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README

This code helps you run the Whole Heart Anatomical Refinement from CCTA using Extrapolation and Parcellation by Hao Xu, et al (KCL) Performs a multilabel segmentation of the CT input.

Run locally

Create conda environment:

conda create -n ccta python=3.8 -y 
conda activate ccta

Install libraries and dependencies

conda install pytorch torchvision -c pytorch -n ccta -y
conda install -c conda-forge pydicom nibabel numpy=1.22 matplotlib gcc -n ccta -y 
conda install -c anaconda scikit-image -n ccta -y

Run with

python run.py --filename /path/to/nifti_file.nii --device cpu --run-locally

Run via Docker container

After installing Docker, run:

docker pull cemrg/ccta:latest 

# to run:
docker run --rm --volume=/path/to:/data cemrg/ccta:latest --filename nifti_file.nii