Segmentation of brain structures during the pre-natal and early post-natal periods is the first step for subsequent analysis of brain development. Segmentation techniques can be roughly divided into two families. The first, which we denote as registration-based techniques, rely on initial estimates derived by registration to one (or several) templates. The second family, denoted as learning-based techniques, relate imaging (and spatial) features to their corresponding anatomical labels. Each approach has its own qualities and both are complementary to each other. In this paper, we explore two ensembling strategies, namely, stacking and cascading to combine the strengths of both families. We present experiments on segmentation of 6-month infant brains and a cohort of fetuses with isolated non-severe ventriculomegaly (INSVM). INSVM is diagnosed when ventricles are midly enlarged and no other anomalies are apparent. Prognosis is diffcult based solely on the degree of ventricular enlargement. In order to find markers for a more reliable prognosis, we use the resulting segmentations to find abnormalities in the cortical folding of INSVM fetuses. Segmentation results show that either combination strategy outperform all of the individual methods, thus demonstrating the capability of learning systematic combinations that lead to an overall improvement. In particular, the cascading strategy outperforms the ensembling one, the former one obtaining top 5, 7 and 13 results (out of 21 teams) in the segmentation of white matter, gray matter and cerebro-spinal fuid in the iSeg2017 MICCAI Segmentation Challenge. The resulting segmentations reveal that INSVM fetuses have a less convoluted cortex. This points to cortical folding abnormalities as potential markers of later neurodevelopmental outcomes.

The first author is co-financed by the Marie Curie FP7-PEOPLE-2012- COFUND Action, Grant agreement no: 600387. This study was partly sup345 ported by Instituto de Salud Carlos III (PI16/00861) integrados en el Plan Nacional de I+D+I y cofinanciados por el ISCIII-Subdirección General de Evaluación y el Fondo Europeo de Desarrollo Regional (FEDER) "Una manera de hacer Europa"; additionally the research leading to these results has received funding from "la Caixa" Foundation. This work is partly supported by the 350 Spanish Ministry of Economy and Competitiveness under the Maria de Maeztu Units of Excellence Programme (MDM-2015-0502).