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I am looking for a binary that can convert mpg files to mj2 (Motion JPEG 2000) files via terminal in Linux server.

Are there any?

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I do not believe you can output to mj2 container with ffmpeg, but you can encode to JPEG 2000 with ffmpeg and use mov or mkv container. You can encode via the native and experimental j2k, or the external library libopenjpeg which requires your ffmpeg to be compiled with --enable-libopenjpeg. Note that the j2k encoder may not support your desired pixel format and also may not provide bit exact outputs compared to the reference encoder:

[FFmpeg-user] Can you encode lossless Motion JPEG 2000 videos with ffmpeg using the right command line arguments?

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Yes you csn do this quite efficiently with the ffmpeg binary.

It is a commandline bin for Linux and Mac (also Win I believe), that is free:

http://ffmpeg.org/

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