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I have iTunes 11.0.2.

For the first time ever I have downloaded some mp4's from youtube - the ones that say share with anyone and everyone if you can, so I thought I would.

I was able to upload or add them to the library in itunes, and they play fine there.

But when I go to sync them to my ipod, it is like the mp4's don't exist and the nothing happens when I click the apply button to sync, even though the mp4's are all checked.

Does anyone know how I can sync these mp4's to my ipod from itunes?

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Have you tried to convert the files. Under file menu create new version, at this point it gives you three options, create iPhone or iPod version, create iPad or ATV version, and create AAC version. I haven't tried this, but found this option while checking out iTunes 11, not sure if this was in earlier versions. –  rclyde Mar 8 '13 at 19:40
    
@rclyde, you should post this as an answer (minus the first sentence), because that is the answer and you should get credit for this. iOS devices and iPods only support a subset of the MP4 format, and this menu option reconverts them. –  bispymusic Mar 8 '13 at 22:09
    
I have tired to create a new version like you suggested, where you suggested, and the first few times itunes froze, and after restarting a couple of times it now tells me: "One or more videos were not converted because they are already in the correct format". –  Jammie Mar 9 '13 at 3:26
    
iPod doesn't play any mp4 you put into. It supports only fixed number of resolutions, so you should convert your video before sync. I recommend handbrake to convert video. –  Eir Nym Mar 9 '13 at 8:19
    
I downloaded handbrake, converted two of the mp4 videos with it. I then deleted those same videos that were currently in itunes. Then I uploaded the new handbrake converted ones, once in itunes they will play, when I tried to sync them with my ipod, the same result as above, its like they don't exist and they won't sync. As a side note, handbrake seems to be a cpu hog, it took all of the cpu's resources and shot the mac's temp up to 240 degees F with a cooling pad. It usually runs from 113 F to 140 F with a cooling pad. –  Jammie Mar 10 '13 at 13:03
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