The line you have provided is the recommended mechanism for ensuring that the MRtrix3 executable directories are added to the
PATH environment variable every time you start a new terminal session; that's what allows you to run MRtrix3 commands by their name alone, rather than providing the full path to their location every time. The command that @jdtournier requested will print the contents of that environment variable, which may provide a clue as to why your system is not finding these commands.
For instance: the
$(pwd) part of that line inserts text corresponding to the path of the current working directory; this is why this line must be executed from the directory in which MRtrix3 is installed.
Furthermore, your command is ignoring the existing contents of
PATH and completely over-writing it with only those three directory locations; this may affect your ability to execute other commands within your terminal. Is there a reason why you are not using the command as it appears in the documentation? i.e.:
echo "export PATH=$(pwd)/release/bin:$(pwd)/scripts:$PATH" >> ~/.bashrc