can I change the codec used for recording in FMS

I'm developing a web client that record the user speech and send it to the FMS that communicate with a speech processing application...My problem is that I must convert the flv file to wav using ffmpeg, but there are some flv codec that are not supported by ffmpeg .
Can I change or choose the codec used by FMS to encode and record the audio file?And if it's possible,How can do this?

thanks