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Neural-Systems-at-UIO / nutil

https://nutil.readthedocs.io/en/latest/
GNU General Public License v3.0
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Nutil crashing immediately after start #321

Open antonybcampos opened 3 weeks ago

antonybcampos commented 3 weeks 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 3 weeks 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 3 weeks 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!!

sharoncy commented 3 weeks ago

@antonybcampos I meant the .flat file output from QuickNII, I don't need the raw images (although it would be useful to see a screenshot of one of your raw images to get a better understanding of your data).

maxnoblemm commented 3 days ago

Hi there,

I am having the same issue. I am following the Quint pipeline on a windows PC. I have followed the documentation closely. However, when try to run Nutil it immediately crashes and leaves no report or any information in the output file I have it set to. I can provide examples and files if needed.

Majpuc commented 2 days ago

Hi Max,

Sorry to hear that you experience issues with Nutil. The most common cause of crashing is if you are running a process through a network. Therefore we recommend to run Nutil locally: https://nutil.readthedocs.io/en/latest/FAQ.html If you still experience issues, please send your .json file from VisuAlign (or QuickNII), atlasmaps (are the .flat files output from QuickNII), some example segmentations and corresponding atlasmaps, and your .nut file from Nutil (this lists your Nutil settings). Please send them to support@ebrains.eu. Thank you!

maxnoblemm commented 2 days ago

Hi Maja,

Unfortunately, I am running this on a local network. I have already sent my .json, atlas maps, some examples and the .nut file to the support email.

Thanks,

Max

On Thu, Nov 21, 2024 at 12:29 AM Maja @.***> wrote:

Hi Max,

Sorry to hear that you experience issues with Nutil. The most common cause of crashing is if you are running a process through a network. Therefore we recommend to run Nutil locally: https://nutil.readthedocs.io/en/latest/FAQ.html If you still experience issues, please send your .json file from VisuAlign (or QuickNII), atlasmaps (are the .flat files output from QuickNII), some example segmentations and corresponding atlasmaps, and your .nut file from Nutil (this lists your Nutil settings). Please send them to @.*** Thank you!

— Reply to this email directly, view it on GitHub https://github.com/Neural-Systems-at-UIO/nutil/issues/321#issuecomment-2490367498, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASZJTXRFOKIVA6LH7CCBAWD2BWKV5AVCNFSM6AAAAABQYMK2YKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJQGM3DONBZHA . You are receiving this because you commented.Message ID: @.***>

sharoncy commented 1 day ago

The crashing issues were resolved for the first user following a re-install of Nutil (v1.0.5) directly from Github onto the C: drive. For documentation purposes (in case it is useful for other users), here is the response I gave via EBRAINS support, and the response I received:

My advice: "I recommend removing Nutil from your system, re-installing on the C:drive, and testing again (I see your files are all on the C:drive, this is good). If this doesn't fix it, you could try the latest version of Nutil, available for download here: https://github.com/Neural-Systems-at-UIO/nutil/releases/tag/v1.0.5 . This version is a pre-release, but it has passed our validation steps so should be fine to use. It has several new features, including the option to extract coordinates corresponding to the centroids of objects, which many people have requested. If you're still having problems, I suggest trying on a different computer. "

Users response: "I am happy to report that the newest version and a fresh install seems to be working for us. Both on my office computer (Win10) and on our shared lab workstation (Win7). I am not sure exactly what the issue was, but for this version I made sure to download the zip file from Github directly to the C: drive, extracted it with 7zip, and then just ran the Nutil.cmd file straight from that folder. From there, I just tested it on the same files, making sure that they were also saved on the C: drive."