[FSL] [TitleIndex] [WordIndex] 

Contents

  1. Introduction
  2. Mac Os X

    Contents

    1. Prerequisites
    2. FSL Install Script
    3. Running the installer
      1. Installing as root user on Linux
      2. Configuring your account for FSL usage using the install script
    4. Checking the installation
    5. Running the GUIs
    6. Advanced usage
      1. Using FSL MATLAB libraries
      2. Manual installation
  3. Linux
  4. Windows
  5. Source Code
  6. Shell Setup
  7. FAQ

Prerequisites

Before you install FSL you should first ensure that you have the X11 windowing system installed. Mac OS X 10.5-10.7 come with this pre-installed, but on Mac OS X 10.8 you will need to install the version available from the XQuartz web page (you'll almost certainly need X11 later for things other than FSL anyway).

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 GUIs

To run a GUI version of a program you can either type its capitalised name with an additional '_gui' appended in the terminal (e.g. Bet_gui), or you can start the main FSL GUI by just typing fsl.

If this doesn't work the see the FAQ for how to go about fixing this.

Advanced usage

Using FSL MATLAB libraries

The fsl_installer.sh script sets this up for you so you will not need to do this if you have used the installer.

FSL ships with several Matlab scripts for loading NIFTI files. These libraries are dependant on FSL environment variables which aren't set in the Mac OS X Desktop environment, so won't run in a Matlab session started from the /Applications/MATLAB.app launcher. You can configure MATLAB by adding the following to your ~/matlab/startup.m file (create it if it doesn't already exist) (assuming FSL is installed in /usr/local!): 

setenv( 'FSLDIR', '/usr/local/fsl');
fsldir = getenv('FSLDIR');
fsldirmpath = sprintf('%s/etc/matlab',fsldir);
path(path, fsldirmpath);
clear fsldir fsldirmpath;

Manual installation

  1. Verify 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 downloaded FSL distribution file.

    • Open up a Terminal (you can find this application in the Utilities folder inside the Applications folder).

    • In the terminal, change to the directory where you downloaded the FSL distribution, e.g. 
      cd ~/Downloads
    • Check the file with 
      fsl=`ls -1 fsl-4.*-macosx.tar.gz`; md5 $fsl | diff -q - $fsl.md5

      NB

      ` is on the key to the left of Z on the UK Mac keyboard, or to the left of 1 on the US Mac keyboard

    • If there is a problem with the download then you will receive a message like: 
      Files .... and .... differ
  2. Unpack the FSL distribution
    • In the terminal, change to the directory where you want FSL installed, e.g. 
      cd /usr/local
    • Unpack the fsl download file - for example, if you downloaded it onto your Downloads folder, 
      tar -zxvf ~/Downloads/fsl-*-macosx.tar.gz

      (omit the z in the -zxvf if your computer has already uncompressed the tarfile for you). This will create a directory called fsl in the current directory which will contain all the required files for FSL and FSLView. Note that you might need to add sudo to the start of the tar command if you don't automatically have the right to create files in /usr/local.

  3. Install the applications
    • To get a double-clickable FSLView application, open a file browser in the top-level fsl directory, e.g. 
      open /usr/local/fsl

      and alt-cmd-drag the fslview.app directory into your Applications folder - the Finder will display an curly arrow when you do this to signify you are creating a link to the original program.

  4. Configure your shell

2012-09-05 11:30