I agree to the terms and condition mentioned in the above two license pages (download Mac OS X version). Uncompress the downloaded FMRLAB files.% tar xvfz.tgz. Mac OS X 10.5-10.7 come with this pre-installed, but on Apple's 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). The FSL install script will warn you if it is unable to find X11 on your computer.

Goals Tracker by FSL' is a web-based mobile app that helps users to develop and stick to their goals. User can identify the required investment amount for achieving their specific goals like. If you wish to install FSLeyes independently of FSL, you can download and install a standalone version from the FSLeyes home page, using these instructions. Download the zip or tar.gz file for your platform. Unzip/untar the downloaded file to a location of your choice. Software Download. If you’d like to transfer the data stored in your FreeStyle Libre reader to your computer (PC or Mac) so you can take a closer look, then you’ll need to download the FreeStyle Libre software. Just click on the link below and follow the instructions.

  1. Mac Os X


    1. Advanced usage

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 Apple's 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). The FSL install script will warn you if it is unable to find X11 on your computer.

Note for Yosemite (10.10) users: even if you have previously installed X11, you will need to either reinstall XQuartz or fix symlinks (sudo ln -s /opt/X11 /usr/X11R6 ; sudo ln -s /opt/X11 /usr/X11) to get FSL to work.

The fslinstaller.py script carries out the installation of FSL, configuring your environment to enable you to run FSL from your terminals.

if you use Mathworks' MATLAB it will configure your startup.m file to allow you to use the FSL MATLAB functions and on OS X platforms it will also install FSLView into /Applications.

Administrative privileges may be required

Installation into certain folders on your computer (eg the default, /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 (an administration account on OS X) 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.

The installer requires access to the internet to be able to download the FSL software appropriate for your platform and 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; assuming that you wish to install into /usr/local (the default) then just press the Return key when the installer asks where to install to. For example if you downloaded to your Downloads folder:

Once the install completes Linux users should log out (System > Log out) and log back in to complete the FSL setup. If you are accessing the Linux computer via a remote SSH session then close the SSH session and re-login. Apple OS X users should open a new terminal window to begin using FSL.

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: This should display the name of the directory that you installed FSL in.
  • Check that your path is correct by typing: which should display a line like: (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, if desired, by using the testing and evaluation suite FEEDS.

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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, otherwise you are ready to run FSL.

Using FSL MATLAB libraries

The fslinstaller script sets this up for you so you should not need to do this. However, if the installer cannot configure MATLAB for some reason you may need to do this by hand.

FSL ships with several Matlab scripts for loading NIFTI files. These libraries are dependant on FSL environment variables which aren't set in the 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!):

Manual installation

  1. Use the installer to download the install file
  2. Verify the download
    • The installer reports the expected MD5 sum for the download.
    • 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 (it will be the folder you were in when you ran the installer, e.g.
    • Check the file with
    • The hexadecimal number should match that reported after the download.
  3. Unpack the FSL distribution
    • In the terminal, change to the directory where you want FSL installed, e.g.
    • Unpack the fsl download file - for example, if you downloaded it onto your Downloads folder,

      (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.

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

      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.

  5. Configure your shell

For more information on controlling the installer, run it with the -h option - there are options for downloading the install files without installation (for example for installing on multiple computers) and specifying the installation location.

Downloading the install file without installing the software

If you have to install FSL on many computers, or perhaps on a machine that doesn't have access to the internet then you can use the installer to download the FSL distribution for later use. To do this, run the installer with the -o option:

This will download the install package to the current folder and print the expected MD5 checksum for this file to the screen. To install this downloaded file, use the -f and -C options, eg:

replacing MD5sum with the hexadecimal number printed when you downloaded the file.

Scripting installation

If your computers have access to the internet then you can automate the installation process using the -q and -d options to prevent questions being asked and to specify the install location respectively. Where they cannot access our download site then you can download the install file as above and then use the -q, -d, -f and -C options with appropriate values to fully automate the install. For more details run the installer with the -h option.

  1. Introduction


    1. Running FSL
    2. Using FSL with a GridEngine (or similar) computing cluster

FSL is available ready to run for Mac OS X and Linux (Centos or Debian/Ubuntu) - with Windows computers being supported with a Linux Virtual Machine. We also provide source code if you run an OS not directly supported by us.

We strongly recommend that the FSL software is downloaded and installed using our new install script available from the link below:

  • Download FSL

Once you have downloaded the installer, fslinstaller.py, you can use it to install FSL on your computer by following these instructions:

  • Mac OS X

  • Linux

  • Windows

  • Source Compilation

After you have installed FSL for the first time, you can follow these instructions to apply upgrades/patches (e.g. from version 5.0.0 to 5.0.1):

  • Patches

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Shell setup

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/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 Mac OS X, 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.

There are several options you can set to change the way FSL behaves. These options are set using environment variables, see our page on FSL environment variables for details on what can be configured, or look in the files ${FSLDIR}/etc/fslconf/fsl.sh (if you use BASH/DASH) or ${FSLDIR}/etc/fslconf/fsl.csh (if you use CSH/TCSH)(what shell am I using?).

When the shell setup commands are sourced, default settings are applied. You can override these defaults by creating a folder .fslconf in your home folder and creating a file fsl.sh (BASH users) or fsl.csh (TCSH users) within it. This file should contain new definitions for any settings you wish to change.

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For example, to change the output file format of the FSL tools to NIFTI pairs, do the following:

  1. Create the configuration folder
  2. Fliqlo screensaver windows. Create the fsl.sh (or fsl.csh) file with the FSLOUTPUTTYPE environment variable set to NIFTI_PAIR For BASH users:

    For TCSH users:

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Alternatively, if the fsl.sh file already exists you can edit it with the text editor of your choice.

DO NOT copy the centrally installed files into ~/.fslconf

If you copy the ${FSLDIR}/etc/fslconf/fsl.sh or ${FSLDIR}/etc/fslconf/fsl.sh into ~/.fslconf you will cause a loop that will stop you from being able to log in!

We recommend that you only change the FSL settings that differ from the defaults in your ~/.fslconf/fsl.sh (or fsl.csh) and nothing else.

If you wish to change the settings for all users you can create the file /etc/fslconf/fsl.sh (or /etc/fslconf/fsl.csh) on a machine by machine basis. Where you wish to store the settings centrally, we also check the file /usr/local/etc/fslconf/fsl.sh (or fsl.csh equivalent) so you could perhaps NFS mount this folder.


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.

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  • 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, simply edit ${FSLDIR}/bin/fsl_sub - hopefully the comments in this file are sufficient to make this fairly painless, particularly for labs using a GE variant. For clustering software other than GE, note that fsl_sub makes use of a GE feature allowing the submission of a text file containing a list of commands (one per line) to be run in parallel.

Running bedpostX on a GPU or GPU cluster

We now have a CUDA implementation of bedpostX which gives 100x speedup on a single GPU compared to a single CPU core. Running the CUDA version of bedpostX requires some special settings as explained below.

  • Requirements:
    • Linux CentOS 6 or CentOS 6.5
    • NVIDIA GPU with compute capability 2.0 or superior
    • (FSL version 5.0.6 and CUDA Toolkit 5.0) or (FSL version 5.0.7/5.0.8 and CUDA Toolkit 5.5) or (FSL version 5.0.9 and CUDA Toolkit 6.5)
    • SGE for multi-GPU (or optionally SGE for single-GPU)
  • Running:
    • Without SGE (single GPU): Simply run bedpostx_gpu <dataDirectory> [options]

    • With SGE:
      • The environment variable SGE_ROOT must be set

      • In addition, the variable FSLGECUDAQ must be set with the name of your GPUs queue (which may have 1 or several GPUs)

      • Simply run bedpostx using the usual call: bedpostx <dataDirectory> [options]

      • By default, bedpostx will divide the dataset into 4 parts submitted as 4 different jobs. Therefore, if there are 4 GPUs (4 slots in the CUDA queue), they can be processed in parallel. In order to use a different number of parts, use the -NJOBS option. For instance, for using 8 GPUs, run as follows: bedpostx <dataDirectory> -NJOBS 8 [options]

  • Please reference the following paper when using the GPU version of bedpostx:
    • [Hernandez 2013] Hernandez M, Guerrero GD, Cecilia JM, Garcia JM, Inuggi A, Jbabdi S, Behrens TEJ, Sotiropoulos SN, (2013) Accelerating Fibre Orientation Estimation from Diffusion Weighted Magnetic Resonance Imaging Using GPUs. PLoS ONE 8(4):e61892