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---
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
│
...
``` |