This project contains the Tumor Segmentation Pipeline used to train a model to segment brain tumors from MRIs as part of the Brain Tumor Segmentation (BraTS) Continuous Challenge. Data from the 2021 competition was used. Participation was also used as part of a group project in a Temple University graduate Computer Science course. The final report can be found here.

The pipeline heavily uses the MONAI module, which uses a PyTorch backend. The pipeline trains MONAI's built-in Residual UNet autoencoder neural network with BraTS data, and runs a test loop with the best model weights found during training. Models are saved in the trained_models directory, and are used in the run_model.py script.

A GPU is required in order to train a model in a reasonable timeframe. When using a GeForce RTX 3060 Ti 8GB GPU, each training epoch took ~20 minutes, so training over 150 epochs took over 2 days.

• Install pyenv via instructions at https://github.com/pyenv/pyenv-virtualenv and update .*rc file accordingly
• Install Python 3.9 pyenv install 3.9.16
• Create venv pyenv virtualenv 3.9.16 brats
• Activate venv pyenv local brats
• Install dependencies pip install -r requirements.txt

• Download zip of training data from the BraTS competition
  • If not affiliated with this specific team, request access to competition data from Synapse here and download training data zip directly from their site.
• Move the file to ./local_data
• Unzip the file
  • unzip RSNA_ASNR_MICCAI_BraTS2021_TrainingData_16July2021.zip
    • Exact filename will differ between competition years
• Rename top level folder to train

Script for training a model.

python train_model.py --model [unet,segresnet] --epochs [1..n]

By default, unet and 150 are used.

The model with the best validation score will be saved to trained_models/<model name>-model.pth. Script will print test validation score, and results can be viewed via TensorBoard by running tensorboard --logdir runs or make results.

Training Loss and Validation Score data can also be exported from TensorBoard. If exported in a *.json, it can be used in the generate_graphs.py script to generate a plot of the loss and validation over each epoch. Note that this script is not paramaterized, so paths, etc. will need to be updated within the script, or set to match its current contents.

Script for running an Optuna study for determining ideal model hyperparameters. Hyperparameters being tested can be modified within the nn.optunet.Optunet class.

Run the tune_hyperparameters.py script, selecting one of the parameters in the list for each argument.

python tune_hyperparameters.py -m [unet,segresnet] -e [1..n] --trials [1..n]

A model type must be selected, but by default, 50 epochs and 20 trials are used.

Note that the script can be stopped at any time with Ctrl+C and results will be retained in MLflow.

To view the results of the study in MLflow, run mlflow server or make optuna_results.

Script for running a trained model on an MRI.

Run the run_model.py script, specifying the following arguments.

python run_model.py -m <path to model> -i <path to NIfTI subdirectory containing all channel images and segmentation>

The script will generate a MatPlotLib image including three slices of the input image, the ground truth segmentation, and the segmentation generated by the model.