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Nov 28, 2022
ed1b6a1 · Nov 28, 2022

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Supervised image registration using DL (D3)

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Requirements

  • Pytorch 1.10.1

    Support both CUDA and CPU, you can install pytorch 1.10.1 with the following command (more information can be found in the link: https://pytorch.org/get-started/previous-versions/):

    #Linux and Windows
    
    # CUDA 10.2
    conda install pytorch==1.10.1 torchvision==0.11.2 torchaudio==0.10.1 cudatoolkit=10.2 -c pytorch
    
    # CUDA 11.3
    conda install pytorch==1.10.1 torchvision==0.11.2 torchaudio==0.10.1 cudatoolkit=11.3 -c pytorch -c conda-forge
    
    # CPU Only
    conda install pytorch==1.10.1 torchvision==0.11.2 torchaudio==0.10.1 cpuonly -c pytorch
    
  • SimpleITK 2.2.0

  • numpy 22.2.2

Instructions

  • Reg_Main.py is the main tool to first predict the transformations between pairwise images, followed by deforming the source image by a geodesic shooting algorithm; ***Note the provided pre-trained registration model ('PretrainedReg.tar') is on 3D brain images with the size of 128 3 .

  • Reg_Tools.py includes some utility functions;

  • uEpdiff.py is the main code of forward shooting by FLASH;