Atlas-Based Segmentation of Pathological Brains Using a Model of Tumor Growth. - Meritxell Bach Cuadra; J. Gomez; Patric Hagmann; Claudio Pollo; Jean-Guy Villemure; Benoit M. Dawant; Jean-Philippe Thiran (MICCAI (1), 2002)

White Matter Mapping in DT-MRI Using Geometric Flows. - Lisa Jonasson; Patric Hagmann; Xavier Bresson; Reto Meuli; Olivier Cuisenaire; Jean-Philippe Thiran (EUROCAST, 2003)

A New Brain Segmentation Framework. - Torsten Butz; Patric Hagmann; Eric Tardif; Reto Meuli; Jean-Philippe Thiran (MICCAI (2), 2003)

DTI mapping of human brain connectivity: statistical fibre tracking and virtual dissection. - Patric Hagmann; Jean-Philippe Thiran; Lisa Jonasson; Pierre Vandergheynst; Stephanie Clarke; Philippe Maeder; Reto Meuli (NeuroImage, 2003)

Representing Diffusion MRI in 5D for Segmentation of White Matter Tracts with a Level Set Method. - Lisa Jonasson; Patric Hagmann; Xavier Bresson; Jean-Philippe Thiran; Van J. Wedeen (IPMI, 2005)

White matter fiber tract segmentation in DT-MRI using geometric flows. - Lisa Jonasson; Xavier Bresson; Patric Hagmann; Olivier Cuisenaire; Reto Meuli; Jean-Philippe Thiran (Medical Image Anal., 2005)

From diffusion MRI to brain connectomics. - Patric Hagmann (2005)

Fibertract segmentation in position orientation space from high angular resolution diffusion MRI. - Patric Hagmann; Lisa Jonasson; Thomas Deffieux; Reto Meuli; Jean-Philippe Thiran; Van J. Wedeen (NeuroImage, 2006)

A level set method for segmentation of the thalamus and its nuclei in DT-MRI. - Lisa Jonasson; Patric Hagmann; Claudio Pollo; Xavier Bresson; Cecilia Richero Wilson; Reto Meuli; Jean-Philippe Thiran (Signal Process., 2007)

Representing Diffusion MRI in 5-D Simplifies Regularization and Segmentation of White Matter Tracts. - Lisa Jonasson; Xavier Bresson; Jean-Philippe Thiran; Van J. Wedeen; Patric Hagmann (IEEE Trans. Medical Imaging, 2007)

Diffusion spectrum magnetic resonance imaging (DSI) tractography of crossing fibers. - Van J. Wedeen; R. P. Wang; Jeremy D. Schmahmann; Thomas Benner; Wen-Yih Isaac Tseng; Guangping Dai; Deepak N. Pandya; Patric Hagmann; Helen D'Arceuil; Alex J. de Crespigny (NeuroImage, 2008)

Modeling the Impact of Lesions in the Human Brain. - Jeffrey Alstott; Michael Breakspear; Patric Hagmann; Leila Cammoun; Olaf Sporns (PLoS Comput. Biol., 2009)

The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes. - Stephan Gerhard; Alessandro Daducci; Alia Lemkaddem; Reto Meuli; Jean-Philippe Thiran; Patric Hagmann (Frontiers Neuroinformatics, 2011)

Classifying minimally disabled multiple sclerosis patients from resting state functional connectivity. - Jonas Richiardi; Markus Gschwind; Samanta Simioni; Jean-Marie Annoni; Beatrice Greco; Patric Hagmann; Myriam Schluep; Patrik Vuilleumier; Dimitri Van De Ville (NeuroImage, 2012)

Structural connectomics in brain diseases. - Alessandra Griffa; Philipp S. Baumann; Jean-Philippe Thiran; Patric Hagmann (NeuroImage, 2013)

Comparing connectomes across subjects and populations at different scales. - Djalel Eddine Meskaldji; Elda Fischi Gomez; Alessandra Griffa; Patric Hagmann; Stephan Morgenthaler; Jean-Philippe Thiran (NeuroImage, 2013)

Efficient Total Variation Algorithm for Fetal Brain MRI Reconstruction. - Sébastien Tourbier; Xavier Bresson; Patric Hagmann; Jean-Philippe Thiran; Reto Meuli; Meritxell Bach Cuadra (MICCAI (2), 2014)

Multi-scale integration and predictability in resting state brain activity. - Artemy Kolchinsky; Martijn P. van den Heuvel; Alessandra Griffa; Patric Hagmann; Luis M. Rocha; Olaf Sporns; Joaquín Goñi (Frontiers Neuroinformatics, 2014)

Automatic brain extraction in fetal MRI using multi-atlas-based segmentation. - Sébastien Tourbier; Patric Hagmann; Maud Cagneaux; Laurent Guibaud; Subrahmanyam Gorthi; Marie Schaer; Jean-Philippe Thiran; Reto Meuli; Meritxell Bach Cuadra (Image Processing, 2015)

Improved statistical evaluation of group differences in connectomes by screening-filtering strategy with application to study maturation of brain connections between childhood and adolescence. - Djalel Eddine Meskaldji; Lana Vasung; David Romascano; Jean-Philippe Thiran; Patric Hagmann; Stephan Morgenthaler; Dimitri Van De Ville (NeuroImage, 2015)

An efficient total variation algorithm for super-resolution in fetal brain MRI with adaptive regularization. - Sébastien Tourbier; Xavier Bresson; Patric Hagmann; Jean-Philippe Thiran; Reto Meuli; Meritxell Bach Cuadra (NeuroImage, 2015)

Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity. - Adrián Ponce-Alvarez; Gustavo Deco; Patric Hagmann; Gian Luca Romani; Dante Mantini; Maurizio Corbetta (PLoS Comput. Biol., 2015)

Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling. - Adrián Ponce-Alvarez; Biyu J. He; Patric Hagmann; Gustavo Deco (PLoS Comput. Biol., 2015)

Generative models of the human connectome. - Richard F. Betzel; Andrea Avena-Koenigsberger; Joaquín Goñi; Ye He; Marcel A. de Reus; Alessandra Griffa; Petra E. Vértes; Bratislav Misic; Jean-Philippe Thiran; Patric Hagmann; Martijn P. van den Heuvel; Xi-Nian Zuo; et al. (NeuroImage, 2016)

Effect of Field Spread on Resting-State Magneto Encephalography Functional Network Analysis: A Computational Modeling Study. - Silvana Silva Pereira; Rikkert Hindriks; Stefanie Mühlberg; Eric Maris; Freek van Ede; Alessandra Griffa; Patric Hagmann; Gustavo Deco (Brain Connect., 2017)

Routes Obey Hierarchy in Complex Networks. - Attila Csoma; Attila Korösi; Gábor Rétvári; Zalán Heszberger; József Bíró; Mariann Slíz; Andrea Avena-Koenigsberger; Alessandra Griffa; Patric Hagmann; András Gulyás (CoRR, 2017)

Transient networks of spatio-temporal connectivity map communication pathways in brain functional systems. - Alessandra Griffa; Benjamin Ricaud; Kirell Benzi; Xavier Bresson; Alessandro Daducci; Pierre Vandergheynst; Jean-Philippe Thiran; Patric Hagmann (NeuroImage, 2017)

Automated template-based brain localization and extraction for fetal brain MRI reconstruction. - Sébastien Tourbier; Clemente Velasco-Annis; Vahid Taimouri; Patric Hagmann; Reto Meuli; Simon K. Warfield; Meritxell Bach Cuadra; Ali Gholipour (NeuroImage, 2017)

Holographic Visualisation and Interaction of Fused CT, PET and MRI Volumetric Medical Imaging Data Using Dedicated Remote GPGPU Ray Casting. - Magali Fröhlich; Christophe Bolinhas; Adrien Depeursinge; Antoine Widmer; Nicolas Chevrey; Patric Hagmann; Christian Simon; Vivianne B. C. Kokje; Stéphane Gobron (POCUS/BIVPCS/CuRIOUS/CPM@MICCAI, 2018)

Effective connectivity inferred from fMRI transition dynamics during movie viewing points to a balanced reconfiguration of cortical interactions. - Matthieu Gilson; Gustavo Deco; Karl J. Friston; Patric Hagmann; Dante Mantini; Viviana Betti; Gian Luca Romani; Maurizio Corbetta (NeuroImage, 2018)

Time-varying effective EEG source connectivity: the optimization of model parameters. - Maria Rubega; David Pascucci; Joan Rué Queralt; Pieter van Mierlo; Patric Hagmann; Gijs Plomp; Christoph M. Michel (EMBC, 2019)

Distinct modes of functional connectivity induced by movie-watching. - Murat Demirtas; Adrián Ponce-Alvarez; Matthieu Gilson; Patric Hagmann; Dante Mantini; Viviana Betti; Gian Luca Romani; Karl J. Friston; Maurizio Corbetta; Gustavo Deco (NeuroImage, 2019)

A spectrum of routing strategies for brain networks. - Andrea Avena-Koenigsberger; Xiaoran Yan; Artemy Kolchinsky; Martijn P. van den Heuvel; Patric Hagmann; Olaf Sporns (PLoS Comput. Biol., 2019)

T2 Mapping from Super-Resolution-Reconstructed Clinical Fast Spin Echo Magnetic Resonance Acquisitions. - Hélène Lajous; Tom Hilbert; Christopher W. Roy; Sébastien Tourbier; Priscille de Dumast; Thomas Yu; Jean-Philippe Thiran; Jean-Baptiste Ledoux; Davide Piccini; Patric Hagmann; Reto Meuli; Tobias Kober; et al. (MICCAI (2), 2020)

An Anatomically-Informed 3D CNN for Brain Aneurysm Classification with Weak Labels. - Tommaso Di Noto; Guillaume Marie; Sébastien Tourbier; Yasser Alemán-Gómez; Guillaume Saliou; Meritxell Bach Cuadra; Patric Hagmann; Jonas Richiardi (MLCN/RNO-AI@MICCAI, 2020)

Connectome spectral analysis to track EEG task dynamics on a subsecond scale. - Katharina Glomb; Joan Rué Queralt; David Pascucci; Michaël Defferrard; Sébastien Tourbier; Margherita Carboni; Maria Rubega; Serge Vulliémoz; Gijs Plomp; Patric Hagmann (NeuroImage, 2020)

Simulated Half-Fourier Acquisitions Single-shot Turbo Spin Echo (HASTE) of the Fetal Brain: Application to Super-Resolution Reconstruction. - Hélène Lajous; Tom Hilbert; Christopher W. Roy; Sébastien Tourbier; Priscille de Dumast; Yasser Alemán-Gómez; Thomas Yu; Hamza Kebiri; Jean-Baptiste Ledoux; Patric Hagmann; Reto Meuli; Vincent Dunet; et al. (UNSURE/PIPPI@MICCAI, 2021)

Diagnostic Surveillance of High-Grade Gliomas: Towards Automated Change Detection Using Radiology Report Classification. - Tommaso Di Noto; Chirine Atat; Eduardo Gamito Teiga; Monika Hegi; Andreas Hottinger; Meritxell Bach Cuadra; Patric Hagmann; Jonas Richiardi (PKDD/ECML Workshops (2), 2021)

Weak labels and anatomical knowledge: making deep learning practical for intracranial aneurysm detection in TOF-MRA. - Tommaso Di Noto; Guillaume Marie; Sébastien Tourbier; Yasser Alemán-Gómez; Oscar Esteban; Guillaume Saliou; Meritxell Bach Cuadra; Patric Hagmann; Jonas Richiardi (CoRR, 2021)

FaBiAN: A Fetal Brain magnetic resonance Acquisition Numerical phantom. - Hélène Lajous; Christopher W. Roy; Tom Hilbert; Priscille de Dumast; Sébastien Tourbier; Yasser Alemán-Gómez; Jérôme Yerly; Thomas Yu; Hamza Kebiri; Kelly Payette; Jean-Baptiste Ledoux; Reto Meuli; et al. (CoRR, 2021)

Multiscale communication in cortico-cortical networks. - Vincent Bazinet; Reinder Vos de Wael; Patric Hagmann; Boris C. Bernhardt; Bratislav Misic (NeuroImage, 2021)

The connectome spectrum as a canonical basis for a sparse representation of fast brain activity. - Joan Rué Queralt; Katharina Glomb; David Pascucci; Sébastien Tourbier; Margherita Carboni; Serge Vulliémoz; Gijs Plomp; Patric Hagmann (NeuroImage, 2021)

Transfer learning with weak labels from radiology reports: application to glioma change detection. - Tommaso Di Noto; Meritxell Bach Cuadra; Chirine Atat; Eduardo Gamito Teiga; Monika Hegi; Andreas Hottinger; Patric Hagmann; Jonas Richiardi (CoRR, 2022)

Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping. - Sébastien Tourbier; Joan Rué Queralt; Katharina Glomb; Yasser Alemán-Gómez; Emeline Mullier; Alessandra Griffa; Mikkel Schöttner; Jonathan Wirsich; Mustafa Anil Tuncel; Jakub Jancovic; Meritxell Bach Cuadra; Patric Hagmann (J. Open Source Softw., 2022)

Towards Automated Brain Aneurysm Detection in TOF-MRA: Open Data, Weak Labels, and Anatomical Knowledge. - Tommaso Di Noto; Guillaume Marie; Sébastien Tourbier; Yasser Alemán-Gómez; Oscar Esteban; Guillaume Saliou; Meritxell Bach Cuadra; Patric Hagmann; Jonas Richiardi (Neuroinformatics, 2023)

The coupling between the spatial and temporal scales of neural processes revealed by a joint time-vertex connectome spectral analysis. - Joan Rué Queralt; Valentina Mancini; Vincent Rochas; Caren Latrèche; Peter J. Uhlhaas; Christoph M. Michel; Gijs Plomp; Stephan Eliez; Patric Hagmann (NeuroImage, 2023)

Introducing Edge-Wise Graph Signal Processing: Application to Connectome Fingerprinting. - Thomas William Arthur Bolton; Mikkel Schöttner; Jagruti Patel; Patric Hagmann (ISBI, 2024)

Assessing workflow impact and clinical utility of AI-assisted brain aneurysm detection: a multi-reader study. - Tommaso Di Noto; Sofyan Jankowski; Francesco Puccinelli; Guillaume Marie; Sébastien Tourbier; Yasser Alemán-Gómez; Oscar Esteban; Ricardo Corredor-Jerez; Guillaume Saliou; Patric Hagmann; Meritxell Bach Cuadra; Jonas Richiardi (CoRR, 2025)

Structural Connectome Harmonization Using Deep Learning: The Strength of Graph Neural Networks. - Jagruti Patel; Thomas William Arthur Bolton; Mikkel Schöttner; Anjali Tarun; Sébastien Tourbier; Yasser Alemán-Gómez; Jonas Richiardi; Patric Hagmann (CoRR, 2025)

The added value for MRI radiomics and deep-learning for glioblastoma prognostication compared to clinical and molecular information. - Daniel Abler; O. Pusterla; A. Joye-Kühnis; Nicolaus Andratschke; Meritxell Bach; A. Bink; S. M. Christ; Patric Hagmann; B. Pouymayou; E. Pravatà; Piotr Radojewski; Mauricio Reyes 001; et al. (CoRR, 2025)

Comparing and Scaling fMRI Features for Brain-Behavior Prediction. - Mikkel Schöttner Sieler; Thomas William Arthur Bolton; Jagruti Patel; Patric Hagmann (CoRR, 2025)

Predicting Cognition from fMRI:A Comparative Study of Graph, Transformer, and Kernel Models Across Task and Rest Conditions. - Jagruti Patel; Mikkel Schöttner; Thomas William Arthur Bolton; Patric Hagmann (CoRR, 2025)