KiTS19 is part of the MICCAI 2019 Challenge. The goal of this challenge is to accelerate the development of reliable kidney and kidney tumor semantic segmentation methodologies.
- Python >= 3.6
- PyTorch >= 1.0.0
pip install -r requirements.txt
Make sure to install git-lfs before cloning! Clone kits19 repository (~54 GB)
git clone https://github.com/neheller/kits19.gitConversion nii.gz to npy for easy to read slice (~140 GB)
python conversion_data.py -d "kits19/data" -o "data"python train_res_unet.py -e 100 -b 32 -l 0.0001 -g 4 -s 512 512 -d "data" --log "runs/ResUNet" --eval_intvl 5 --cp_intvl 5 --vis_intvl 0 --num_workers 8python get_roi.py -b 32 -g 4 -s 512 512 --org_data "kits19/data" --data "data" -r "runs/ResUNet/checkpoint/best.pth" -o "data/roi.json"python train_dense_unet.py -e 100 -b 32 -l 0.0001 -g 4 -s 512 512 -d "data" --log "runs/DenseUNet" --eval_intvl 5 --cp_intvl 5 --vis_intvl 0 --num_workers 8python eval_dense_unet.py -b 32 -g 4 -s 512 512 -d "data" -r "runs/DenseUNet/checkpoint/best.pth" --vis_intvl 0 --num_workers 8 -o "out"python post_processing.py -d "out" -o "out_proc"
We are the 21st of total 106 teams.
- Refactor code
- Describe method
- Show result
- Write argument help
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