Installing FSL on Apple Mac

Thanks to Robert Coghill for sponsoring the Apple port.

To install FSL on a Mac you need to do the following:

  1. Check that you have the X11 window system installed
    Do this by looking for the X11 application in the Utilities folder within the Applications folder; by default Macs don't generally come with this installed (you'll almost certainly need X11 later for things other than FSL anyway.)
    If you do not have X11 then install it from the OS X Install CD. Insert the CD, open it in a file browser, scroll down to the Optional Installs, then click on Applications -> X11.

  2. Unpack the FSL distribution

  3. Install the applications
    To get a clickable application icon FSLView, open a file browser in the toplevel fsl directory, e.g.
          open /usr/local/fsl
    and drag the fslview.app directory into your Applications folder or your Desktop.

  4. Find out which shell you are running
    In a terminal, type:
          help
    the output will be either a list of commands, in which case you are using the bash shell, or an error saying "command not found" or similar message, in which case you are using the tcsh or csh shell.

  5. Set up your user environment
    If you are using the bash shell then do the following -

    If you are using the tcsh or the csh shell then follow the above instructions, but instead type the following in the terminal:

      cd 
      touch .cshrc
      open -a TextEdit .cshrc
       
    and add the following to the .cshrc file (as opened in TextEdit, but after selecting plain text mode - as above):
      setenv FSLDIR /usr/local/fsl
      source ${FSLDIR}/etc/fslconf/fsl.csh
      setenv PATH ${FSLDIR}/bin:${PATH}
     
    then change the /usr/local/fsl as instructed above, and save the file.

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

    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. See the FSL FAQ for more information about this.

  7. Running the GUIs
    Once you have checked the environment and command line programs, as described above, then start X11 (click on it in the Utilities folder inside the Applications folder) . All of the FSL GUIs should now work. 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.

  8. Customising FSL
    To customise FSL for particular ouput datatypes etc., see the page on Customising FSL.

  9. Further help
    If any problems occur when installing or running the FSL tools, please consult the FSL FAQ. This also contains instructions on how to join and use the FSL email list to ask specific questions which are not covered in the FAQ.