Using MATLAB to read .mov files from HyperDeck Studio Pro 2

I have been using a Blackmagic Design HyperDeck Studio Pro 2 to record uncompressed .mov files but I can't seem to read these files into Matlab or Corel Video Studio (this is the only other video software I have). Ideally I would like to edit and analyze the videos in Matlab but there does not seem to be enough/correct header information contained in the .mov file to allow Matlab to open it. I have also tried converting the .mov files to other formats but the lack of header/codec info seem to prevent the other file types from being opened in Matlab as well. Any help regarding settings for the recorder that would avoid this problem or options for converting/editing the files I have would be great.