Is it possible to customise filename for submitted label?

[MalikTeng]

I'm working with a 3D slicer and the monai-label plugin for heart MR image segmentation. I want to automatically keep track of the specific monai bundle used for labeling by adding its name as a suffix to the label file. Is this feasible, or do you have a better approach?

[diazandr3s]

Hi @MalikTeng,

This is a great question.

Are you starting MONAI Label pointing to a local folder? If yes, this is the class we use to manage the local datastore: https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/datastore/local.py#L86

That class creates and modifies the datastore_V.json* file we use to keep track of the volumes and labels.

These are the endpoints to modify the datastore: https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/endpoints/datastore.py#L93

When you submit the label using Slicer, this is the method that is called: https://github.com/Project-MONAI/MONAILabel/blob/main/plugins/slicer/MONAILabel/MONAILabel.py#L1433

and this is the endpoint: https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/endpoints/datastore.py#L93

One idea would be to modify the save_label method by adding more information to the submitted label name.

Hope this helps,

[MalikTeng]

Hi @diazandr3s,

Much appreciated your advice! It seems that I can address the issue by making some adjustments to specific sections of the code within those two scripts, which might need to clone and install the MONAI Label repository on my local machine. However, I couldn't locate precise instructions on how to do this correctly.

Could you please guide me to the relevant documentation or resources that can assist me in this process?

Many thanks!

[diazandr3s]

Hi @MalikTeng,

Instructions for this sort of customization would be the code itself.
Have you tried to modify the datastore to change the prediction name? Here is the part where this happens: https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/datastore/local.py#L496

[MalikTeng]

Hi @diazandr3s,

To enable bundle name tracking in the MONAI Label plugin with 3D Slicer, I followed these steps:

1. Clone and Install MONAI Label: Clone the MONAI Label repository to your local machine and install it in edit mode. For example, clone to ~/MONAILabel and install using the command pip install -e ..

2. Modify MONAILabel.py: In the MONAILabel.py script, located at ~/Slicer-5.4.0-linux-amd64/slicer.org/Extensions-31938/MONAILabel/lib/Slicer-5.4/qt-scripted-modules, alter the self.logic.save_label call. Add the bundle name used for segmentation by including self.ui.segmentationModelSelector.currentText to the params argument, forming a dictionary like {"label_info": label_info, "model": model}. Here, model represents the bundle name.

3. Update local.py: In the cloned MONAI Label repository, navigate to ~/MONAILabel/monailabel/datastore/local.py. In function save_label, modify the label_tag in the logger info and label path lines to label_info.get("model"). This change ensures the bundle name passed in step 2 is used.

After these modifications, MONAI Label will save labels in folders named after the bundle's name. Note that this solution might vary based on different 3D Slicer versions and may require repeating the first step after updates to the MONAI Label plugin.

Looking forward to your feedback!

[diazandr3s]

Thanks for sharing this, @MalikTeng
It makes sense.