search

Neural-Systems-at-UIO / nutil

https://nutil.readthedocs.io/en/latest/
GNU General Public License v3.0
12 stars 5 forks source link

Nutil crashing immediately after start #321

Open antonybcampos opened 2 days ago

antonybcampos commented 2 days ago

Hi!

I am using the QUINT workflow to identify brain regions of cFOS+ cells comparing non-treated versus stress-treated animals. I stained my tissue with cFOS and NeuN. I can provide a sample of some images if needed, and also our current outputs. We have followed the pipeline but, unfortunately, once we reach Nutil and assign all the settings for the run, it crashes immediately.

I would appreciate any input on the type of files or the outputs generated throughout the pipeline. Thanks, Brayan

sharoncy commented 10 hours ago

Hi @antonybcampos. I'm sorry to hear you're having problems. Are you using the Windows or Mac version of Nutil? The Mac version is known to be corrupt, so if you're using this one you'll have to switch to the Windows version. If this is not the issue, I'll need some more info to investigate. The easiest would be if you could send me some example files, I can then do a test run. I'll need your .json file from VisuAlign (or QuickNII), some example segmentations and corresponding atlasmaps (I don't need files for all your sections, just for a few sections), and your .nut file from Nutil (this lists your Nutil settings). Please send them to support@ebrains.eu, stating that your question is related to "brain atlases" and for "Sharon Yates". I'll then get back to you.

antonybcampos commented 1 hour ago

Hi, @sharoncy! Thank you so much for your kind response. We are running everything on Windows. We will prepare this folder with a few sample images and send it to that mail.

I was wondering if the corresponding atlasmaps are the .flat files output from QuickNII? Are those what you meant, or did you mean the raw images/maps that are input for deepslice > QuickNII as well?

We appreciate your support!!