Hi Elizabeth,

As we released Nutil v1.1 recently, I did a test run to check that the custom region file for Allen CCFv3 2017 is incorporated correctly in Nutil. I wasn't able to replicate the issue (the error message did not come up for me), so I'm not sure what's going on in your case. As a workaround, we provide the default "custom region" file for CCFv3 2017 as part of the Nutil package (in the "CustomRegion" folder). If you select "custom" instead of "default" for customised reports, you can navigate to this .xlsx template (CustomRegionMouse_2017.xlsx) and then run the analysis as normal. The custom regions are basically compilations of reference atlas regions, this feature allows you to define your own regions-of-interest, potentially saving a post-processing step in the analysis. 

If you're still having problems, feel free to send me an example dataset (to: support@ebrains.eu , stating that the issue its related to brain atlases and that it's for Sharon Yates). I'll need a segmentation file corresponding to one or a few of your sections, corresponding atlas maps, your .JSON file from VisuAlign (or QuickNII if you haven't used VisuAlign) and your .NUT file from Nutil. 

Best regards,

Sharon