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Installation

Users need to install both MONAI and nnU-Net to utilize the nnunet runner.

MONAI

Users can follow the link to install dev branch of MONAI. The following command shows the example to install MONAI and Necessary dependencies.

# install latest monai (pip install monai)
pip install git+https://github.com/Project-MONAI/MONAI#egg=monai

# install dependencies
pip install fire nibabel
pip install "scikit-image>=0.19.0"

nnU-Net (V2)

To run components of nnU-Net V2, users need to properly install PyTorch on their own or adopt Pytorch docker containers maintained by NVIDIA. And other dependent libraries can be installed by running basic commands.

# install dependencies
pip install --upgrade git+https://github.com/MIC-DKFZ/acvl_utils.git
pip install --upgrade git+https://github.com/MIC-DKFZ/dynamic-network-architectures.git

# install nnunet
pip install nnunetv2

# install hiddenlayer (optional)
pip install --upgrade git+https://github.com/julien-blanchon/hiddenlayer.git

The official instruction can be found here.