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FSL Install Script
The fslinstaller.py script carries out the installation of FSL, configuring your environment to enable you to run FSL from your terminals.
if you use Mathworks' MATLAB it will configure your startup.m file to allow you to use the FSL MATLAB functions and on OS X platforms it will also install FSLView into /Applications.
Running the installer (on Mac or Linux)
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
The Terminal application can be found in /Applications/Utilities
In the terminal change to the folder containing the downloaded file and run it (for example if you downloaded to your Downloads folder):
cd ~/Downloads
python fslinstaller.py
The installer requires access to the internet to be able to download the FSL software appropriate for your platform. 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.
Administrative privileges may be required
Installation into certain folders on your computer (eg 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 any rights to use sudo (an administration account on OS X) then the installer will fail and will need to be run 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.
Once the install completes Linux users should log out (System > 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 OS X users should open a new terminal window to begin using FSL.
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):
cd ~/Desktop
su -c "python fslinstaller.py"
and entering the root account password. You should now configure your user account to enable FSL using the instructions in the following section.
For more information on controlling the installer, run it with the -h option - there are options for downloading the install files without installation (for example for installing on multiple computers) and specifying the installation location.
Downloading the install file without installing the software
If you have to install FSL on many computers, or perhaps on a machine that doesn't have access to the internet then you can use the installer to download the FSL distribution for later use. To do this, run the installer with the -o option:
python fslinstaller.py -o
This will download the install package to the current folder and print the expected MD5 checksum for this file to the screen. To install this downloaded file, use the -f and -C options, eg:
python fslinstaller.py -f fsl-centos6_54.tar.gz -C `MD5sum`
replacing MD5sum with the hexadecimal number printed when you downloaded the file.
Scripting installation
If your computers have access to the internet then you can automate the installation process using the -q and -d options to prevent questions being asked and to specify the install location respectively. Where they cannot access our download site then you can download the install file as above and then use the -q, -d, -f and -C options with appropriate values to fully automate the install. For more details run the installer with the -h option.