Generative Latent Representations of 3D Brain MRI for Multi-Task Downstream Analysis in Down Syndrome

Generative models have emerged as powerful tools in medical imaging, enabling tasks such as segmentation, anomaly detection, and high-quality synthetic data generation. These models typically rely on learning meaningful latent representations, which are particularly valuable given the high-dimensional nature of 3D medical images like brain magnetic resonance imaging (MRI) scans. Despite their potential, latent representations remain underexplored in terms of their structure, information content, and applicability to downstream clinical tasks. Investigating these representations is crucial for advancing the use of generative models in neuroimaging research and clinical decision-making. In this work, we develop multiple variational autoencoders (VAEs) to encode 3D brain MRI scans into compact latent space representations for generative and predictive applications. We systematically evaluate the effectiveness of the learned representations through three key analyses: (i) a quantitative and qualitative assessment of MRI reconstruction quality, (ii) a visualisation of the latent space structure using Principal Component Analysis, and (iii) downstream classification tasks on a proprietary dataset of euploid and Down syndrome individuals brain MRI scans. Our results demonstrate that the VAE successfully captures essential brain features while maintaining high reconstruction fidelity. The latent space exhibits clear clustering patterns, particularly in distinguishing individuals with Down syndrome from euploid controls.

BioFace3D: A fully automatic pipeline for facial biomarkers extraction of 3D face reconstructions segmented from MRI

Facial dysmorphologies have emerged as potential critical indicators in the diagnosis and prognosis of genetic, psychotic and rare disorders. While in certain conditions these dysmorphologies are severe, in other cases may be subtle and not perceivable to the human eye, requiring precise quantitative tools for their identification. Manual coding of facial dysmorphologies is a burdensome task and is subject to inter- and intra-observer variability. To overcome this gap, we present BioFace3D as a fully automatic tool for the calculation of facial biomarkers using facial models reconstructed from magnetic resonance images. The tool is divided into three automatic modules for the extraction of 3D facial models from magnetic resonance images, the registration of homologous 3D landmarks encoding facial morphology, and the calculation of facial biomarkers from anatomical landmarks coordinates using geometric morphometrics techniques.