Debian/Ubuntu users

Non-LTS Debian/Ubuntu users should install FSL from the Neurodebian site - and read the setup instructions.

Quick start for Debian/Ubuntu users

As of fsl 5.0 all you need do is add ". /etc/fsl/5.0/" to the end of your .profile file. When you next login you should find the fsl programs are available.

When I run the installer it says there is a new version and then crashes

Version 3.0.0 has a bug in the self-update code. To get a newer version of the installer you will need to re-download the installer.

I'm running macOS and when I try to launch a FSL GUI I get `command not found` errors

The file system that macOS uses can't distinguish between upper and lower case filenames, so Feat and feat are the same. Consequently, the GUIs on the macOS release are called Toolname_gui for example Feat_gui.

I'm running Mac OS X 10.5 and find that the FSL GUIs crash or don't seem to be working properly

We no longer support the use of FSL on Mac OS X 10.5 and would strongly recommend you upgrade (if possible) to a later version, OS X 10.12 being the current version. The version of X11 that Apple included with Mac OS X 10.5 has a significant number of bugs which can effect usage - especially with the clipboard handling. We would recommend that all users install the latest version of the XQuartz package available from

I'm running MATLAB on macOS and can't get the FSL NIFTI libraries to work

Look at the FslInstallation/MacOsX page for details on using these libraries with MATLAB.

I'm running Mac OS X 10.5/10.6 and the FSL GUIs don't work

We no longer support Mac OS X 10.4-10.8, so this has been kept for historical interest

Have you upgraded from Mac OS X 10.4? If so then you may have a .bash_profile (or .tcshrc or .cshrc) that breaks this behaviour. If you installed using the script then download the current version and re-run it using the `-e` option.

I'm running Mac OS X 10.4 and the FSL GUIs don't work

We no longer support Mac OS X 10.4-10.8, so this has been kept for historical interest

To run the FSL GUIs you need to be running the X11 program which can be found in /Applications/Utilities - it's icon is a white square with a black X superimposed on it. If you have this program running and you get an error like:

Error: Can't open display:

then you need to configure the Apple Terminal application to setup X11 correctly. You can do this by running the FSL installer with the -e option.

FSLView issues

Also, see the FslView/Faq for some installation issues you might come across with FSLView.



FslInstallation/Faq (last edited 13:26:43 22-01-2018 by MatthewWebster)