed. You can run the fslinstaller.py script as described above - you will be prompted for your password when necessary.

For single-user installations, we recommend that you do not use sudo when running the fslinstaller.py script. Instead, run the script as your normal user - you will be prompted for your root password as needed.

If you do not have permission to use sudo then the installer will fail and you will need to either install into a folder belonging to your user or to run the installer as the root user. If you run the fslinstaller.py script with sudo, or as the root user, see the FSL configuration page for details on how to setup your user account for FSL.

Running the FSL GUIs

The file system that macOS uses can't distinguish between upper and lower case filenames, so Feat and feat are treated the same. Consequently, the FSL GUIs on the macOS release are called <Toolname>_gui, for example Feat_gui.

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.

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 may need to migrate your FSL configuration commands. See the configuration page for more details.