Attenuation Correction Synthesis for Hybrid PET-MR Scanners. - Ninon Burgos; Manuel Jorge Cardoso; Marc Modat; Stefano Pedemonte; John C. Dickson; Anna Barnes; John S. Duncan; David Atkinson; Simon R. Arridge; Brian F. Hutton; Sébastien Ourselin (MICCAI (1), 2013)

Simulated Field Maps: Toward Improved Susceptibility Artefact Correction in Interventional MRI. - Martin Kochan; Pankaj Daga; Ninon Burgos; Mark White 001; Manuel Jorge Cardoso; Laura Mancini; Gavin Winston; Andrew W. McEvoy; John S. Thornton; Tarek A. Yousry; John S. Duncan; Danail Stoyanov; et al. (IPCAI, 2014)

Joint Parametric Reconstruction and Motion Correction Framework for Dynamic PET Data. - Jieqing Jiao; Alexandre Bousse; Kris Thielemans; Pawel Markiewicz; Ninon Burgos; David Atkinson; Simon R. Arridge; Brian F. Hutton; Sébastien Ourselin (MICCAI (1), 2014)

Attenuation Correction Synthesis for Hybrid PET-MR Scanners: Application to Brain Studies. - Ninon Burgos; Manuel Jorge Cardoso; Kris Thielemans; Marc Modat; Stefano Pedemonte; John C. Dickson; Anna Barnes; Rebekah Ahmed; Colin J. Mahoney; Jonathan M. Schott; John S. Duncan; David Atkinson; et al. (IEEE Trans. Medical Imaging, 2014)

Detail-Preserving PET Reconstruction with Sparse Image Representation and Anatomical Priors. - Jieqing Jiao; Pawel Markiewicz; Ninon Burgos; David Atkinson; Brian F. Hutton; Simon R. Arridge; Sébastien Ourselin (IPMI, 2015)

Multi-atlas synthesis for computer assisted diagnosis: Application to cardiovascular diseases. - Maria A. Zuluaga; Ninon Burgos; Andrew Mayall Taylor; Sébastien Ourselin (ISBI, 2015)

Robust CT Synthesis for Radiotherapy Planning: Application to the Head and Neck Region. - Ninon Burgos; Manuel Jorge Cardoso; Filipa Guerreiro; Catarina Veiga; Marc Modat; Jamie McClelland; Antje-Christin Knopf; Shonit Punwani; David Atkinson; Simon R. Arridge; Brian F. Hutton; Sébastien Ourselin (MICCAI (2), 2015)

Subject-specific Models for the Analysis of Pathological FDG PET Data. - Ninon Burgos; Manuel Jorge Cardoso; Alex F. Mendelson; Jonathan M. Schott; David Atkinson; Simon R. Arridge; Brian F. Hutton; Sébastien Ourselin (MICCAI (2), 2015)

Simulated field maps for susceptibility artefact correction in interventional MRI. - Martin Kochan; Pankaj Daga; Ninon Burgos; Mark White 001; Manuel Jorge Cardoso; Laura Mancini; Gavin P. Winston; Andrew W. McEvoy; John S. Thornton; Tarek A. Yousry; John S. Duncan; Danail Stoyanov; et al. (Int. J. Comput. Assist. Radiol. Surg., 2015)

Voxelwise atlas rating for computer assisted diagnosis: Application to congenital heart diseases of the great arteries. - Maria A. Zuluaga; Ninon Burgos; Alex F. Mendelson; Andrew Mayall Taylor; Sébastien Ourselin (Medical Image Anal., 2015)

Joint Segmentation and CT Synthesis for MRI-only Radiotherapy Treatment Planning. - Ninon Burgos; Filipa Guerreiro; Jamie McClelland; Simeon Nill; David Dearnaley; Nandita deSouza; Uwe Oelfke; Antje-Christin Knopf; Sébastien Ourselin; M. Jorge Cardoso (MICCAI (2), 2016)

Individual Analysis of Molecular Brain Imaging Data Through Automatic Identification of Abnormality Patterns. - Ninon Burgos; Jorge Samper-González; Anne Bertrand; Marie Odile Habert; Sébastien Ourselin; Stanley Durrleman; M. Jorge Cardoso; Olivier Colliot (CMMI/RAMBO/SWITCH@MICCAI, 2017)

Yet Another ADNI Machine Learning Paper? Paving the Way Towards Fully-Reproducible Research on Classification of Alzheimer's Disease. - Jorge Samper-González; Ninon Burgos; Sabrina Fontanella; Hugo Bertin; Marie Odile Habert; Stanley Durrleman; Theodoros Evgeniou; Olivier Colliot (MLMI@MICCAI, 2017)

Short Acquisition Time PET Quantification Using MRI-Based Pharmacokinetic Parameter Synthesis. - Catherine J. Scott; Jieqing Jiao; M. Jorge Cardoso; Andrew Melbourne; Enrico De Vita; David Thomas 002; Ninon Burgos; Pawel Markiewicz; Jonathan M. Schott; Brian F. Hutton; Sébastien Ourselin (MICCAI (2), 2017)

A multi-centre evaluation of eleven clinically feasible brain PET/MRI attenuation correction techniques using a large cohort of patients. - Claes Nøhr Ladefoged; Ian Law; Udunna Anazodo; Keith St. Lawrence; David Izquierdo-Garcia; Ciprian Catana; Ninon Burgos; M. Jorge Cardoso; Sébastien Ourselin; Brian F. Hutton; Inés Mérida; Nicolas Costes 001; et al. (NeuroImage, 2017)

Direct Parametric Reconstruction With Joint Motion Estimation/Correction for Dynamic Brain PET Data. - Jieqing Jiao; Alexandre Bousse; Kris Thielemans; Ninon Burgos; Philip S. J. Weston; Jonathan M. Schott; David Atkinson; Simon R. Arridge; Brian F. Hutton; Pawel Markiewicz; Sébastien Ourselin (IEEE Trans. Medical Imaging, 2017)

Reproducible evaluation of classification methods in Alzheimer's disease: framework and application to MRI and PET data. - Jorge Samper-González; Ninon Burgos; Simona Bottani; Sabrina Fontanella; Pascal Lu; Arnaud Marcoux; Alexandre Routier; Jérémy Guillon; Michael Bacci; Junhao Wen 002; Anne Bertrand; Hugo Bertin; et al. (CoRR, 2018)

Reproducible evaluation of diffusion MRI features for automatic classification of patients with Alzheimers disease. - Junhao Wen 002; Jorge Samper-González; Simona Bottani; Alexandre Routier; Ninon Burgos; Thomas Jacquemont; Sabrina Fontanella; Stanley Durrleman; Stéphane Epelbaum; Anne Bertrand; Olivier Colliot (CoRR, 2018)

An Automated Pipeline for the Analysis of PET Data on the Cortical Surface. - Arnaud Marcoux; Ninon Burgos; Anne Bertrand; Marc Teichmann; Alexandre Routier; Junhao Wen 002; Jorge Samper-González; Simona Bottani; Stanley Durrleman; Marie Odile Habert; Olivier Colliot (Frontiers Neuroinformatics, 2018)

Reproducible evaluation of classification methods in Alzheimer's disease: Framework and application to MRI and PET data. - Jorge Samper-González; Ninon Burgos; Simona Bottani; Sabrina Fontanella; Pascal Lu; Arnaud Marcoux; Alexandre Routier; Jérémy Guillon; Michael Bacci; Junhao Wen 002; Anne Bertrand; Hugo Bertin; et al. (NeuroImage, 2018)

Reproducible evaluation of methods for predicting progression to Alzheimer's disease from clinical and neuroimaging data. - Jorge Samper-González; Ninon Burgos; Simona Bottani; Marie Odile Habert; Theodoros Evgeniou; Stéphane Epelbaum; Olivier Colliot (Image Processing, 2019)

Convolutional Neural Networks for Classification of Alzheimer's Disease: Overview and Reproducible Evaluation. - Junhao Wen 002; Elina Thibeau-Sutre; Jorge Samper-González; Alexandre Routier; Simona Bottani; Stanley Durrleman; Ninon Burgos; Olivier Colliot (CoRR, 2019)

Visualization approach to assess the robustness of neural networks for medical image classification. - Elina Thibeau-Sutre; Olivier Colliot; Didier Dormont; Ninon Burgos (Image Processing, 2020)

Convolutional neural networks for classification of Alzheimer's disease: Overview and reproducible evaluation. - Junhao Wen 002; Elina Thibeau-Sutre; Mauricio Diaz-Melo; Jorge Samper-González; Alexandre Routier; Simona Bottani; Didier Dormont; Stanley Durrleman; Ninon Burgos; Olivier Colliot (Medical Image Anal., 2020)

Deep learning for brain disorders: from data processing to disease treatment. - Ninon Burgos; Simona Bottani; Johann Faouzi; Elina Thibeau-Sutre; Olivier Colliot (Briefings Bioinform., 2021)

Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies. - Alexandre Routier; Ninon Burgos; Mauricio Diaz-Melo; Michael Bacci; Simona Bottani; Omar El-Rifai; Sabrina Fontanella; Pietro Gori; Jérémy Guillon; Alexis Guyot; Ravi Hassanaly; Thomas Jacquemont; et al. (Frontiers Neuroinformatics, 2021)

Predicting the progression of mild cognitive impairment using machine learning: A systematic, quantitative and critical review. - Manon Ansart; Stéphane Epelbaum; Giulia Bassignana; Alexandre Bône; Simona Bottani; Tiziana Cattai; Raphaël Couronné; Johann Faouzi; Igor Koval; Maxime Louis; Elina Thibeau-Sutre; Junhao Wen 002; et al. (Medical Image Anal., 2021)

Reproducible Evaluation of Diffusion MRI Features for Automatic Classification of Patients with Alzheimer's Disease. - Junhao Wen 002; Jorge Samper-González; Simona Bottani; Alexandre Routier; Ninon Burgos; Thomas Jacquemont; Sabrina Fontanella; Stanley Durrleman; Stéphane Epelbaum; Anne Bertrand; Olivier Colliot (Neuroinformatics, 2021)

Individualised, interpretable and reproducible computer-aided diagnosis of dementia: towards application in clinical practice. - Ninon Burgos (2022)

MRI Field Strength Predicts Alzheimer's Disease: a Case Example of Bias in the ADNI Data Set. - Elina Thibeau-Sutre; Baptiste Couvy-Duchesne; Didier Dormont; Olivier Colliot; Ninon Burgos (ISBI, 2022)

Homogenization of brain MRI from a clinical data warehouse using contrast-enhanced to non-contrast-enhanced image translation with U-Net derived models. - Simona Bottani; Elina Thibeau-Sutre; Aurélien Maire; Sebastian Ströer; Didier Dormont; Olivier Colliot; Ninon Burgos (Image Processing, 2022)

ClinicaDL: An open-source deep learning software for reproducible neuroimaging processing. - Elina Thibeau-Sutre; Mauricio Diaz-Melo; Ravi Hassanaly; Alexandre Routier; Didier Dormont; Olivier Colliot; Ninon Burgos (Comput. Methods Programs Biomed., 2022)

Interpretability of Machine Learning Methods Applied to Neuroimaging. - Elina Thibeau-Sutre; Sasha Collin; Ninon Burgos; Olivier Colliot (CoRR, 2022)

Reproducibility in machine learning for medical imaging. - Olivier Colliot; Elina Thibeau-Sutre; Ninon Burgos (CoRR, 2022)

Fourier Disentangled Multimodal Prior Knowledge Fusion for Red Nucleus Segmentation in Brain MRI. - Guanghui Fu; Gabriel Jimenez 001; Sophie Loizillon; Rosana El Jurdi; Lydia Chougar; Didier Dormont; Romain Valabrègue; Ninon Burgos; Stéphane Lehéricy; Daniel Racoceanu; Olivier Colliot (CoRR, 2022)

Automatic quality control of brain T1-weighted magnetic resonance images for a clinical data warehouse. - Simona Bottani; Ninon Burgos; Aurélien Maire; Adam Wild; Sebastian Ströer; Didier Dormont; Olivier Colliot (Medical Image Anal., 2022)

A2V: A Semi-Supervised Domain Adaptation Framework for Brain Vessel Segmentation via Two-Phase Training Angiography-to-Venography Translation. - Francesco Galati; Daniele Falcetta; Rosa Cortese; Barbara Casolla; Ferran Prados; Ninon Burgos; Maria A. Zuluaga (BMVC, 2023)

Unsupervised Anomaly Detection in 3D Brain FDG PET: A Benchmark of 17 VAE-Based Approaches. - Ravi Hassanaly; Camille Brianceau; Olivier Colliot; Ninon Burgos (DGM4MICCAI, 2023)

Semi-supervised Domain Adaptation for Automatic Quality Control of FLAIR MRIs in a Clinical Data Warehouse. - Sophie Loizillon; Olivier Colliot; Lydia Chougar; Sebastian Ströer; Yannick Jacob; Aurélien Maire; Didier Dormont; Ninon Burgos (DART@MICCAI, 2023)

Exploiting hospital data warehouses: the challenges of image quality and heterogeneity (Conference Presentation). - Ninon Burgos (Image Processing, 2023)

Simulation based evaluation framework for deep learning unsupervised anomaly detection on brain FDG-PET. - Ravi Hassanaly; Simona Bottani; Benoît Sauty; Olivier Colliot; Ninon Burgos (Image Processing, 2023)

Transfer learning from synthetic to routine clinical data for motion artefact detection in brain T1-weighted MRI. - Sophie Loizillon; Simona Bottani; Aurélien Maire; Sebastian Ströer; Didier Dormont; Olivier Colliot; Ninon Burgos (Image Processing, 2023)

How can data augmentation improve attribution maps for disease subtype explainability. - Elina Thibeau-Sutre; Jelmer M. Wolterink; Olivier Colliot; Ninon Burgos (Image Processing, 2023)

Frequency Disentangled Learning for Segmentation of Midbrain Structures from Quantitative Susceptibility Mapping Data. - Guanghui Fu; Gabriel Jimenez 001; Sophie Loizillon; Lydia Chougar; Didier Dormont; Romain Valabrègue; Ninon Burgos; Stéphane Lehéricy; Daniel Racoceanu; Olivier Colliot (CoRR, 2023)

Leveraging healthy population variability in deep learning unsupervised anomaly detection in brain FDG PET. - Maëlys Solal; Ravi Hassanaly; Ninon Burgos (CoRR, 2023)

Data Augmentation in High Dimensional Low Sample Size Setting Using a Geometry-Based Variational Autoencoder. - Clément Chadebec; Elina Thibeau-Sutre; Ninon Burgos; Stéphanie Allassonnière (IEEE Trans. Pattern Anal. Mach. Intell., 2023)

Evaluation of MRI-based machine learning approaches for computer-aided diagnosis of dementia in a clinical data warehouse. - Simona Bottani; Ninon Burgos; Aurélien Maire; Dario Saracino; Sebastian Ströer; Didier Dormont; Olivier Colliot (Medical Image Anal., 2023)

Confidence Intervals Uncovered: Are We Ready for Real-World Medical Imaging AI? - Evangelia Christodoulou; Annika Reinke; Rola Houhou; Piotr Kalinowski; Selen Erkan; Carole H. Sudre; Ninon Burgos; Sofiène Boutaj; Sophie Loizillon; Maëlys Solal; Nicola Rieke; Veronika Cheplygina; et al. (MICCAI (10), 2024)

Preface for International Conference on Medical Imaging with Deep Learning 2024. - Ninon Burgos; Caroline Petitjean; Maria Vakalopoulou; Stergios Christodoulidis; Pierrick Coupé; Hervé Delingette; Carole Lartizien; Diana Mateus (MIDL, 2024)

Detecting Brain Anomalies in Clinical Routine with the β-VAE: Feasibility Study on Age-Related White Matter Hyperintensities. - Sophie Loizillon; Yannick Jacob; Aurélien Maire; Didier Dormont; Olivier Colliot; Ninon Burgos; Apprimage Study Group (MIDL, 2024)

Evaluation of pseudo-healthy image reconstruction for anomaly detection with deep generative models: Application to brain FDG PET. - Ravi Hassanaly; Camille Brianceau; Maëlys Solal; Olivier Colliot; Ninon Burgos (CoRR, 2024)

Automated MRI Quality Assessment of Brain T1-weighted MRI in Clinical Data Warehouses: A Transfer Learning Approach Relying on Artefact Simulation. - Sophie Loizillon; Simona Bottani; Stéphane Mabille; Yannick Jacob; Aurélien Maire; Sebastian Ströer; Didier Dormont; Olivier Colliot; Ninon Burgos (CoRR, 2024)

Automatic motion artefact detection in brain T1-weighted magnetic resonance images from a clinical data warehouse using synthetic data. - Sophie Loizillon; Simona Bottani; Aurélien Maire; Sebastian Ströer; Didier Dormont; Olivier Colliot; Ninon Burgos (Medical Image Anal., 2024)

Contrast-enhanced to non-contrast-enhanced image translation to exploit a clinical data warehouse of T1-weighted brain MRI. - Simona Bottani; Elina Thibeau-Sutre; Aurélien Maire; Sebastian Ströer; Didier Dormont; Olivier Colliot; Ninon Burgos (BMC Medical Imaging, 2024)

Automatic quality control of brain 3D FLAIR MRIs for a clinical data warehouse. - Sophie Loizillon; Simona Bottani; Aurélien Maire; Sebastian Ströer; Lydia Chougar; Didier Dormont; Olivier Colliot; Ninon Burgos (Medical Image Anal., 2025)

False Promises in Medical Imaging AI? Assessing Validity of Outperformance Claims. - Evangelia Christodoulou; Annika Reinke; Pascaline Andrè; Patrick Godau; Piotr Kalinowski; Rola Houhou; Selen Erkan; Carole H. Sudre; Ninon Burgos; Sofiène Boutaj; Sophie Loizillon; Maëlys Solal; et al. (CoRR, 2025)

Unsupervised anomaly detection using Bayesian flow networks: application to brain FDG PET in the context of Alzheimer's disease. - Hugues Roy; Reuben Dorent; Ninon Burgos (CoRR, 2025)