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skaliy committed Aug 17, 2023
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# Endometrial cancer segmentation
The primary objective of this repository is to reproduce the results reported in [Automated segmentation of endometrial cancer on MR images using deep learning](https://link.springer.com/content/pdf/10.1038/s41598-020-80068-9.pdf). In addition, we have looked at improving the segmentation performance using multi-sequence MR images (T2w, VIBE, and ADC) as reported in the study [Automatic segmentation of uterine endometrial cancer on multi-sequence MRI using a convolutional neural network](https://www.nature.com/articles/s41598-021-93792-7).

The trained weights and exported learner are available on [HugginFace](https://huggingface.co/skaliy/endometrial_cancer_segmentation).
The trained weights and exported learner are available on [Huggin Face](https://huggingface.co/skaliy/endometrial_cancer_segmentation).
Test our model live with the Gradio app for VIBE on [Hugging Face Spaces](https://skaliy-endometrial-cancer-segmentation-app.hf.space). To run the application on your local system, follow the instructions below.

## How to use
1. Clone this repository.
1. Clone this repository:
```bash
git clone git@github.com:MMIV-ML/fastMONAI.git
```
2. Install fastMONAI by following the instructions provided [here](https://github.com/MMIV-ML/fastMONAI/tree/master).
3. (<b>Optional</b>) Run the `01_ec_training.ipynb` `03_ec_training-multi.ipynb` notebook to train your own model.
4. Run the 02-ec-inference.ipynb or inference_script.py to perform inference with the trained model for VIBE images.
5. Run the 04-ec-inference-multi.ipynb to perform inference with the trained model for T2w, VIBE, and ADC images.
3. (<b>Optional</b>) Run the `01_ec_training.ipynb` `03_ec_training_multi.ipynb` notebook to train your own model.
4. Run the `02_ec_inference.ipynb`, `inference_script.py` or `app.py` to perform inference with the trained model for VIBE images.
5. Run the `04_ec_inference_multi.ipynb` or `inference_script_multi.py` to perform inference with the trained model for T2w, VIBE, and ADC images.

If you choose to use `inference_script.py`, please follow these steps:
If you choose to use `inference_script.py` or `inference_script_multi.py`, please follow these steps:

- Make the script executable using the following command in the terminal: `chmod +x inference_script.py`
- Run the script by executing the following command in the terminal: `python inference_script.py IMG_PATH`
- Make the script executable using the following command in the terminal:
```bash
chmod +x inference_script.py
```
- Run the script by executing the following command in the terminal:
```bash
python inference_script.py IMG_PATH
```

If you choose to use `app.py`, please execute the following command in the terminal:
```bash
gradio app.py
```

## Results for VIBE
The box plot of the predictions on the validation set:
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