Precon_all: A species-agnostic automated pipeline for non-human cortical surface reconstruction

Benn, R. A.; Xu, T.; Mars, R. B.; Boch, M.; Roumazeilles, L.; Heuer, K.; Toro, R.; Margulies, D. S.; Manzano-Patron, J. P.; Montesinos, P.; Galan-Arriola, C.; Lopez-Martin, G.; Sanchez-Gonzalez, J.; Duff, E. P.; Ibanez, B.

doi:10.1101/2025.04.16.649072

bioRxiv · 10.1101/2025.04.16.649072

Precon_all: A species-agnostic automated pipeline for non-human cortical surface reconstruction

Benn, R. A.·Xu, T.·Mars, R. B.·Boch, M.·Roumazeilles, L.·Heuer, K.·Toro, R.·Margulies, D. S.·Manzano-Patron, J. P.·Montesinos, P.·Galan-Arriola, C.·Lopez-Martin, G.·Sanchez-Gonzalez, J.·Duff, E. P.·Ibanez, B.

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Abstract

Cortical surface reconstruction has changed how we study brain morphology and geometry. However, extending these methods to non-human species has been limited by the lack of standardized pipelines, anatomical templates, and variability in imaging protocols. To address these challenges, we present Precon_all, an open-source, species-agnostic pipeline that automates cortical surface reconstruction for non-human neuroimaging. It runs reliably across a wide range of anatomical structures and imaging conditions and has been successfully applied to datasets from primates, carnivores, and artiodactyls. Its modular framework mirrors human neuroimaging workflows, supports manual quality control, and produces outputs compatible with FreeSurfer and Connectome Workbench. In doing so, it substantially reduces technical barriers to non-human neuroimaging. As data-sharing initiatives continue to expand access to non-human imaging datasets, Precon_all provides a scalable and standardized solution that supports the broader adoption of surface-based methods for studying cortical evolution through comparative neuroscience.

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Benn, R. A., Xu, T., Mars, R. B., Boch, M., Roumazeilles, L., Heuer, K., Toro, R., Margulies, D. S., Manzano-Patron, J. P., Montesinos, P., Galan-Arriola, C., Lopez-Martin, G., Sanchez-Gonzalez, J., Duff, E. P., Ibanez, B.. 2025-04-20. Precon_all: A species-agnostic automated pipeline for non-human cortical surface reconstruction. https://doi.org/10.1101/2025.04.16.649072

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