Using ffmpeg to apply mpdecimate and recreating the folder structure with fixed files to another partition

I have 4.390 video files across 638 folders/subfolders. These files have problems with the framerate and I was able to fix using the command

ffmpeg -i in.mkv -vf mpdecimate out.mkv

How can I use a command line command or batch, so I can apply this fix in all folders and subfolders saving the fixed files to another drive, replicating the same folder tree, and also, using the same names in output files?