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I've recovered some files from an hdd that weren't supposed to be deleted in the first place, but they have seeking problems/crash the players. Since they have the right size, I'm thinking it might be a problem of corrupt index/header, so I'm trying to find a way to fix them. It's easy to find examples on how to fix corrupt .avi files with mencoder, but .wmv seems trickier.

Also, I realize there might not be a way to fix these files, but I figure I might as well as try. As far as players go, I've tried opening it with vlc/mplayer/windows media player.

I can use anything on Windows XP/7 and Ubuntu, as long as it's free. Since the files are 200mb+ and there are quite a few, I don't think trial software would work.

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You can try ffmpeg -i yourfile.wmv -vcodec copy -acodec copy output.wmv, possibly with the option -er 1 up to -er 4 (turns on error concealment). –  slhck Jun 4 '11 at 11:44
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Maybe a bit late now but if you have not solved it yet I recall trying a few things to fix wmv files sometime ago but this was the only one I stored to a disk and as far as I can recall it was free to use. There is also a linux and command line versions.

http://www.radioactivepages.com/asfbin.aspx

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I never used it for wmv but you may try this:

http://www.cgsecurity.org/wiki/PhotoRec

it has an ugly command line user interface and it has some problems under win7 (run it as administrator) but the results for pictures are impressive:

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