Utilizing deep learning via the 3D U-net neural network for the delineation of brain stroke lesions in MRI image

Abstract

The segmentation of acute stroke lesions plays a vital role in healthcare by assisting doctors in making prompt and well-informed treatment choices. Although Magnetic Resonance Imaging (MRI) is a time-intensive procedure, it produces high-fidelity images widely regarded as the most reliable diagnostic tool available. Employing deep learning techniques for automated stroke lesion segmentation can offer valuable insights into the precise location and extent of affected tissue, enabling medical professionals to effectively evaluate treatment risks and make informed assessments. In this research, a deep learning approach is introduced for segmenting acute and sub-acute stroke lesions from MRI images. To enhance feature learning through brain hemisphere symmetry, pre-processing techniques are applied to the data. To tackle the class imbalance challenge, we employed a strategy of using small patches with balanced sampling during training, along with a dynamically weighted loss function that incorporates f1-score and IOU-score (Intersection over Union). Furthermore, the 3D U-Net architecture is used to generate predictions for complete patches, employing a high degree of overlap between patches to minimize the requirement for subsequent post-processing steps. The 3D U-Net model, utilizing ResnetV2 as the pre-trained encoder for IOU-score and Seresnext101 for f1-score, stands as the leading state-of-the-art (SOTA) model for segmentation tasks. However, recent research has introduced a novel model that surpasses these metrics and demonstrates superior performance compared to other backbone architectures. The f1-score and IOU-score were computed for various backbones, with Seresnext101 achieving the highest f1-score and ResnetV2 performing the highest IOU-score. These calculations were conducted using a threshold value of 0.5. This research proposes a valuable model based on transfer learning for the classification of brain diseases in MRI scans. The achieved f1-score using the recommended classifiers demonstrates the effectiveness of the approach employed in this study. The findings indicate that Seresnext101 attains the highest f1-score of 0.94226, while ResnetV2 achieves the best IOU-score of 0.88342, making it the preferred architecture for segmentation methods. Furthermore, the study presents experimental results of the 3D U-Net model applied to brain stroke lesion segmentation, suggesting prospects for researchers interested in segmenting brain strokes and enhancing 3D U-Net models.