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FSL is available ready to run for 64bit Centos 5 and Centos 6 and also for Debian/Ubuntu (from http://neuro.debian.net/pkgs/fsl.html). 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

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.

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.

fsl_installer.sh - Version 1.6 09/02/2012

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
    • 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 ~/Desktop
sh fsl_installer.sh

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.

Administrative privileges may be required

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 configuring your account for FSL section for details on how to use the installer to setup your user account for 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 "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.

For more information on controlling the installer, run it with the -h option.

Configuring your account for FSL usage using the install script

In addition to installing the FSL programs, the install script is also capable of configuring your user account to enable you to run the FSL programs.

If your user account was used to run the installer when installing the FSL programs, this will have already been done, but you may also want to configure additional accounts. This is especially useful where you had to install as the root user on a Linux computer as your account would not have been setup.

To configure the current computer account for FSL, first identify where FSL has been installed (/usr/local/fsl by default) and execute the installer with the -e option, eg:

sh /usr/local/fsl/doc/fsl/fsl_installer.sh -e

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 5.5
    (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 at this point 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.

Advanced usage

Manual installation

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

  1. Check the download

    Visit our checksums page to download the MD5 sum file that matches the .tar.gz package you have downloaded. Make sure that the .md5 file is in the same directory as the .tar.gz file and in a terminal, type:

    md5sum -c name of .md5 file
    for example
    md5sum -c fsl-4.1.3-centos5_64.tar.gz.md5
    The verification will take a few minutes and if there is a problem with the download then you will receive a message like:
    • Files .... and .... differ
  2. 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 32bit distribution to your home directory, type

     cd /usr/local
     tar zxvf ~/fsl-*-centos5-32.tar.gz
  3. Configure your shell

2012-09-05 11:30