Unknown issue with running dataset in Quantifier

Neural-Systems-at-UIO / nutil

https://nutil.readthedocs.io/en/latest/

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Unknown issue with running dataset in Quantifier #267

Closed ingvildeb closed 2 years ago

ingvildeb commented 2 years ago

Hi! I have a dataset that just won't run in Quantifier. I have many files with similar paths and using the same (custom) atlas that have run perfectly and am not able to understand why this one doesn't.

The .nut file is located here: Y:\2021_Bjerke_CalciMap-project\Analyses\Nutil\P35\Calbindin and all the paths are on the server. I would greatly appreciate help investigating this.

sharoncy commented 2 years ago

Ingvild and I looked at this yesterday. The reason it didn't run is because there was a FLAT file missing. The other warnings came up because there were sections in the .json that had not been anchored since they fell outside of the reference atlas: the warning messages did not give this info so it was hard to figure out. Removing these sections from the .json fixed the problem.This is not a use case we have come across before, which is why the warning messages didn't describe the problem sufficiently. Consider revising the warning messages.

sharoncy commented 2 years ago

I will add a new issue to review/revise the warning messages. This issue can be closed. 26.08.22.

Majpuc commented 2 years ago

Very good. Is the reason for the missing flat file identified? faulty export?

ingvildeb commented 2 years ago

No, it was a section that had been excluded during anchoring (image removed from QuickNII and VisuAlign files) but there was still a segmentation image for it, so just a mistake on my side.