Fast, Sequence Adaptive Parcellation of Brain MR Using Parametric Models. - Oula Puonti; Juan Eugenio Iglesias; Koen Van Leemput (MICCAI (1), 2013)

Brain Tumor Segmentation Using a Generative Model with an RBM Prior on Tumor Shape. - Mikael Agn; Oula Puonti; Per Munck af Rosenschöld; Ian Law; Koen Van Leemput (Brainles@MICCAI, 2015)

Simultaneous Whole-Brain Segmentation and White Matter Lesion Detection Using Contrast-Adaptive Probabilistic Models. - Oula Puonti; Koen Van Leemput (Brainles@MICCAI, 2015)

An Ensemble of 2D Convolutional Neural Networks for Tumor Segmentation. - Mark Lyksborg; Oula Puonti; Mikael Agn; Rasmus Larsen 001 (SCIA, 2015)

Fast and sequence-adaptive whole-brain segmentation using parametric Bayesian modeling. - Oula Puonti; Juan Eugenio Iglesias; Koen Van Leemput (NeuroImage, 2016)

Computational Analysis of Brain Images: Towards a Useful Tool in Clinical Practice. - Oula Puonti (2016)

An automatically generated texture-based atlas of the lungs. - Yashin Dicente Cid; Oula Puonti; Alexandra Platon; Koen Van Leemput; Henning Müller; Pierre-Alexandre Poletti (Computer-Aided Diagnosis, 2018)

Skull segmentation from MR scans using a higher-order shape model based on convolutional restricted Boltzmann machines. - Oula Puonti; Koen Van Leemput; Jesper Duemose Nielsen; Christian Bauer 006; Hartwig Roman Siebner; Kristoffer Hougaard Madsen; Axel Thielscher (Image Processing, 2018)

Head models of healthy and depressed adults for simulating the effects of non-invasive brain stimulation. - Nya Mehnwolo Boayue; Gábor Csifcsák; Oula Puonti; Axel Thielscher; Matthias Mittner (F1000Research, 2018)

Automatic skull segmentation from MR images for realistic volume conductor models of the head: Assessment of the state-of-the-art. - Jesper Duemose Nielsen; Kristoffer Hougaard Madsen; Oula Puonti; Hartwig R. Siebner; Christian Bauer 006; Camilla Gøbel Madsen; Guilherme B. Saturnino; Axel Thielscher (NeuroImage, 2018)

Accurate anatomical head segmentations: a data set for biomedical simulations. - Silvia Farcito; Oula Puonti; Hazael Montanaro; Guilherme B. Saturnino; Jesper Duemose Nielsen; Camilla Gøbel Madsen; Hartwig R. Siebner; Esra Neufeld; Niels Kuster; Bryn A. Lloyd; Axel Thielscher (EMBC, 2019)

A modality-adaptive method for segmenting brain tumors and organs-at-risk in radiation therapy planning. - Mikael Agn; Per Munck af Rosenschöld; Oula Puonti; Michael J. Lundemann; Laura Mancini; Anastasia Papadaki; Steffi Thust; John Ashburner; Ian Law; Koen Van Leemput (Medical Image Anal., 2019)

Accurate and robust whole-head segmentation from magnetic resonance images for individualized head modeling. - Oula Puonti; Koen Van Leemput; Guilherme B. Saturnino; Hartwig R. Siebner; Kristoffer H. Madsen; Axel Thielscher (NeuroImage, 2020)

Value and limitations of intracranial recordings for validating electric field modeling for transcranial brain stimulation. - Oula Puonti; Guilherme B. Saturnino; Kristoffer Hougaard Madsen; Axel Thielscher (NeuroImage, 2020)

SynthSeg: Domain Randomisation for Segmentation of Brain MRI Scans of any Contrast and Resolution. - Benjamin Billot; Douglas N. Greve; Oula Puonti; Axel Thielscher; Koen Van Leemput; Bruce Fischl; Adrian V. Dalca; Juan Eugenio Iglesias (CoRR, 2021)

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, 2021)

On the reconstruction of magnetic resonance current density images of the human brain: Pitfalls and perspectives. - Hasan H. Eroglu; Oula Puonti; Cihan Göksu; Fróði Gregersen; Hartwig R. Siebner; Lars G. Hanson; Axel Thielscher (NeuroImage, 2021)

Accurate and Explainable Image-Based Prediction Using a Lightweight Generative Model. - Chiara Mauri; Stefano Cerri; Oula Puonti; Mark Mühlau; Koen Van Leemput (MICCAI (8), 2022)

Mapping cortico-subcortical sensitivity to 4 Hz amplitude modulation depth in human auditory system with functional MRI. - Søren Asp Fuglsang; Kristoffer H. Madsen; Oula Puonti; Jens Hjortkjær; Hartwig R. Siebner (NeuroImage, 2022)

A Lightweight Causal Model for Interpretable Subject-level Prediction. - Chiara Mauri; Stefano Cerri; Oula Puonti; Mark Mühlau; Koen Van Leemput (CoRR, 2023)

Brain-ID: Learning Robust Feature Representations for Brain Imaging. - Peirong Liu; Oula Puonti; Xiaoling Hu 002; Daniel C. Alexander; Juan Eugenio Iglesias (CoRR, 2023)

SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining. - Benjamin Billot; Douglas N. Greve; Oula Puonti; Axel Thielscher; Koen Van Leemput; Bruce Fischl; Adrian V. Dalca; Juan Eugenio Iglesias (Medical Image Anal., 2023)

A head template for computational dose modelling for transcranial focused ultrasound stimulation. - SeyedSina Hosseini; Oula Puonti; Bradley E. Treeby; Lars G. Hanson; Axel Thielscher (NeuroImage, 2023)

Evaluating the influence of anatomical accuracy and electrode positions on EEG forward solutions. - Jesper Duemose Nielsen; Oula Puonti; Rong Xue; Axel Thielscher; Kristoffer Hougaard Madsen (NeuroImage, 2023)

Anatomical details affect electric field predictions for non-invasive brain stimulation in non-human primates. - Kathleen Mantell; Nipun D. Perera; Sina Shirinpour; Oula Puonti; Ting Xu; Jan Zimmermann; Arnaud Falchier; Sarah R. Heilbronner; Axel Thielscher; Alexander Opitz (NeuroImage, 2023)

Brain-ID: Learning Contrast-Agnostic Anatomical Representations for Brain Imaging. - Peirong Liu; Oula Puonti; Xiaoling Hu 002; Daniel C. Alexander; Juan Eugenio Iglesias (ECCV (12), 2024)

Quantifying White Matter Hyperintensity and Brain Volumes in Heterogeneous Clinical and Low-Field Portable MRI. - Pablo Laso; Stefano Cerri; Annabel Sorby-Adams; Jennifer Guo; Farrah Mateen; Philipp Goebl; Jiaming Wu; Peirong Liu; Hongwei Bran Li; Sean I. Young; Benjamin Billot; Oula Puonti; et al. (ISBI, 2024)

P-Count: Persistence-Based Counting of White Matter Hyperintensities in Brain MRI. - Xiaoling Hu 002; Annabel Sorby-Adams; Frederik Barkhof; W. Taylor Kimberly; Oula Puonti; Juan Eugenio Iglesias (TGI3@MICCAI, 2024)

PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI. - Peirong Liu; Oula Puonti; Annabel Sorby-Adams; W. Taylor Kimberly; Juan Eugenio Iglesias (MICCAI (12), 2024)

Registration by Regression (RbR): A Framework for Interpretable and Flexible Atlas Registration. - Karthik Gopinath; Xiaoling Hu 002; Malte Hoffmann; Oula Puonti; Juan Eugenio Iglesias (WBIR, 2024)

H-SynEx: Using synthetic images and ultra-high resolution ex vivo MRI for hypothalamus subregion segmentation. - Lívia Rodrigues 001; Martina Bocchetta; Oula Puonti; Douglas N. Greve; Ana Carolina Londe; Marcondes França; Simone Appenzeller; Juan Eugenio Iglesias; Letícia Rittner (CoRR, 2024)

PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI. - Peirong Liu; Oula Puonti; Annabel Sorby-Adams; William T. Kimberly; Juan Eugenio Iglesias (CoRR, 2024)

High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models. - Lívia Rodrigues 001; Martina Bocchetta; Oula Puonti; Douglas N. Greve; Ana Carolina Londe; Marcondes França; Simone Appenzeller; Letícia Rittner; Juan Eugenio Iglesias (CoRR, 2024)

Learn2Synth: Learning Optimal Data Synthesis Using Hypergradients. - Xiaoling Hu 002; Oula Puonti; Juan Eugenio Iglesias; Bruce Fischl; Yaël Balbastre (CoRR, 2024)

Hierarchical Uncertainty Estimation for Learning-based Registration in Neuroimaging. - Xiaoling Hu 002; Karthik Gopinath; Peirong Liu; Malte Hoffmann; Koen Van Leemput; Oula Puonti; Juan Eugenio Iglesias (ICLR, 2025)

"Recon-all-clinical": Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI. - Karthik Gopinath; Douglas N. Greve; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Oula Puonti; Juan Eugenio Iglesias (Medical Image Anal., 2025)

A lightweight generative model for interpretable subject-level prediction. - Chiara Mauri; Stefano Cerri; Oula Puonti; Mark Mühlau; Koen Van Leemput (Medical Image Anal., 2025)

Towards quantitative intensity analysis of conventional T1-weighted images in multiple sclerosis. - Tun Wiltgen; Julian McGinnis; Ronja C. Berg; Cui Ci Voon; Oula Puonti; Katrin Giglhuber; Carl Ganter; Claus Zimmer; Bernhard Hemmer; Benedikt Wiestler; Jan Kirschke; Christine Preibisch; et al. (NeuroImage, 2025)

Reference-Free 3D Reconstruction of Brain Dissection Photographs with Machine Learning. - Lin Tian; Sean I. Young; Jonathan Williams Ramirez; Dina Zemlyanker; Lucas J. Deden-Binder; Rogeny Herisse; Theresa R. Connors; Derek H. Oakley; Bradley T. Hyman; Oula Puonti; Matthew S. Rosen; Juan Eugenio Iglesias (CoRR, 2025)

From Low Field to High Value: Robust Cortical Mapping from Low-Field MRI. - Karthik Gopinath; Annabel Sorby-Adams; Jonathan Williams Ramirez; Dina Zemlyanker; Jennifer Guo; David Hunt; Christine L. Mac Donald; C. Dirk Keene; Timothy S. Coalson; Matthew F. Glasser; David C. Van Essen; Matthew S. Rosen; et al. (CoRR, 2025)

End-to-end Cortical Surface Reconstruction from Clinical Magnetic Resonance Images. - Jesper Duemose Nielsen; Karthik Gopinath; Andrew Hoopes; Adrian V. Dalca; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Axel Thielscher; Juan Eugenio Iglesias; Oula Puonti (CoRR, 2025)

Scalable Segmentation for Ultra-High-Resolution Brain MR Images. - Xiaoling Hu 002; Peirong Liu; Dina Zemlyanker; Jonathan Williams Ramirez; Oula Puonti; Juan Eugenio Iglesias (CoRR, 2025)

Conditional diffusion models for guided anomaly detection in brain images using fluid-driven anomaly randomization. - Ana Lawry Aguila; Peirong Liu; Oula Puonti; Juan Eugenio Iglesias (CoRR, 2025)