Availability of FSL
FSL is available ready to run for macOS (Intel and M1/M2) and Linux, with Windows computers being supported via the Windows Subsystem for Linux (WSL). Source code is downloaded and installed part of a standard installation, if you wish to compile the code yourself.
We strongly recommend that the FSL software is downloaded and installed using the fslinstaller.py script available from the link below:
Once you have downloaded the installer, fslinstaller.py, you can use it to install FSL on your computer by following these instructions (click on the appropriate link now, as the next steps for installing are described in the linked pages, not in the sections immediately below here):
To download older ( prior to FSL 6.0.6 ) versions of the FSL, the previous version of the installer can be downloaded here.
The FSL Install script will setup your computer such that you can run the FSL tools from a terminal. See our shell setup guide for details on what this script does. On Linux computers it can also be used to configure FSL for all users on the computer.
Starting the programs
Once your account is configured for FSL use, you can run the FSL tools from the command line; the tools are stored in $FSLDIR/share/fsl/bin and this location will have been added to your terminal's search locations for ease of use.
In general, command-line programs are lower case (e.g. bet), with the GUI version capitalised (e.g. Bet), except on macOS, where you need to append _gui because it can't tell the difference between upper and lower case filenames (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.
Using FSL with a GridEngine (or similar) computing cluster
Several of the more compute-intensive tools can take advantage of cluster computing, via Son of Grid Engine or http://gridscheduler.sourceforge.net/| Open Grid Scheduler]] (both forks of Sun Grid Engine). We would largely recommend using Son of Grid Engine if you are building a cluster from scratch on a Centos system as they provide RPMs to ease installation. Debian/Ubuntu users should look to install the gridengine package.
Cluster aware tools
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.
BEDPOSTX (FDT) low-level diffusion processing will run all slices in parallel.
FSLVBM 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, refer to the fsl_sub documentation.
Running FSL tools on a GPU or GPU cluster
Some FSL tools are able to be accelerated with CUDA-compatible NVIDIA GPUs - this includes bedpostx_gpu, eddy and probtrackx2_gpu. These tools are compiled against the CUDA 10.2 toolkit, but should work with any GPU that supports CUDA 10.2 or newer.