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/
    β”œβ”€β”€ case00001.nii.gz
    β”œβ”€β”€ case00002.nii.gz
    β”œβ”€β”€ case00003.nii.gz
    β”œβ”€β”€ ...

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 difftumor_final.sif

This is how outputs_data organizes

    $outputs_data/
    β”œβ”€β”€ case00001
    β”œβ”€β”€ case00002
    β”œβ”€β”€ case00003
        │── ct.nii.gz
        └── predictions
            β”œβ”€β”€ liver.nii.gz
            β”œβ”€β”€ pancreas.nii.gz
            β”œβ”€β”€ kidney.nii.gz
            β”œβ”€β”€ liver_tumor.nii.gz
            β”œβ”€β”€ pancreas_tumor.nii.gz
            β”œβ”€β”€ kidney_tumor.nii.gz
    β”‚
    ...
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