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Does anyone know if medium or small raw files are supported with dual iso? I can't seem to find any info about it.
I tried a timelapse last night with small raw set on my 6D.  I get an error when converting using cr2hdr (latest from https://bitbucket.org/a_d_/magic-lantern/downloads):

Input FIle : DUAL6977.cr2
Canon Eos 6D detected
Full Size : 2736 x 1824
Active Area : 2736 x 1824
Error: dcraw output is not a valid PGM file

Thanks for any help and for all the work guys!

Thanks engardeknave for this.  It's Great!

Is there a way to set the CR2 image path to a folder instead of the dialog box? 

*EDIT*

Never mind, I figured it out.  Just had to read through it..   
For others like me, I changed:

inputfolder=InputBox("Enter the path to the dual ISO shots.","Dual ISO Script")

to

inputfolder="D:\NewPhotos\DUALISO"