README.md

---
license: apache-2.0
---
# Instructions

### 1-Download
Download the singularity container.
```
wget https://huggingface.co/qicq1c/SuPreM/resolve/main/suprem_final.sif
```
### 2-Data preparation
This is how `inputs_data` organizes
```
    $inputs_data/
    ├── casename00001
    │   └── ct.nii.gz
    ├── casename00002
    │   └── ct.nii.gz
    ├── casename00003
    │   └── ct.nii.gz
    ...
```

### 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.
```
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
    │
    ...
```