Hello, 

When running the nutil quantifier using the Waxholm Space Atlas v4, the RefAtlasRegion report is missing in the 'reports' folder within the output folder. 

Is it not possible to get the RefAtlasRegion report using this atlas?

Thank you in advance, 

Britt 

Hi Britt,

I did some testing here, Nutil v0.8.0 generates RefAtlasRegion reports for WHSv4 as it should (did you use this version of Nutil?). So I'm not sure what's happening on your end. If you send me a test dataset (at least one segmentation in png format, corresponding atlas map in flat format, the json file from QuickNII or VisuAlign containing the anchoring information and the nut file from Nutil) then I can try to replicate the error. 

Sharon Yates (s.c.yates@medisin.uio.no)

Hi Sharon, 

Thank you very much for your quick reply! 

I will have a look at the Nutil version and otherwise send you a test dataset tomorrow.

Best,

Britt 

Hi again Sharon, 

I am afraid I still cannot get the RefAtlasRegion reports to work. After making some changes to the nutil input, I now get the output file but all object counts are N/A. 

I have sent you an email with example files that I am using. 

Thank you!

Britt 

Hi Britt,

Nutil doesn't generate object counts if you switch on the "object splitting". Try switching the "object splitting" off. See more info here https://nutil.readthedocs.io/en/latest/Q...

Hope this helps,

Sharon 

Originally posted by Britt van de Gevel:

Hi again Sharon, 

I am afraid I still cannot get the RefAtlasRegion reports to work. After making some changes to the nutil input, I now get the output file but all object counts are N/A. 

I have sent you an email with example files that I am using. 

Thank you!

Britt 

Hi Sharon, 

Thank you for your reply. 

I have re-downloaded nutil and also have had object splitting off. I have now realised that while nutil is creating individual section reports, I get this error which makes the programme quit:

'The instruction at 0x00007FF8CFDA2D0D references memory at 0x0000000000000003. The memory could not be written.'

The hard drive I'm working on has 998 GB free to use. 

Do you know how I can solve this error?

Best wishes, 

Britt 

Hi again,

I am not sure why the program quits in your case, but a common cause of crashes is that the connection between Nutil and the images is cut during the processing time. This can occur if the Nutil software is stored in a different location to the images (for example, Nutil stored on the C: drive and the images stored on another server). Try testing with both the software and the images on the C: drive. If this doesn't fix your problem, you could send me a dataset so that I can test - a json file from QuickNII/VisuAlign, a segmentation (png) and corresponding atlasmap (flat format) and the NUT file containing your Nutil parameters (s.c.yates@medisin.uio.no). ;

Best wishes,

Sharon

Originally posted by Britt van de Gevel:

Hi Sharon, 

Thank you for your reply. 

I have re-downloaded nutil and also have had object splitting off. I have now realised that while nutil is creating individual section reports, I get this error which makes the programme quit:

'The instruction at 0x00007FF8CFDA2D0D references memory at 0x0000000000000003. The memory could not be written.'

The hard drive I'm working on has 998 GB free to use. 

Do you know how I can solve this error?

Best wishes, 

Britt 

Hi Sharon,

Thank you for your advice! The problem might be that I had too much data I put in in one go. 

Splitting the data into smaller chunks and making sure nutil and the data are both on the C: drive seems to have fixed the issue of the RefAtlas regions report - especially when I turn off the coordinates. 

To get one final RefAtlas regions report for the whole data series, would you suggest to take the sum of the cell counts in the whole series (all sections combined) RefAtlas regions report per chunks I've divided the data into? 

Best, 

Britt