Hi Paul,
First off thank you for your help and quick response. I added the -oob_value flag and it worked!
Just a little context to answer your questions, although it is not all that interesting/relevant to anybody except me lol. The script I used wasn't from proc.py. This is a relatively old data set with 2 days of scanning, day 1 was analyzed in surface but day 2 wasn't. So I applied the part of the day 1 script related to the surface transformation to the day 2 data and it didn't include the oob flag.
