Stefano Cerri

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'm also one of the lead organizers of the FOMO25 Challenge at MICCAI 2025, a challenge on self-supervised learning for medical imaging. 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. I was also part of the 15 PhD students of the Translational Brain Imaging Train Network (TRABIT).

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.

FOMO300K dataset
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
arXiv preprint, 2025
Paper Dataset
Cross-disorder brain structures
Cross-disorder comparison of Brain Structures among 4,842 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
medRxiv preprint, 2025
Paper
Longitudinal segmentation example
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
Paper Code Wiki
🏆 NICL 2024 Best Paper Award!
Tumor survival prediction
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
Paper
SAMSEG lesion segmentation
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
Paper Code Wiki
Longitudinal lesion model
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
Paper Code Wiki
VAE generated samples
Semi-supervised Variational Autoencoder for Survival Prediction
Sveinn Pálsson*, Stefano Cerri*, Andrea Dittadi*, Koen Van Leemput
BrainLes 2019 workshop, BRATS challenge, MICCAI 2019
Paper Code

Software

I'm actively maintaining the segmentation code of SAMSEG, included in FreeSurfer.

3D brain segmentation
Contrast-Adaptive Whole-Brain and Lesion Segmentation Tool
Paper Code Wiki
VAE CNN architecture
Semi-supervised Variational Autoencoder CNN architecture for modeling of 3D brain images and classification
Paper Code
Longitudinal segmentation
Longitudinal Contrast-Adaptive Whole-Brain and Lesion Segmentation Tool
Paper1 Paper2 Code Wiki