Project-MONAI / Project-MONAI/tutorials
can not edit the inference labels for the radilogy app
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- Dominant language
- Jupyter Notebook
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Description
I follow the tutorial monailabel_radiology_spleen_segmentation_OHIF.ipynb and can start the app. When I want to edit the inference labels as shown below:
I can not find the "segmentation" tool buttons and no upleft pannel either.
The info looks like this:
{
"name": "MONAILabel - Radiology (0.8.1)",
"description": "DeepLearning models for radiology",
"version": "0.8.1",
"labels": [
"spleen"
],
"models": {
"segmentation_spleen": {
"type": "segmentation",
"labels": {
"spleen": 1
},
"dimension": 3,
"description": "A pre-trained model for volumetric (3D) segmentation of the spleen from CT image",
"config": {
"device": [
"NVIDIA GeForce RTX 3090:0",
"NVIDIA GeForce RTX 3090:1",
"NVIDIA GeForce RTX 3090:2",
"NVIDIA GeForce RTX 3090:3"
]
}
},
"Histogram+GraphCut": {
"type": "scribbles",
"labels": {
"spleen": 1
},
"dimension": 3,
"description": "A post processing step with histogram-based GraphCut for Generic segmentation",
"config": {
"num_bins": 64,
"lamda": 1,
"sigma": 0.1,
"device": [
"NVIDIA GeForce RTX 3090:0",
"NVIDIA GeForce RTX 3090:1",
"NVIDIA GeForce RTX 3090:2",
"NVIDIA GeForce RTX 3090:3"
]
}
},
"GMM+GraphCut": {
"type": "scribbles",
"labels": {
"spleen": 1
},
"dimension": 3,
"description": "A post processing step with GMM-based GraphCut for Generic segmentation",
"config": {
"num_mixtures": 20,
"lamda": 5,
"sigma": 0.5,
"device": [
"NVIDIA GeForce RTX 3090:0",
"NVIDIA GeForce RTX 3090:1",
"NVIDIA GeForce RTX 3090:2",
"NVIDIA GeForce RTX 3090:3"
]
}
}
},
"trainers": {
"segmentation_spleen": {
"description": "Train Spleen Segmentation Model",
"config": {
"name": "train_01",
"pretrained": true,
"device": [
"NVIDIA GeForce RTX 3090:0",
"NVIDIA GeForce RTX 3090:1",
"NVIDIA GeForce RTX 3090:2",
"NVIDIA GeForce RTX 3090:3"
],
"max_epochs": 50,
"early_stop_patience": -1,
"val_split": 0.2,
"train_batch_size": 1,
"val_batch_size": 1,
"multi_gpu": true,
"gpus": "all",
"dataset": [
"SmartCacheDataset",
"CacheDataset",
"PersistentDataset",
"Dataset"
],
"dataloader": [
"ThreadDataLoader",
"DataLoader"
],
"tracking": [
"mlflow",
"None"
],
"tracking_uri": "",
"tracking_experiment_name": ""
},
"labels": {
"spleen": 1
}
}
},
"strategies": {
"random": {
"description": "Random Strategy"
},
"first": {
"description": "Get First Sample"
},
"last": {
"description": "Get Last Sample"
}
},
"scoring": {},
"train_stats": {
"segmentation_spleen": {}
},
"datastore": {
"total": 1,
"completed": 0,
"label_tags": {}
}
}
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with monailabel_radiology_spleen_segmentation_OHIF.ipynb and reproduce the reported app workflow using the displayed MONAI Label 0.8.1 configuration. Compare the available interface with the screenshot, focusing on the missing segmentation tools and upper-left panel. Done means the tutorial exposes the controls needed to edit inference labels, with the reproduction steps documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, pytorch
- Domain
- frontend
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100