To run bse from the command line, you need to either specify the path to the bse command or add the path to your PATH variable. For example, if you unpacked the BrainSuite programs to your home directory, which I’ll call wwu94, then the path would be:
In Linux BASH, you can type this command:
to add BrainSuite’s program directory to the start of your path. Then, when you call bse, it should run.
You can also call the programs on the command line like this:
which tells the shell the precise location of the program.
Please give that a try.