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 macOS)

• Check that your environment is correct by typing:

  echo $FSLDIR
  

  This should display the name of the directory that you installed FSL in.
• Check that your path is correct by typing:

  flirt -version
  

  which should display a line like:

  FLIRT version 6.0

  (although the version number might be different).
• Check that the miniconda environment installation completed successfully:

  which imcp
  

  • which should display a line like:

  /usr/local/fsl/share/fsl/bin/imcp

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.