metadata
license: apache-2.0
Instructions
1-Data preparation
This is how inputs_data organizes
$inputs_data/
├── casename00001
│ └── ct.nii.gz
├── casename00002
│ └── ct.nii.gz
├── casename00003
│ └── ct.nii.gz
...
2-Download
You can choose to use the docker image (recommand) or the singularity container.
Download the docker image.
docker pull qchen99/suprem:v1
or
Download the singularity container.
wget https://huggingface.co/qicq1c/SuPreM/resolve/main/suprem_final.sif
3-Inference
You can directly perform inference on your own data. Simply modify inputs_data into your data path and adjust outputs_data to specify the desired output location for the segmentation results.
Use Docker
sudo docker container run --gpus "device=0" -m 128G --rm -v $inputs_data:/workspace/inputs/ -v $outputs_data:/workspace/outputs/ qchen99/suprem:v1 /bin/bash -c "sh predict.sh"
or
Use Singularity
SINGULARITYENV_CUDA_VISIBLE_DEVICES=0 singularity run --nv -B $inputs_data:/workspace/inputs -B $outputs_data:/workspace/outputs suprem_final.sif
This is how outputs_data organizes
$outputs_data/
├── casename00001
├── casename00002
├── casename00003
│── combined_labels.nii.gz
└── segmentations
├── aorta.nii.gz
├── gall_bladder.nii.gz
├── kidney_left.nii.gz
├── kidney_right.nii.gz
├── liver.nii.gz
├── pancreas.nii.gz
├── postcava.nii.gz
├── spleen.nii.gz
├── stomach.nii.gz
│
...