# 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)