youness-elbrag/Skull-Striping

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

PythonApache-2.0

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
```