FSL

DOWNLOADING AND INSTALLING

Downloading

FSL is available precompiled for the Linux and Mac OS X operating systems. Windows is supported via a Linux Virtual Machine. The sources are also available if you want to compile it yourself.

Download FSL

Installation instructions

Running

Make sure the following is present somewhere in your shell setup file (.bashrc, .profile, .cshrc etc., depending on what shell you use), changing "/usr/local/fsl" to wherever you have installed FSL:

bash / sh / kshFSLDIR=/usr/local/fsl . ${FSLDIR}/etc/fslconf/fsl.sh PATH=${FSLDIR}/bin:${PATH} export FSLDIR PATH

tcsh / cshsetenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH}

To run the FSL tools from the command line, you can find the tools in $FSLDIR/bin. In general command-line programs are lower case (e.g. 'bet'). In general the GUI version is capitalised (e.g. 'Bet'), except on Mac, where '_gui' is appended because those file systems can't tell the difference between upper and lower case (e.g. 'Bet_gui').

To bring up a simple GUI which is just a menu of the main individual FSL GUI tools, just type fsl.

Customising (for different output datatypes, etc.)

There are several environment variables which FSL uses to determine certain user preferences, such as the output file format (NIFTI_GZ, NIFTI_PAIR, etc). The defaults for these are set when you source the setup file as shown above (i.e., ${FSLDIR}/etc/fslconf/fsl.sh or ${FSLDIR}/etc/fslconf/fsl.csh). If you wish to change these defaults then you need to:

cd
mkdir .fslconf
cd .fslconf

and in this directory create a file called fsl.sh or fsl.csh, depending on the shell that you use, setting any or all of the variables that appear in the central ${FSLDIR}/etc/fslconf/fsl.sh or ${FSLDIR}/etc/fslconf/fsl.csh files.

DO NOT copy the central files into ~/.fslconf/ as it will cause a loop that will stop your login from working.

It is recommended that the files ~/.fslconf/fsl.sh or ~/.fslconf/fsl.csh only include a few variable definitions and nothing more. Note that whoever installs FSL can also edit the central files in $FSLDIR/etc/fslconf to change the preferences for all users.

Setting up FSL to use a SunGridEngine (or similar) computing cluster

Several of the more compute-intensive tools can now take advantage of cluster computing, via SunGridEngine (SGE):

FEAT will run multiple first-level analyses in parallel if they are setup all together in one GUI setup. At second level, if full FLAME (stages 1+2) is selected then all the slices are processed in parallel.
MELODIC will run multiple single-session analyses (or single-session preprocessing if a multi-session/subject analysis is being done) in parallel if they are setup all together in one GUI setup.
TBSS will run all registrations in parallel.
BEDPOST (FDT) low-level diffusion processing will run all slices in parallel.
FSL-VBM will run all registrations in parallel, both at the template-creation stage and at the final registrations stage.
POSSUM will process all slices in parallel.

All the above tools interact with a compute cluster via a single central script fsl_sub; if no cluster is available then this script silently runs all the requested jobs in series. To customise FSL for your local compute cluster and clustering software, simply edit ${FSLDIR}/bin/fsl_sub - hopefully the comments in this file are sufficient to make this fairly painless, particularly for labs using SGE. For other clustering software than SGE, note that fsl_sub makes use of an SGE feature allowing the submission of a text file containing a list of commands (one per line) to be run in parallel.