Yes, NX Nastran can be run independently. The only thing to look out for is your license type. You probably have a bundled license if it came with femap. In that case, you need to specify "prog=bundle" on the nastran command line.
The easiest thing to do is make a run from within femap, then examine the .log file to see the command line that femap used to launch the job. If you use the same input deck and same command line, the job should run.
Note that bundle and desktop licenses impose 2 primary restrictions (compared to an enterprise license):