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Can FFmpeg or FFmbc be used to do this and if so, what are the parameters? If not, is there any low cost or no cost transcoding software available to do this?

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This should get you started.

ffmpeg -i in.flv -c:v dnxhd -s hd1080 -b 36M out.mov

http://itbroadcastanddigitalcinema.com/ffmpeg_howto.html#Encoding_VC-3

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