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 (/Applications/Utilities/Terminal.app) window.

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:

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:

  • /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 may be of use, particularly when scripting installs.

You can automate the installation process using the -q and -d options to prevent questions being asked and to specify the install location respectively.


FslInstallation/FslInstaller (last edited 14:34:34 18-04-2018 by MatthewWebster)