Trying to run MONAI Label to autosegment heart

[coronaryangina001]

Hello! I'm trying to use the segmentation pre-trained model in the radiology app to autosegment out some hearts that I plan on 3d printing! I've gotten the MonAI Label server working on my computer using Anaconda in this tutorial: https://www.youtube.com/watch?v=8y1OBQs2wis&t=154s. I've been able to upload my own data onto the server but I can't get any of the programs (deepedit, deepgrow, or segmentation) to work! I'll attach some images to maybe help.

I can't figure out why the "Model" section in auto Segmentation or SmartEdit/Deepgrow won't populate but I suspect that's where the problem lies.

Here is the command I used to start the server:

Thanks in advance for the help!

[coronaryangina001]

^the blacked out part is the directory for my CT scan that I'm using

[coronaryangina001]

I figured it out! I had to re-install my conda environment and then go in and re-install monailabel! Problem now is that when I run autosegmentation it just spits out a blob.

[coronaryangina001]

this is what its throwing on startup, I re-installed pytorch w/ CUDA so it would see my graphics card:

[diazandr3s]

Hi @coronaryangina001,

That'd be great! Is that something I could feasibly do myself?

Yes, you could train the model following this tutorial: https://github.com/Project-MONAI/tutorials/tree/main/auto3dseg#performance-benchmarking

Regarding MONAI Label, I see it started without issues. Have you tried fetching the next image? Which file format are you using to start the server?

[coronaryangina001]

I'll check that out as soon as I get the server issue fixed again.

I have, I'm using the exact same file I've been using. Is it something to do with 3d slicer not recognizing the "segmentation" app running?

I can retrieve my CT just fine using "next sample"

this won't let me select anything, last time this happened I installed a clean environment and that fixed it (which was the origin of this post) but now that isn't working.

[coronaryangina001]

Okay. I have a really really weird result going on. The "model" section is NOT letting me select anything in slicer 5.7.0 (latest release) but on the older slicer 5.2.2 it works. I'll post photos:

I think there is something wrong with the MonAi plugin maybe?

[coronaryangina001]

Okay. I think I got it figured out. If you have the old Nvidia AI Assissted Annotation downloaded then it causes that box to be greyed out. I uninstalled it and now it all works again:

[diazandr3s]

It's cut off, but that part about something not being installed correctly might be the issue.

That's true. I see it shows 0.0 seconds on the logits. The inference is not complete.