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Notebook to demo the suggested nnUNet MONAI Bundle #1939

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Notebook to demo the suggested nnUNet MONAI Bundle #1939

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@SimoneBendazzoli93 SimoneBendazzoli93 commented Feb 5, 2025 •
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Fixes #1938

Description

Notebook tutorial to demonstrate the suggested solution for wrapping nnUNet into a MONAI Bundle (Project-MONAI/MONAI#8328)

The notebook includes code to:

  1. Train a nnUNet model using the nnUNetV2Runner implementation
  2. Wrap the trained model into a MONAI Bundle-compatible model
  3. Run Inference using the MONAI Bundle syntax
  4. Instructions on how to generate the MONAI Bundle to run the nnUNet training step with the MONAI Bundle syntax.

Checks

  • Avoid including large-size files in the PR.
  • Clean up long text outputs from code cells in the notebook.
  • For security purposes, please check the contents and remove any sensitive info such as user names and private key.
  • Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the ./figure folder
  • Notebook runs automatically ./runner.sh -t <path to .ipynb file>

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pre-commit-ci bot and others added 10 commits February 5, 2025 15:39
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Signed-off-by: simben <[email protected]>
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Enhance nnUNet MONAI Bundle Notebook with data handling and configura…
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…tion updates
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Merge branch 'main' into main
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DCO Remediation Commit for simben <[email protected]>
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Tutorial for using nnUNet MONAI Bundle
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