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First steps
PoisonConvert only works properly if you do a little preparation on your Synology-NAS:
You can use any program that will do the job (e.g. putty on windows, terminal on OS X).
User: root
Password: Your admin-password
The program needs ffmpeg installed on your DiskStation. Unfortunately, in most cases, there is an outdated version of ffmpeg installed that doesn´t understand the „new“ syntax (e.g. „-c:a“ instead of „acodec“). So you have to install ffmpeg yourself. In order to simplify this process, I've written a script that installs ffmpeg together with libx264 and libfaac on Synology DiskStation. Please check out this thread: Automatic installation of x264, ffmpeg, etc....
Compiling ffmpeg will bring you ffprobe and qt-faststart on the DiskStastion too.
Make sure you have ipkg installed on the DiskStation. Numerous tutorials can be found on the web (like: link). If you have done that, install ipkgs bash:
ipkg update
ipkg install bash
Ipkg is not required anymore. You can use the Synology installer script to automatically install PoisonConvert on your DiskStation (take a look at the readme for more information).