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
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
Hi Sharon,
Thanks for the quick response. It is still giving the same error.
I am using Nutil v1.1, I just downloaded this yesterday on a different computer as I was trying to run quantifier on my laptop and the whole program would shut down and close before even starting the analysis. I have left all the advanced settings on default, so the customised reports is 'default'. I did save the .NUT file directly before starting.
I do have two colours on my segmentations (red and blue) because I had to run object classification- but I don't think that should be a problem as the object colour (red) is selected.
Thanks for your help,
Elizabeth
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
Hi Sharon,
Thank you so much for all your help. Putting the customised report in seems to ahve fixed whatever the issue was and everything appears to be running smoothly now.
Thanks again,
Elizabeth
Originally posted by Sharon Christine Yates:
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