Sorry, I don't know whats wrong with me, I did indeed put a huge bug in the script and every time I looked at it, I kept thinking, "no, its supposed to delete the temp file".  I even pasted in the bug when I posted here.  You are correct Isaac, this is a bug, and its one that I introduced.  I'm afraid you have to change that first remove line from:
rm -f irfretroicor.nii irfretroicor+orig.????

to:
rm -f irfretroicor.nii

I don't know how I left this in there, I'm really sorry because I know that first off, its a lot of work to get any new tool started, and secondly this one takes a lot of time to run.
Erik