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Does anyone know of a good software (preferably free) to convert the 3D videos from the Fujifilm W3 3D camera into side-by-side 3D format in a batch processing manner?

I know the FinePix software does that but it does one at a time. With the bug in the original camera firmware that turns off recording every minute, I have so many clips that converting one by one is practically impossible. (I know there is a firmware upgrade, but I haven't done it yet, and I have a whole bunch of videos to convert.) I can't watch the videos on my LG Cinema 3D unless I play them through my camera (which is not practical either), or convert them to side-by-side.

Another advantage of converting to side-by-side is that the file size reduces to 15% of the file size generated by the camera without any noticeable change in quality.