Yes. Cartographer may run from a command line, but it's still a Windows app.
Cartographer comes with a sample command file for FF1 that demonstrates two different ways to extract the same script, as well as a batch file you can run instead of opening a command prompt. Just right-click on Cartographer.bat, select "Edit", and you can modify it in Notepad so that it will extract the script from the ROM using your custom command file. Once you're done, just double-click on Cartographer.bat and it will run the command.