Unnecessary duplication of files

[ForrestCKoch]

Todo: see #1
@atsuch highlights the issue

BTW, why is it necessary to move around the input images so many times (Study dir --> originalImg --> subjects/mri/orig)? Why not keep one copy of original image (that may be gunzipped) in one input dir (either Study dir or originalImg) and leave it untouched, and place unzipped one in another?

and my response

re: the repeated movement of files -- I completely agree. The duplication of files (and their unzipping) wastes space and unnecessarily complicates things. I have only become involved in this project relatively recently and wasn't involved in any of the early design choices. Since it "works" and it is so deeply ingrained in the codebase this is currently a lower priority issue for me; however, I agree this should be changed in the future.