= 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). The `fslinstaller,py` source code can be viewed [[https://git.fmrib.ox.ac.uk/fsl/conda/installer|here]].

= Running the installer (on macOS or Linux) =

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 `fslinstaller.py` file and run it with python; assuming that you wish to install into `~/fsl/` (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:

{{{#!highlight bash numbers=disable
cd ~/Downloads
python fslinstaller.py
}}}
<<Anchor(python_name)>>
{{{#!wiki note
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 [[https://bugs.python.org/issue43404#msg388144|here]].
}}}
 
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.

{{{#!wiki note
'''Installing FSL into a different location'''

By default, FSL is installed into your user account home directory (at `~/fsl/`), and so does not require administrative privileges. If you wish to install FSL to a different location (e.g. `/usr/local/fsl/`), 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 - the script will prompt you for your password when necessary.

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. Should you install as `root`, see the [[FslInstallation/ShellSetup|configuring your account for FSL]] section for details on how to setup your user account for FSL.
}}}


== 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 fslinstaller.py -h` for a list of all available options.