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/
βββ case00001.nii.gz
βββ case00002.nii.gz
βββ case00003.nii.gz
βββ ...
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/
βββ case00001
βββ case00002
βββ case00003
βββ ct.nii.gz
βββ predictions
βββ liver.nii.gz
βββ pancreas.nii.gz
βββ kidney.nii.gz
βββ liver_tumor.nii.gz
βββ pancreas_tumor.nii.gz
βββ kidney_tumor.nii.gz
β
...