This is a pipeline made for $Citation needed
Ensure you have podman and Nvidia container toolkit installed. Contact repo owner for docker image
Start with:
git clone https://github.com/Rigshospitalet-KFNM/HeadNeckPETGTV --recurse-submodules
Install virtual environment
python3 -m venv venv
source venv/bin/activate
pip install submodules/dicom_node
Then install dcm2niix and niftyreg found in the submodules
This pipeline is controlled by environment variables, set them using
export NAME=VALUE
- PIPELINE_ARCHIVE_PATH - Path, where the dicom node stores images temporary
- PIPELINE_WORKING_PATH - Path, where the dicom node executes the process function
- PIPELINE_LOG_PATH - Path, to the log file
- PIPELINE_DCM2NIIX - Path, to the dcm2niix executable
- PIPELINE_RESAMPLE - Path, to the reg_resample executable
- PIPELINE_AE_TITLE - Optional List of str, comma seperated, spaces are stripped. Accepted AE title, if present only ae titles in list is accepted
- PIPELINE_SEGMENTATION_ARCHIVE - Optional Path of directory, if present segmentation are saved to this directory.