Dear Dan,

This is a problem specifically with the munger script. munger is quite fussy about certain input file and directory names. There are couple of odd things here:

> Reference brain stem is ref
> JOB ID =
> Start time is: 1489437302 seconds
> Root directory is /d/Data/cmtk_registration
> Changing to root directory: images_FB
> Setting image root to: images_FB


1. The reference brain stem is ref. Your reference brain is:

Nov01_2016_B3ZD.nrrd

It is better to use names without underscores. These have a special meaning for munger and things may be fragile if your names do not conform to expectations.

2. There might be a problem with the name of the directory containing your input images. It should normally be called images not images_FB.

Best,

Greg.