About
I'm a postdoctoral researcher at the Pioneer Centre for AI and at the Copenhagen Research Centre for Biological and Precision Psychiatry , developing automatic models for analyzing brain MRI data. I'm the recipient of a Lundbeck Foundation Postdoc Fellowship and part of the Lundbeck Foundation Investigator Network (LFIN) . I co-led the FOMO25 and FOMO26 challenges at MICCAI 2025 and 2026, focused on foundation models for brain MRI. Previously, I was a research fellow at the Athinoula A. Martinos Center for Biomedical Imaging . I obtained my PhD at the Technical University of Denmark (DTU) , supervised by Koen Van Leemput .
Past Experiences
Research Fellow , Athinoula A. Martinos Center for Biomedical Imaging, 2021–2023
PhD Degree , Medical Image Analysis, Technical University of Denmark, 2018–2021
Machine Learning Intern , Horus Technology, 2017
Master Degree , Computer Science, Politecnico di Milano, 2015–2017
Bachelor Degree , Computer Science, Politecnico di Milano, 2012–2015
Publications
Selected publications, for a full list see Google Scholar .
BINDER: A Latent Variable Model for Probabilistic Medical Image Registration
Stefano Cerri*, Amirhossein HassankhaniØ, Yaël Balbastre, Koen Van Leemput
arXiv preprint, 2026
Towards Brain MRI Foundation Models for the Clinic: Findings from the FOMO25 Challenge
Stefano Cerri*, Asbjørn Munk*, Vardan Nersesjan, Christian Hedeager Krag, Jakob Ambsdorf, ..., Michael Eriksen Benros, Juan Eugenio Iglesias, Mads Nielsen
arXiv preprint, 2026
A large-scale heterogeneous 3D magnetic resonance brain imaging dataset for self-supervised learning
Stefano Cerri*, Asbjørn Munk*, Jakob Ambsdorf, Julia Machnio, Sebastian Nørgaard Llambias, Vardan Nersesjan, Christian Hedeager Krag, Peirong Liu, Pablo Rocamora García, Mostafa Mehdipour Ghazi, Mikael Boesen, Michael Eriksen Benros, Juan Eugenio Iglesias, Mads Nielsen
Scientific Data, 2026
Cross-disorder comparison of Brain Structures among 4,836 Individuals with Mental Disorders and Controls utilizing Danish population-based Clinical MRI Scans
Stefano Cerri, Vardan Nersesjan, Kiril Vadimovic Klein, Enric Cristòbal Cóppulo, Sebastian Nørgaard Llambias, Mostafa Mehdipour Ghazi, Mads Nielsen, Michael Eriksen Benros
Molecular Psychiatry, 2026
An Open-Source Tool for Longitudinal Whole-Brain and White Matter Lesion Segmentation
Stefano Cerri, Douglas N. Greve, Andrew Hoopes, Henrik Lundell, Hartwig R. Siebner, Mark Mühlau, Koen Van Leemput
NeuroImage Clinical, Vol. 38, 2023, 103354
🏆 NICL 2024 Best Paper Award!
Predicting survival of glioblastoma from automatic whole-brain and tumor segmentation of MR images
Sveinn Pálsson, Stefano Cerri, Hans Skovgaard Poulsen, Thomas Urup, Ian Law, Koen Van Leemput
Scientific Reports, Vol. 12, 2022, 19744
A Contrast-Adaptive Method for Simultaneous Whole-Brain and Lesion Segmentation in Multiple Sclerosis
Stefano Cerri, Oula Puonti, Dominik S. Meier, Jens Wuerfel, Mark Mühlau, Hartwig R. Siebner, Koen Van Leemput
NeuroImage, Vol. 225, 2021, 117471
A Longitudinal Method for Simultaneous Whole-Brain and Lesion Segmentation in Multiple Sclerosis
Stefano Cerri, Andrew Hoopes, Douglas N. Greve, Mark Mühlau, Koen Van Leemput
3rd MLCN workshop, MICCAI 2020
Semi-supervised Variational Autoencoder for Survival Prediction
Sveinn Pálsson*, Stefano Cerri*, Andrea Dittadi*, Koen Van Leemput
BrainLes 2019 workshop, BRATS challenge, MICCAI 2019
Software
I'm actively maintaining the segmentation code of SAMSEG, included in FreeSurfer .
Contrast-Adaptive Whole-Brain and Lesion Segmentation Tool
BINDER: Bayesian INference for DEformable Registration
Semi-supervised Variational Autoencoder CNN architecture for modeling of 3D brain images and classification
Longitudinal Contrast-Adaptive Whole-Brain and Lesion Segmentation Tool
