Error in Nvidia AIAA

You can ask MONAILabel developers to help you port the old model into a MONAILabel app.

@diazandr3s

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Thanks for the ping, @lassoan

@Pari_TF, have you considered using MONAI Label (GitHub - Project-MONAI/MONAILabel: MONAI Label is an intelligent open source image labeling and learning tool.)?

It is easy to get a pretrained model for lung segmentation using MONAI Label. Are you using a public dataset?

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Thanks for your reply. No, I haven’t used MONAI Label. That’s great. I will try it. Thank you so much. Yes, I’m working on a public dataset.

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I am using my own data to segment lung nodules. The training set has been using the annotation_lung_tumor model of Nvidia AIAA. Now that the test set is ready, I found that the above model is no longer available, which caused me a lot of trouble. Can you help me add the old model to MONAI Label, thanks.

Do you know which dataset they used to get that pretrained model? I think it is Task06_Lung (MSD - Google Drive) from the Medical Segmentation Decathlon but I’m not sure.

If that’s the dataset, you should be able to get a pretrained model fairly easy. Do you have a GPU-based PC?

It is indeed a model pre-trained with the Task06_Lung dataset, and we use boundary-point based segmentation of lung tumor on CT (AIAA for 3D Slicer). But now the model is not found in NVIDIA. Also, we have GPU-based PC.

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I was going to try this out but I am consistently running into

monailabel apps --download --name deepedit --output apps
Using PYTHONPATH=/home/rbumm:
App deepedit => /usr/monailabel/sample-apps/deepedit not exists

after a

pip install monailabel

This is with and w/o an elevated bash on Windows 10 Ubuntu WSL. Any ideas?

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@rbumm there were recently some changes in folder structure. Please try out the monailabel-weekly instead (pip install monailabel-weekly)

Then download the radiology app as follows:

monailabel apps --download --name radiology --output apps

As an example you could download and use the spleen dataset:

monailabel datasets --download --name Task09_Spleen --output datasets

Then start the server using the Deepedit model:

monailabel start_server --app apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models deepedit

Here you can see more details: GitHub - Project-MONAI/MONAILabel: MONAI Label is an intelligent open source image labeling and learning tool.

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Thanks, Andres, tried this already - pip uninstalled monailabel and pip installed monailabel-weekly, but there is a similar message:

monailabel apps --download --name radiology --output apps
Using PYTHONPATH=/home/rbumm:
App radiology => /usr/monailabel/sample-apps/radiology not exists

Probably a permission problem.

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This is strange :confused:
Probably the weekly installation wasn’t clean. Please do a clean installation using a clean Python virtual environment.

Needed to install monailabel via github to make this working in Windows 10 WSL (see here).

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Hi @rbumm,

My bad, I just realised the weekly version doesn’t install the candidate release 0.4.0 :slightly_frowning_face:
In order to use the radiology app you should either use directly the GitHub repo as you did or install directly the candidate release:

pip install monailabel==0.4.0rc3

Please let me know how that goes. Happy to help.

Andres