Tumor Segmentation in Brain MRI Images
The goal of this project is to segment tumors in brain MRI images based on deepMedic. This project has been tested and works on both Windows and Ubuntu.
Install the required packages using the requirements.txt file:
pip3 install requirements.txt
Install GDCM package based on your operating system:
- Linux:
sudo apt update
sudo apt install libgdcm2.4
sudo apt install libgdcm-tools
- Windows:
Download and install GDCM from http://gdcm.sourceforge.net/ or https://sourceforge.net/projects/gdcm/
Note: Install the CUDA and cuDNN requirements if you want to use the GPU.
Run wsgi.py if you want to have a local web service and run client_test_request.py to send a local request to the service.
Server-side:
python3 wsgi.py
Client-side:
python3 client_test_request.py
Run project_runner.py to execute the main project process directly:
python3 project_runner.py
You should define the project output path and data path in the project_runner or client_test_request script. You must also define the processor between cpu or cuda as GPU. A sample data is placed in the dicom_images folder. Also, the saved model is placed in the model folder.
Note for large images: Large 3D CNNs are computationally expensive. Consider downsampling the images or reducing the size of the network if you encounter computational difficulties.
It should be noted that this project was done for MarcoPax company.
Developed by Farrokh Karimi