README.md

metadata

license: apache-2.0

DiffTumor

The Singularity container is designed for the prediction of abdominal tumors, specifically targeting the liver, pancreas, and kidneys. It utilizes a segmentation model sourced from DiffTumor.

Instructions

1-Download

Download the singularity container.

wget https://huggingface.co/qicq1c/DiffTumor/resolve/main/difftumor_final.sif

2-Data preparation

This is how inputs_data organizes

    $inputs_data/
    ├── case00001.nii.gz
    ├── case00002.nii.gz
    ├── case00003.nii.gz
    ├── case000xx.nii.gz
    ├── ...
    ├── case10000.nii.gz

3-Inference

You can directly perform inference on your own data. Simply modify inputs_data to reflect 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 difftumor.sif

This is how outputs_data organizes

    $outputs_data/
    ├── case00001
    ├── case00002
    ├── case00003
        │── ct.nii.gz
        └── predictions
            ├── liver.nii.gz
            ├── pancreas.nii.gz
            ├── kidney.nii.gz
            ├── liver_tumor.nii.gz
            ├── pancreas_tumor.nii.gz
            ├── kidney_tumor.nii.gz