DL-BET

Deep Learning based Brain Extraction Tool

Preprocessing of Small Animal MRI Scans

1. NIFTI conversion from BRUKER raw data
2. Isotropic upsampling
3. N4 Bias field correction

Brain Mask Generation

Installation

1. Create and activate a conda environment.
2. Install PyTorch. Visit https://pytorch.org/get-started/locally/ for installation details.
3. Install other required packages.
4. Clone this repository.

Usage

1. Save training, validation, and test date to a directory called 'dataset'. A randomized 80-10-10 split is suggested. Define folder paths in configs_settings.ini.
2. Run 'python3 DL-BET.py' to begin training model.
3. Run 'python3 DL-BET_test.py' after training has completed to generate test outputs, saved to 'results'.