I'd like to point out that CGI scripts do not receive their arguments via @ARVG, so even if you fix if ($numArgs), your script still won't work. Look at CGI's param method.

Your script itself is extremely unsafe. The user could specify an arbitrary input or output directory name. But that's nothing compared to the user's ability to inject shell commands in $command.

Finally, why shell out to use ImageMagick when it provides a Perl interface? You're forking needlessly, and you're not even checking for success.

Your program needs much work.