Highlight the folder that museplayer.exe is found in. Then hold shift and right-click the folder. You should see “open command window here” as one of the options; select it.
Now you should be able to run:
museplayer -f /path/to/file.muse -C /path/to/new.csv
If you’re having trouble getting the file paths correct, you can instead place the muse file in the same folder as museplayer.exe. That would let you run:
museplayer -f file.muse -C new.csv
Of course, replace
file.muse with the name of your muse file.
Also, if you’re trying to build the project from that bitbucket repository, you can instead install MusePlayer via the Research Tools installer on this page.