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Vascular-Tree-Reconstruction

This repository holds the source code for the papers Divergence Prior and Vessel-tree Reconstruction and Confluent Vessel Trees with Accurate Bifurcations appeared in CVPR19 and CVPR21 respectively.

How to install

The following installation is tested using cmake-3.10.2 under Ubuntu 18.04.3 LTS.

  1. c/c++ compiler: gcc-4.8/g++-4.8
  2. CUDA: 8.0
  3. Dependencies: boost-1.65.0, hdf5-1.10.1, eigen-3.3.4, ITK-4.13.3, flann-1.8.4, cusp-0.5.1
  4. If these dependencies are installed in a custom folder, you may need to help cmake find them by explicitly setting some variables in CMakeLists.txt, CMake/FindEigen.cmake, CMake/FindFlann.cmake and CMake/FindITK.cmake.
  5. Create a new folder Build inside the folder where this repository is cloned.
mkdir Build
cd Build
  1. To build the project
cmake -DCMAKE_INSTALL_PREFIX=[path to install the project] ..
make -j 8
make install

How to use

The example script is contained in the Experiments. To obtain the synthetic vessel volume data, use fetchData.sh. After downloading the data, simply run ExprOutter.sh.

Five stages for vessel tree/centerline extraction:

  1. Do ObjectenessMasureImageFilter (Frangi filtering)

  2. Do NonmaximumSuppressionVolume

    Important

    --thresholdValue --- this is threshold for plots (ROC, angle error)
    
  3. Do GenerateNeighborhoodGraph

  4. Do LevenbergMarquardtMinimizer (use GPU)

    Important

    --lambda  --- curvature coefficient
    --beta  --- divergence coefficient
    --tau  --- the hyperparameter in the oriented curvature
    --voxelPhysicalSize  --- defines allowed error in ||l_p - p||_+
    
  5. Do GenerateTreeTopology

    Important

    --directedLabel   --- a flag used to decide whether to use minimum arborescence or MST
    --root   --- root index needs to be specified if using the minimum arborescence
    

    Code for the minimum arborescence: https://github.com/atofigh/edmonds-alg.git

About

Source code for CVPR 19 (Divergence Prior) & 21 (Confluent Vessel Tree) papers.

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