So ironic, I used to be so tech challenged but have had so many "opportunities" in the last few months to learn more than I have in 5 years.
I too have converted many audio files from MP3 to MP4 to CD and from MP4 to MP3 to CD...........now I have never worked with FLAC of course, since I have never had to, but all these conversions are interesting.
I really listen to songs I play carefully and I have never noticed the difference in any of the conversions I have made whether it be from MP3 to MP4 and to CD and also of course MP4 to CD. The MP3 converter I use when I download music from Amazon is theirs and it is set up to sync into iTunes automatically. I don't hear a difference. And now that I have the FLAC version of Can You Hear Me, I have synced it with iTunes and I hear no difference. Now, no matter how hard I listen there are many more people who have had much more experience and a better trained ear to hear the differences, but it's fun to play with; so fun in fact I downloaded AVS Audio Converter 6.3, and really, I didn't know there were so many audio formats! Now it gets more interesting so I will play around with that! And there's a video converter to play with which is awesome, considering I have a new NOOK. Interesting thing on this converter........you can sync any song to iPhone; but then you can do that with iTunes as well

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No one mentioned video and what kind of quality is lost when converting from dvd digital format into iTunes, but I have done it rather successfully with Handbrake and gotten some good results with RealPlayer, although I see the difference with RealPlayer. The best of course is when I have purchased a dvd with a digital format that loads, one time only of course

, into my iTunes library and of course it's of true digital quality.
Now of course I will say I don't operate a Mac system with Snow Leopard, which would be the best way to run iTunes, but I have my trusted PC; Problem is I have worked so much on the Mac in the last few months I know more about it than my PC!
Now to play with FLAC! Awesome fun these tech thingys are!
Maybe one day I will have to get myself a Mac Air or something cool
