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| An automated installer, `fsl_installer.sh` is available to carry out the installation of (or application of a patch to) FSL, configuring your environment to enable you to run FSL from your terminals. | 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]]. |
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| On Mac OS platforms it will also install FSLView into `/Applications` and if you use Mathworks' MATLAB it will configure your `startup.m` file to allow you to use the FSL MATLAB functions. | = Running the installer (on macOS or Linux) = |
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| [[attachment:fsl_installer.sh]] - Version 1.6 09/02/2012 | 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: |
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| = Running the installer = The installer runs from within a terminal session, so you need to open a terminal: * Linux (Centos) . The Terminal application can be found in `Applications > System Tools > Terminal` menu * Mac |
* Linux (Centos 7) . The Terminal application can be found in `Applications > Utilities > Terminal` menu * macOS |
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| In the terminal change to the folder containing the downloaded file and run it (for example if you downloaded to your Downloads folder): | 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: |
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| cd ~/Desktop sh fsl_installer.sh |
cd ~/Downloads python fslinstaller.py |
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| Assuming that this folder also contains the FSL distribution tar file and you wish to install into `/usr/local` then just press Return when the installer asks a question, to accept the defaults. | <<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`. |
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| {{{#!wiki warning '''Administrative privileges may be required''' |
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`. |
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| Installation into certain folders on your computer (eg `/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 any rights to use `sudo` then the installer will fail and will need to be run as the `root` user. Should you install as `root` see the [[FslInstaller/ShellConfigure|configuring your account for FSL]] section for details on how to use the installer to setup your user account for FSL. | 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. |
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| == 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): {{{#!highlight bash numbers=disable cd ~/Desktop su -c "sh fsl_installer.sh" }}} and entering the `root` account password. You should now configure your user account to enable FSL using the instructions in the following section. |
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| For more information on controlling the installer, run it with the `-h` option. | == 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. |
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 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:
cd ~/Downloads
python fslinstaller.py
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.
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.
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 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.