CT Organ Masking with TotalSegmentation

This project utilizes the TotalSegmentation library to automatically generate masks for organs such as the liver, pancreas, and spleen from CT data. It can process multiple NIfTI files at once and offers an option to handle each organ individually to avoid memory issues.

Features

• Automatically mask organs such as the liver, pancreas, spleen, left, and right kidneys from CT images.
• Option to process each organ individually to prevent memory overload.
• Automatically generate masks for all NIfTI files in the data directory.

Installation

To use this project, you need to install the TotalSegmentation library. Please refer to the link for installation instructions.

Usage

You can run the main.py script to generate masks from CT data:

License

This project uses the TotalSegmentator library, which is licensed under the Apache-2.0 License.

Directory structure

python main.py --data_dir /path/to/your/data

/data/
├── subject1/
│   └── modality1/
│       └── ct.nii.gz
│   └── modality2/
│       └── ct.nii.gz
└── subject2/
    └── modality1/
        └── ct.nii.gz
    └── modality2/
        └── ct.nii.gz