It's been a while since I've used MATLAB from the command line, but the basic approach you should be taking is invoking the OS to run the MATLAB script in question, and telling that script to generate your desired .mat file.

In order to invoke the operating system with Perl, there are two basic approaches you can take.

1. If you want to capture output from the process, then you should use backticks (`). my $result = `matlab`; See Quote and Quote like Operators. Note this captures STDOUT and not STDERR.
2. If you don't care about output, then system is probably the command you want. system('matlab');

See MATLAB documentation for info on how to interact with MATLAB on the command line.

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