Hi,

Sorry to hear you're having issues. There is something going wrong here, you shouldn't get this message for CCFv3 (2017) as a custom region file is built into the Nutil package. Make sure you select "default" for customised reports (if you select "custom" you'll have to provide your own custom region file, more info here: https://nutil.readthedocs.io/en/latest/QuantifierReports.html). Which version of Nutil are you working with? I recommend either v1.1.0 or v0.8.0. Once you have filled in your parameters in the Nutil user interface, do you make sure to save your .NUT file before pressing start. Hopefully these suggestions will fix the issue. If not, let me know and I'll look into it more closely.

Best regards, Sharon

Originally posted by Elizabeth Teasell:

Hi, 

I am trying to run Nutil quantifier and I am getting the error message: You need to provide a custom region file (there is no default custom region file for this atlas).

I have selected Allen mouse brain atlas CCFv3 (2017) as the reference atlas. 

I am not sure what a custom region file is. 

Thanks in advance