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:
 {{{#!highlight bash numbers=disable
echo $FSLDIR
 }}}
 This should display the name of the directory that you installed FSL in.
 * Check that your path is correct by typing:
 {{{#!highlight bash numbers=disable
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:
 {{{#!highlight bash numbers=disable
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.