Introduction
Mac Os X
Linux
Contents
Windows
Source Code
Shell Setup
FAQ

Debian/Ubuntu users

Debian/Ubuntu users can install FSL from the Neurodebian site - http://neuro.debian.net/pkgs/fsl-complete.html and should read their setup instructions.

Quick start for Debian/Ubuntu users

As of fsl 5.0 all you need do is add ". /etc/fsl/5.0/fsl.sh" to the end of your .profile file. When you next login you should find the fsl programs are available.

Prerequisites

FSL is available ready to run for 64bit Centos 5 and Centos 6. As distributed these Linux variants require no additional software to run. See the FAQ for help with running FSL on other Linux platforms (eg SuSE).

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)

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.

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)
- 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; 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

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.

Checking the installation

Test that the environment and command line tools are set up correctly by doing the following:

Start a new Terminal session (File > Open Terminal under Linux/Gnome, Shell > New Window on Mac OS X)
Check that your environment is correct by typing:
```
echo $FSLDIR
```
This should display the name of the directory that you installed FSL in.
Check that your path is correct by typing:
```
      flirt -version
```
which should display a line like:
```
      FLIRT version 6.0
```
(although the version number might be different).

In general, to run the FSL tools from the command line (within a terminal) you need to enter the program name in lower case (e.g. bet). Typing a command on its own (without any arguments or options) gives you a help message for that command.

A more complete test of the FSL installation can be run, if desired, by using the testing and evaluation suite FEEDS.

Running the programs

The FSL command line tools are located in $FSLDIR/bin. In general command-line programs are lower case (e.g. bet); the GUI version capitalised (e.g. Bet).

To bring up a simple GUI which is just a menu of the main individual FSL GUI tools, just type fsl. You are now ready to run FSL

Advanced usage

System-wide configuration

The fslinstaller script is capable of configuring Centos computers such that all user accounts can automatically use FSL without having to configure their accounts themselves. You can do this using the -E option to the installer:

```
python fslinstaller -E
```

This will create files for BASH/sh and (t)csh users in /etc/profile.d which configure the FSL environment variables at login time.

Manual installation

If you don't want to/can't use the installer script then follow these instructions to install FSL.

Download the FSL install file using the installer
```
python fslinstaller -o
```
- This will download the FSL software for your Linux version to the current folder and print out the expect MD5 checksum for this download.
Check the download
```
md5sum fsl-5.x.x-centosY_64.tar.gz
```
- and compare the output to that given by the installer.
Unpacking
To unpack a distribution, you need the UNIX tar utility. First cd to the directory where you want FSL installed (for example /usr/local). Then uncompress and untar the distribution - for example, if you have downloaded the Cent OS 5 64bit distribution to your home directory, type
```
 cd /usr/local
 tar zxvf ~/fsl-*-centos5_64.tar.gz
```
Configure your shell

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_64.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.