Optimizing contrastive learning for cortical folding pattern detection

The human cerebral cortex has many bumps and grooves called gyri and sulci. Even though there is a high inter-individual consistency for the main cortical folds, this is not the case when we examine the exact shapes and details of the folding patterns. Because of this complexity, characterizing the cortical folding variability and relating them to subjects' behavioral characteristics or pathologies is still an open scientific problem. Classical approaches include labeling a few specific patterns, either manually or semi-automatically, based on geometric distances, but the recent availability of MRI image datasets of tens of thousands of subjects makes modern deep-learning techniques particularly attractive. Here, we build a self-supervised deep-learning model to detect folding patterns in the cingulate region. We train a contrastive self-supervised model (SimCLR) on both Human Connectome Project (1101 subjects) and UKBioBank (21070 subjects) datasets with topological-based augmentations on the cortical skeletons, which are topological objects that capture the shape of the folds. We explore several backbone architectures (convolutional network, DenseNet, and PointNet) for the SimCLR. For evaluation and testing, we perform a linear classification task on a database manually labeled for the presence of the "double-parallel" folding pattern in the cingulate region, which is related to schizophrenia characteristics. The best model, giving a test AUC of 0.76, is a convolutional network with 6 layers, a 10-dimensional latent space, a linear projection head, and using the branch-clipping augmentation. This is the first time that a self-supervised deep learning model has been applied to cortical skeletons on such a large dataset and quantitatively evaluated. We can now envisage the next step: applying it to other brain regions to detect other biomarkers.

Identification of Rare Cortical Folding Patterns using Unsupervised Deep Learning

Like fingerprints, cortical folding patterns are unique to each brain even though they follow a general species-specific organization. Some folding patterns have been linked with neurodevelopmental disorders. However, due to the high inter-individual variability, the identification of rare folding patterns that could become biomarkers remains a very complex task. This paper proposes a novel unsupervised deep learning approach to identify rare folding patterns and assess the degree of deviations that can be detected. To this end, we preprocess the brain MR images to focus the learning on the folding morphology and train a beta-VAE to model the inter-individual variability of the folding. We compare the detection power of the latent space and of the reconstruction errors, using synthetic benchmarks and one actual rare configuration related to the central sulcus. Finally, we assess the generalization of our method on a developmental anomaly located in another region. Our results suggest that this method enables encoding relevant folding characteristics that can be enlightened and better interpreted based on the generative power of the beta-VAE. The latent space and the reconstruction errors bring complementary information and enable the identification of rare patterns of different nature. This method generalizes well to a different region on another dataset. Code is available at https://github.com/neurospin-projects/2022_lguillon_rare_folding_detection.