I just wanted to include my experience using Dual ISO somewhere for others that might be having the same struggle with the conversion to dng.
I am running Windows 8 64 bit which might be my problem
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I downloaded the cr2hdr zip folder from this post. I unzipped into the same folder as my dual ISO cr2 image file. I dragged the cr2 image onto cr2hdr and it launched, but it seemed to stop only part way through processing the file. It produced 2 files:
tmp.pgmCamera
tmp.txt
I searched for references to pgmcamera in an attempt to find a solution but found none, at first I thought I had the wrong copy of the .exe. In the end I had to run cr2hdr from the command prompt in order to produce a dng file I could use. After navigating to the correct folder just type:
cr2hdr.exe image.cr2
Where image.cr2 should be replaced with the name of the image you want to process.
I am running Windows 8 64 bit which might be my problem

I downloaded the cr2hdr zip folder from this post. I unzipped into the same folder as my dual ISO cr2 image file. I dragged the cr2 image onto cr2hdr and it launched, but it seemed to stop only part way through processing the file. It produced 2 files:
tmp.pgmCamera
tmp.txt
I searched for references to pgmcamera in an attempt to find a solution but found none, at first I thought I had the wrong copy of the .exe. In the end I had to run cr2hdr from the command prompt in order to produce a dng file I could use. After navigating to the correct folder just type:
cr2hdr.exe image.cr2
Where image.cr2 should be replaced with the name of the image you want to process.