Comparative neuroanatomy has been a challenging research field, even with the methodological innovations in recent years. In this context, cortical surface reconstructions emerged as a new venue to provide further insights on brain morphology, but they are mostly limited to humans and a few other primates, hindering a systematic understanding of diversity in brain anatomy across species.Here, we implemented an innovative pipeline, Stitcher (Mynssen et al., in preparation), to reconstruct the cortical surface of five lesser-known mammals belonging to four orders: Artiodactyla, Carnivora, Cetacea and Pinniped. In our method, manually traced contours in each slice are stitched together to build a surface. We compared Stitcher with a semi-automatic routine, precon_all (https://github.com/neurabenn/precon_all), which combines FreeSurfer and FSL softwares to generate the cortical surfaces, in order to identify pros and cons of each approach.We found that Carnivora and Artiodactyla orders could be reconstructed with both techniques and all their main sulci and gyri were identifiable. Comparison across methods showed great similarity visually and numerically, with volume and area discrepancies not exceeding 5%. However, Cetacea and Pinniped failed the semi-automatic approach, being only successfully reconstructed via the manual method (Figure). Nevertheless, when using Stitcher’s method, the two cortices exhibit the main cortical features identified in the studied species.By contrasting pipelines, we aim to show how to combine different techniques, expanding the possibilities for studying cortical morphology in non-model animals.Figure: cortical reconstruction of a Franciscana Dolphin (Pontoporia blainvillei) using Stitcher pipeline.