I just finished recording 100 GB worth of 10 bit raw on my canon 5D mark 3.
The magic lantern screen on the top right says i have 6GB left. However, when plug the CF card into the card reader there is absolutely nothing on the card viewing it from my computer.
How do i fix this?
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Use a decent card reader. I can recommend Kingston FCR-HS4. See http://www.cameramemoryspeed.com/reviews/card-readers/