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--- |
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license: apache-2.0 |
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--- |
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# Instructions |
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## 1-Data preparation |
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This is how `inputs_data` organizes |
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``` |
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$inputs_data/ |
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├── casename00001 |
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│ └── ct.nii.gz |
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├── casename00002 |
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│ └── ct.nii.gz |
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├── casename00003 |
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│ └── ct.nii.gz |
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... |
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``` |
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## 2-Download |
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You can choose to use the docker image (recommand) or the singularity container. |
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#### Download the docker image. |
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``` |
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docker pull qchen99/suprem:v1 |
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``` |
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or |
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#### Download the singularity container. |
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``` |
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wget https://huggingface.co/qicq1c/SuPreM/resolve/main/suprem_final.sif |
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``` |
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## 3-Inference |
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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. |
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#### Use Docker |
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``` |
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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" |
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``` |
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or |
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#### Use Singularity |
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``` |
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SINGULARITYENV_CUDA_VISIBLE_DEVICES=0 singularity run --nv -B $inputs_data:/workspace/inputs -B $outputs_data:/workspace/outputs suprem_final.sif |
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``` |
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This is how `outputs_data` organizes |
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``` |
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$outputs_data/ |
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├── casename00001 |
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├── casename00002 |
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├── casename00003 |
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│── combined_labels.nii.gz |
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└── segmentations |
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├── aorta.nii.gz |
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├── gall_bladder.nii.gz |
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├── kidney_left.nii.gz |
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├── kidney_right.nii.gz |
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├── liver.nii.gz |
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├── pancreas.nii.gz |
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├── postcava.nii.gz |
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├── spleen.nii.gz |
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├── stomach.nii.gz |
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│ |
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... |
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``` |
