Building and running TotalSegmentator in Docker container

1. Clone this repository

• (Optional) Edit first line of dockerfile if using AMD GPU

2. Navigate to the repository directory
3. Build docker container

docker build -t meglaficus/totally_segment .

4. Have this kind of folder structure ready:

├── files
│   ├── CT
│   │   ├── 00001.nii.gz
│   │   ├── 00002.nii.gz
│   │   ├── 00003.nii.gz
│   │   ├── ...
│   ├── TotalSeg

5. Run the container (change command to include path to "files" directory)

docker run --gpus all -it -v /path/to/files/directory/:/home/app/files --shm-size=24gb meglaficus/totally_segment

6. Execute the program

cd ../home/app
python totally_segment.py
exit

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See https://github.com/wasserth/TotalSegmentator for more info