NEOCIVET: Extraction of Cortical Surface and Analysis of Neonatal Gyrification Using a Modified CIVET Pipeline

Cerebral cortical gyration becomes dramatically more complex in the fetal brain during the 3rd trimester of gestation; the process proceeds in a similar fashion ex utero in children who are born prematurely. To quantify this morphological development, it is necessary to extract the interface between gray matter and white matter. We employed the well-established CIVET pipeline to extract this cortical surface, with point correspondence across subjects, using a surface-based spherical registration. We developed a variant of the pipeline, called NEOCIVET, that addresses the well-known problems of poor and temporally-varying gray/white contrast in neonatal MRI. NEOCIVET includes a tissue classification strategy that combines i) local and global contrast features, ii) neonatal template construction based on age-specific subgroups, and iii) masking of non-interesting structures using label-fusion approaches. These techniques replaced modules that might be suboptimal for regional analysis of poor-contrast neonatal cortex. In the analysis of 43 preterm-born neonates, many with multiple scans (n=65; 28-40 wks PMA at scan), NEOCIVET identified increases in cortical folding over time in numerous cortical regions (mean curvature: +0.004/wk) while folding did not change in major sulci that are known to develop early (corrected p<0.05). Cortical folding increase was disrupted in the presence of severe types of perinatal WM injury. The proposed pipeline successfully mapped cortical structural development, supporting current models of cerebral morphogenesis.