INSTALL.md

Installation

Dataset

Please download these datasets and save to datapath (user-defined).

• 01 AbdonmenAtlas 1.0
• 02 Liver Tumor Segmentation Challenge (LiTS)
• 03 MSD-Pancreas
• 04 KiTS

It can be publicly available datasets (e.g., LiTS) or your private datasets. Currently, we only take data formatted in nii.gz. Download these datasets and save it to the datapath directory.

wget https://huggingface.co/datasets/qicq1c/Pubilcdataset/resolve/main/10_Decathlon/Task03_Liver.tar.gz?download=true # Task03_Liver.tar.gz (28.7 GB)
wget https://huggingface.co/datasets/qicq1c/Pubilcdataset/resolve/main/10_Decathlon/Task07_Pancreas.tar.gz?download=true # Task07_Pancreas.tar.gz (28.7 GB)
wget https://huggingface.co/datasets/qicq1c/Pubilcdataset/tree/main/05_KiTS.tar.gz?download=true # KiTS.tar.gz (28 GB)

Dependency

The code is tested on python 3.8, Pytorch 1.12.

Setup environment

[Optional] If You are using Agave/Sol

module load anaconda3/5.3.0 # only for Agave

module load mamba/latest # only for Sol
mamba create -n difftumor python=3.8

conda create -n difftumor python=3.8
source activate difftumor # or conda activate difftumor
pip install torch==1.12.1+cu113 torchvision==0.13.1+cu113 torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cu113
pip install -r requirements.txt