Did you add the scripts folder to your path? You can do this by calling ./set_path, as explained in the docs. Afterwards, the output of echo $PATH should contain path/to/mrtrix3/scripts in the list.
The set_path script exists in the root directory of your MRtrix3 installation. Therefore to execute it you will need to navigate your current working directory to this root MRtrix3 directory. The “./” in “./set_path” instructs the shell interpreter that you are attempting to execute a file that resides in your current working directory, hence why you need to navigate there first.