FSL installation troublshooting
Problems running getfsl.sh or fslinstaller.py
If the getfsl.sh or fslinstaller.py scripts fail, please save a copy of all of the text that was printed in the terminal, and also check for a log file in your home directory called fsl_installation_<date>.log - if you send us a message, include this information, as it will help us to diagnose the problem.
python: command not found errors
If you have downloaded the fslinstaller.py script, your system must have a Python interpreter installed. Some systems do not have a command called python, and will print errors like python: command not found. If this happens try calling python3 fslinstaller.py or python2 fslinstaller.py.
Some versions of macOS do not have Python installed by default - if you do not have any Python command available, you can download an installer from https://www.python.org. Alternately, Python will be installed as part of Xcode, which you can install by running sudo xcode-select --install.
You do not need a Python interpreter if you use the getfsl.sh script.
SSL: CERTIFICATE_VERIFY_FAILED errors
If you experience SSL certificate errors on macOS, try running the installer with /usr/bin/python fslinstaller.py or /usr/bin/python3 fslinstaller.py. If you have installed Python separately from https://www.python.org, make sure you have run the Install certificates script, as described here.
If you are still experiencing SSL errors, or you are using Linux or WSL, try running the fslinstaller.py script like this:
python fslinstaller.py --skip_ssl_verify
fsl: command not found errors after installing
If you succesfully installed FSL, but are unable to run any FSL commands:
- Make sure you have closed and re-opened your terminal / WSL shell. Another option is to reboot your computer.
- Check your shell configuration to make sure that the FSL initialisation commands were correctly added.
Localisation problems
FSL programs generally require a period to be used as the decimal separator ( e.g. 10.4, 0.235 etc ). If your environment is configured to use a different character such as a comma then this may cause problems. Two potential fixes are to change the LC_NUMERIC variable value by:
- typing the following lines into a terminal locally each time you want to run FSL, or
- globally modifying all terminals by adding the following lines to your shell configuration file (see the page on configuration).