I am also trying to use QuickNII with a custom atlas (specifically marmoset and rhesus macaque) data.

However, just as a proof of principle I tried to generate the *.cutlas file using the QuickNII extras and the Waxholm atlas data V4 instead (found here on this nitrc site) of the V2 used in the demo and it keeps throwing an error at the 'Compressing Segmentation' stage.

The error is this:
'Exception in thread "main" java.lang.NullPointerException: Cannot invoke "java.lang.Integer.intValue()" because the return value of "java.util.Map.get(Object)" is null'
The code does work nicely with the WHS V2 data it's meant to be used with but I can't figure out what has changed in the v4 data (except for having more regions).

Considering this isn't working: would it even be possible to use segmented monkey data in QuickNII? Monkey data would include the MRI, segmentation and labels but no DTI (i.e. dataset like this)

Any help would be greatly appreciated. QuickNII worked great for us for mice and rats so if I can continue using it for our monkey data, that would be fantastic.