Justin,
This doesn't look like a complete output from the console. If you're seeing the "ADIR_ReFace" name, then the code has gotten from the wrapping shell script into the compiled-Matlab function, but what you've given me is missing the banner and the stacktrace that would come from an error in that part of the code. Can you please try to give me a more complete console log? Naively guessing with only what I have, I would try renaming the nifti to something more simplistic. All those periods may be messing up the filename vs. extension parsing. 

Best regards,
Chris Schwarz