Installation instruction for PNL

conda create -y -n hd-bet python=3.6
conda activate hd-bet

git clone [email protected]:pnlbwh/HD-BET.git
cd HD-BET/
pip install .

conda install pytorch torchvision pytorch-cuda=12.1 -c pytorch -c nvidia

The last pytorch-cuda=12.1 makes it possible to run hd-bet on our GPUs that are CUDA v12.* compatible. Both channels -c pytorch -c nvidia are necessary to install dependencies of pytorch-cuda=12.1

After completing installation, you can invoke hd-bet by absolute path without sourcing or activating any environment:

/path/to/miniconda3/envs/hd-bet/bin/hd-bet --help

References:

https://anaconda.org/pytorch/pytorch-cuda/files

https://www.reddit.com/r/pytorch/comments/11z9vkf/pytorch_installation_with_cuda_121/

https://pytorch.org/get-started/locally/