Original labels not loading in 3D Slicer after batch inference #870
Replies: 3 comments 5 replies
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Hi @Nachimak28, thanks for your detailed post. This is great! It's strange why this is happening. Could you please try with the Slicer preview release? If labels are in the |
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Hi @Nachimak28, Thanks for the follow-up. I've just created a PR changing this bit for the segmentation spleen model. You can see here the change: https://github.com/Project-MONAI/MONAILabel/blob/fixSpleenSeg/sample-apps/radiology/lib/configs/segmentation_spleen.py#L49-L51 Please let me know how that goes :) |
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That's helpful.. please go ahead and make the videos.. we can share across.. |
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Hi there,
As per another [discussion](#856) which proved really helpful. I am trying to build a Proof of Concept workflow.
Context: Training a custom 3D segmentation model and hosting the monailabel server in a CPU since we can't afford a GPU letting the monailabel server act as a backend to supply the labels without any training happening then and there.
What all I have done till this point:
Issue faced:
Even if the original labels are present in the
images/labels/original
directory, I dont see the label being loaded in 3D slicer and still have to run the model inference everytime.I also checked the plugin config in 3D slicer's application settings and the Original Labels option is enabled.
I presume I might be doing something wrong with the lib/config and lib/infer app codebase that the original label isn't being transmitted when I press the next sample button.
Here are my config and infer files
Config: https://github.com/Nachimak28/monailabel_custom_model_inference/tree/main/config
Infer: https://github.com/Nachimak28/monailabel_custom_model_inference/blob/main/infers/lung_lesion_seg.py
Note: Both these are simply inspired from the segmentation_spleen.py files as mentioned in the model addition guide with only minor necessary changes.
I also tried a similar experiment with the spleen segmentation example given in the documentation, it still does not load the already present label.
monailabel version: 0.4.0
Slider 3D version: 5.0.2 stable
(would the original label load in a preview release ?)
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