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+# MRI Segmentation Tool
+
+An MRI segmentation tool for lung and heart segmentation using PlatyPy library.
+
+## Environment
+
+- Ubuntu 20.04
+- Python 3.8.10
+
+## Installation
+
+1. Clone this repository:
+```bash
+git clone https://github.com/XiaoKChenEdu/MRI-Segmentation
+cd MRI-Segmentation
+```
+
+2. Install dependencies:
+```bash
+pip install -r requirements.txt
+```
+
+3. Install the custom lung segmentation module:
+```bash
+chmod +x install_lung.sh
+./install_lung.sh
+```
+
+## Dependencies
+
+The following Python packages are required:
+
+- platipy==0.5.1
+- platipy[cardiac]
+- SimpleITK==2.2.1
+- matplotlib==3.7.1
+- numpy==1.24.3
+
+## Project Structure
+
+```
+MRI-Segmentation/
+├── requirements.txt
+├── lung_segmentation.py
+├── lung_segmentation_gui.py
+├── heart_segmentation.py
+├── heart_segmentation_gui.py
+├── input/
+│   └── volumes/
+└── output/
+```
+
+## Usage
+
+### GUI Tools
+
+1. For lung segmentation:
+```bash
+python lung_segmentation_gui.py
+```
+
+2. For heart segmentation:
+```bash
+python heart_segmentation_gui.py
+```
+
+### Command Line Tools
+
+1. For lung segmentation:
+```bash
+python lung_segmentation.py
+```
+
+2. For heart segmentation:
+```bash
+python heart_segmentation.py
+```
+
+## Input Format
+
+The tool accepts NIFTI files (*.nii.gz) as input. Place your input files in the `input/volumes/` directory.
+
+## Output
+
+The segmentation results will be saved in the `output/` directory, organized in subdirectories named after the input file. Each output directory contains:
+- Segmentation masks in NIFTI format (*.nii.gz)
+- Visualization of the segmentation (PNG format)
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