Create README.md

research/spine/README.md

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+# Multi-Center CNN-based spine segmentation from T2w MRI using small amounts of data
+The source code, designed to reproduce our test results and facilitate training and running inference on your own data. 
+The trained weights and exported learners are available on [Huggin Face](https://huggingface.co/skaliy/spine-segmentation).
+
+## Getting started
+### Quick Start
+Yyou can run the notebooks directly in Google Colab.
+
+### Local Setup (Optional)
+1. Clone this repository:
+```bash
+git clone https://github.com/MMIV-ML/fastMONAI
+```
+2. Install fastMONAI by following the instructions provided [here](https://github.com/MMIV-ML/fastMONAI/tree/master).
+3. (<b>Optional</b>) Run the `00-spine-segmentation-training-evaluation.ipynb` notebook to train your own model or to reproduce the test results reported in our paper.
+4. Run the `01-spine-segmentation-inference.ipynb` or `inference_script.py` to perform inference with the trained model on own data
+
+If you choose to use `inference_script.py`
+- 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
+```
+
+## Research PACS 
+Our spine segmentation application deployed in the research PACS system at our hospital: 
+![](figs/research_pacs.png)