Clinical Value of Machine Learning in the Automated Detection of Focal Cortical Dysplasia Using Quantitative Multimodal Surface-Based Features

Objective: To automatically detect focal cortical dysplasia (FCD) lesion by combining quantitative multimodal surface-based features with machine learning and to assess its clinical value.Methods: Neuroimaging data and clinical information for 74 participants (40 with histologically proven FCD type II) was retrospectively included. The morphology, intensity and function-based features characterizing FCD lesions were calculated vertex-wise on each cortical surface and fed to an artificial neural network. The classifier performance was quantitatively and qualitatively assessed by performing statistical analysis and conventional visual analysis.Results: The accuracy, sensitivity, specificity of the neural network classifier based on multimodal surface-based features were 70.5%, 70.0%, and 69.9%, respectively, which outperformed the unimodal classifier. There was no significant difference in the detection rate of FCD subtypes (Pearson’s Chi-Square = 0.001, p = 0.970). Cohen’s kappa score between automated detection outcomes and post-surgical resection region was 0.385 (considered as fair).Conclusion: Automated machine learning with multimodal surface features can provide objective and intelligent detection of FCD lesion in pre-surgical evaluation and can assist the surgical strategy. Furthermore, the optimal parameters, appropriate surface features and efficient algorithm are worth exploring

Automated morphometric analysis and phenotyping of mouse brains from structural µMR images

In light of the utility and increasing ubiquity of mouse models of genetic and neurological disease, I describefully automated pipelines for the investigation of structural microscopic magnetic resonance images of mouse brains – for both high-throughput phenotyping, and monitoring disease. Mouse models offer unparalleled insight into genetic function and brain plasticity, in phenotyping studies; and neurodegenerative disease onset and progression, in therapeutic trials. I developed two cohesive, automatic software tools, for Voxel- and Tensor-Based Morphometry (V/TBM) and the Boundary Shift Integral (BSI), in the mouse brain. V/TBM are advantageous for their ability to highlight morphological differences between groups, without laboriously delineating regions of interest. The BSI is a powerful and sensitive imaging biomarker for the detection of atrophy. The resulting pipelines are described in detail. I show the translation and application of open-source software developed for clinical MRI analysis to mouse brain data: for tissue segmentation into high-quality, subject-specific maps, using contemporary multi-atlas techniques; and for symmetric, inverse-consistent registration. I describe atlases and parameters suitable for the preclinical paradigm, and illustrate and discuss image processing challenges encountered and overcome during development. As proof of principle and to illustrate robustness, I used both pipelines with in and ex vivo mouse brain datasets to identify differences between groups, representing the morphological influence of genes, and subtle, longitudinal changes over time, in particular relation to Down syndrome and Alzheimer’s disease. I also discuss the merits of transitioning preclinical analysis from predominately ex vivo MRI to in vivo, where morphometry is still viable and fewer mice are necessary. This thesis conveys the cross-disciplinary translation of up-to-date image analysis techniques to the preclinical paradigm; the development of novel methods and adaptations to robustly process large cohorts of data; and the sensitive detection of phenotypic differences and neurodegenerative changes in the mouse brai