JianghaoWu/MBH-Seg_monash

Second Stage Test by Monash — Submission 1

1. Download the Docker Image

You can download the latest Docker image from huggingface as monash_latest.tar.gz.

2. Load the Docker Image

To load the Docker image, use the following command:

docker load -i monash_latest.tar.gz

After loading, you will see the message: Loaded image: monash:latest, where monash:latest is the name of the Docker image.

3. Test the Docker Image

To test the Docker container, run:

docker container run --gpus "device=0" --name monash --rm --shm-size=24g -v $PWD/relative_path/test/fold/:/workspace/inputs/ -v $PWD/relative_path/outputs/fold/:/workspace/outputs/ monash:latest /bin/bash -c "sh predict.sh"

If you encounter any permission issues, you may need to run it with sudo:

sudo docker container run --gpus "device=0" --name monash --rm --shm-size=24g -v $PWD/relative_path/test/fold/:/workspace/inputs/ -v $PWD/relative_path/outputs/fold/:/workspace/outputs/ monash:latest /bin/bash -c "sh predict.sh"

Parameters:

• --gpus "device=0": Select the appropriate GPU ID.
• Replace relative_path/test/fold with the relative path to your test folder, which should contain Nifti files (.nii.gz). This path is relative to your current working directory.
• Replace relative_path/outputs/fold with the relative path to your desired output folder, which will store the results. This path is also relative to your current working directory.
• monash:latest: This is the Docker image name, which will be displayed after loading the image in step 2.

or using absolute path:

docker container run --gpus "device=0" --name monash --rm --shm-size=24g -v /absolute/path/to/your/test/fold/:/workspace/inputs/ -v /absolute/path/to/my/team/outputs/fold/:/workspace/outputs/ monash:latest /bin/bash -c "sh predict.sh"

• Replace /absolute/path/to/your/test/fold/ with the absolute path to your test folder, which should contain Nifti files (.nii.gz).
• Replace /absolute/path/to/my/team/outputs/fold/ with the absolute path to your desired output folder, where the output results will be stored.