/rembrandt-mri

Code used for the REMBRANDT MRI paper

Primary LanguagePython

Code used for the REMBRANDT MRI paper to extract PyRadiomics features from Rembrandt MRI data

Prerequisites

  • Python installed on your machine, version 3.5 or higher.
  • Pandas installed
  • Download data folder on your machine

Install PyRadiomics

  • Depending on your environment use either pip or conda to install PyRadiomics : python -m pip install pyradiomics conda install -c radiomics pyradiomics

How the python code works

  • There is a loop that walks through the directory tree (the root folder data). It uses the function os.walk() . The parameters to pass are
    • dirName: The next directory it found.
    • subdirList: A list of sub-directories in the current directory.
    • fileList: A list of files in the current directory.
  • For each patient, the PyRadiomics features are extracted and saved in a data frame.
  • Save your final data frame into a csv