MRI-to-CT Synthesis With Cranial Suture Segmentations Using A Variational Autoencoder Framework

Abstract: Quantifying normative pediatric cranial development and suture ossification is crucial for diagnosing and treating growth-related cephalic disorders. Computed tomography (CT) is widely used to evaluate cranial and sutural deformities; however, its ionizing radiation is contraindicated in children without significant abnormalities. Magnetic resonance imaging (MRI) offers radiation free scans with superior soft tissue contrast, but unlike CT, MRI cannot elucidate cranial sutures, estimate skull bone density, or assess cranial vault growth. This study proposes a deep learning driven pipeline for transforming T1 weighted MRIs of children aged 0.2 to 2 years into synthetic CTs (sCTs), predicting detailed cranial bone segmentation, generating suture probability heatmaps, and deriving direct suture segmentation from the heatmaps. With our in-house pediatric data, sCTs achieved 99% structural similarity and a Frechet inception distance of 1.01 relative to real CTs. Skull segmentation attained an average Dice coefficient of 85% across seven cranial bones, and sutures achieved 80% Dice. Equivalence of skull and suture segmentation between sCTs and real CTs was confirmed using two one sided tests (TOST p < 0.05). To our knowledge, this is the first pediatric cranial CT synthesis framework to enable suture segmentation on sCTs derived from MRI, despite MRI's limited depiction of bone and sutures. By combining robust, domain specific variational autoencoders, our method generates perceptually indistinguishable cranial sCTs from routine pediatric MRIs, bridging critical gaps in non invasive cranial evaluation.