Jonathan Zopes

Moritz Platscher, Jonathan Zopes, Christian Federau

Deep learning based disease detection and segmentation algorithms promise to improve many clinical processes. However, such algorithms require vast amounts of annotated training data, which are typically not available in the medical context due to data privacy, legal obstructions, and non-uniform data acquisition protocols. Synthetic databases with annotated pathologies could provide the required amounts of training data. We demonstrate with the example of ischemic stroke that an improvement in lesion segmentation is feasible using deep learning based augmentation. To this end, we train different image-to-image translation models to synthesize magnetic resonance images of brain volumes with and without stroke lesions from semantic segmentation maps. In addition, we train a generative adversarial network to generate synthetic lesion masks. Subsequently, we combine these two components to build a large database of synthetic stroke images. The performance of the various models is evaluated using a U-Net which is trained to segment stroke lesions on a clinical test set. We report a Dice score of $\mathbf{72.8}$% [$\mathbf{70.8\pm1.0}$%] for the model with the best performance, which outperforms the model trained on the clinical images alone $\mathbf{67.3}$% [$\mathbf{63.2\pm1.9}$%], and is close to the human inter-reader Dice score of $\mathbf{76.9}$%. Moreover, we show that for a small database of only 10 or 50 clinical cases, synthetic data augmentation yields significant improvement compared to a setting where no synthetic data is used. To the best of our knowledge, this presents the first comparative analysis of synthetic data augmentation based on image-to-image translation, and first application to ischemic stroke.

Jonathan Zopes, Moritz Platscher, Silvio Paganucci et al.

Purpose: To implement a brain segmentation pipeline based on convolutional neural networks, which rapidly segments 3D volumes into 27 anatomical structures. To provide an extensive, comparative study of segmentation performance on various contrasts of magnetic resonance imaging (MRI) and computed tomography (CT) scans. Methods: Deep convolutional neural networks are trained to segment 3D MRI (MPRAGE, DWI, FLAIR) and CT scans. A large database of in total 851 MRI/CT scans is used for neural network training. Training labels are obtained on the MPRAGE contrast and coregistered to the other imaging modalities. The segmentation quality is quantified using the Dice metric for a total of 27 anatomical structures. Dropout sampling is implemented to identify corrupted input scans or low-quality segmentations. Full segmentation of 3D volumes with more than 2 million voxels is obtained in less than 1s of processing time on a graphical processing unit. Results: The best average Dice score is found on $T_1$-weighted MPRAGE ($85.3\pm4.6\,\%$). However, for FLAIR ($80.0\pm7.1\,\%$), DWI ($78.2\pm7.9\,\%$) and CT ($79.1\pm 7.9\,\%$), good-quality segmentation is feasible for most anatomical structures. Corrupted input volumes or low-quality segmentations can be detected using dropout sampling. Conclusion: The flexibility and performance of deep convolutional neural networks enables the direct, real-time segmentation of FLAIR, DWI and CT scans without requiring $T_1$-weighted scans.