Post-Processing

the automated tool to Post-Processing the data Brain Tumor include n4 bias Correction and Skull Stripinng

• PostProcessig dataset Brast2020;

  this tool built based on top of BET algorithm that publish from FSL and N4baisCorrection we automated the process and handle the data in 3D shape

  • installation Requires packages

      pip install -r requirements.txt

  • tool description ;

    we develpoed a simple tool that helps to Post Processing the dstaset

    • N4 bais Correction field this will increase the Low intensity of the image to run :
      

    python Postprocessing.py --config 'data_Brast.yaml' --path Processed --n4baiscorrection 

    • Skull Stripping this technic helps to reduce tissues such skull and midbrain .. only we do care about in our project is brain tissues to tun it :
      

    python Postprocessing.py --config 'data_Brast.yaml' --path Processed --skull_stripping 

  • Virtualization dataset Brast2020;

    • vitualize few samples from the data you need to run this command

      • the Options to plot the corrected with oring img type_plot:
      1. option 1 -> Anat
      2. option 2 -> epi
      3. option 3 -> img

      python virtaulizer.py --corrected_samples --type_plot option  

    • for rendering the images in 3D or 2d slices you will need to run

      python virtaulizer.py --v2Drender

    • this commaned may takes will depends on the GPU perfomence you have

      python virtualizer.py --v3Drender