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Books and Theses
- 2022
[b1]Ninon Burgos:
Individualised, interpretable and reproducible computer-aided diagnosis of dementia: towards application in clinical practice. Sorbonne University, Paris, France, 2022
Journal Articles
- 2024
- [j18]Simona Bottani, Elina Thibeau-Sutre, Aurélien Maire, Sebastian Ströer, Didier Dormont, Olivier Colliot, Ninon Burgos:
Contrast-enhanced to non-contrast-enhanced image translation to exploit a clinical data warehouse of T1-weighted brain MRI. BMC Medical Imaging 24(1): 67 (2024) - [j17]Sophie Loizillon
, Simona Bottani, Aurélien Maire, Sebastian Ströer, Didier Dormont, Olivier Colliot, Ninon Burgos:
Automatic motion artefact detection in brain T1-weighted magnetic resonance images from a clinical data warehouse using synthetic data. Medical Image Anal. 93: 103073 (2024) - 2023
- [j16]Simona Bottani, Ninon Burgos, Aurélien Maire, Dario Saracino, Sebastian Ströer, Didier Dormont, Olivier Colliot:
Evaluation of MRI-based machine learning approaches for computer-aided diagnosis of dementia in a clinical data warehouse. Medical Image Anal. 89: 102903 (2023) - [j15]Clément Chadebec, Elina Thibeau-Sutre, Ninon Burgos, Stéphanie Allassonnière:
Data Augmentation in High Dimensional Low Sample Size Setting Using a Geometry-Based Variational Autoencoder. IEEE Trans. Pattern Anal. Mach. Intell. 45(3): 2879-2896 (2023) - 2022
- [j14]Elina Thibeau-Sutre, Mauricio Diaz-Melo, Ravi Hassanaly, Alexandre Routier, Didier Dormont, Olivier Colliot, Ninon Burgos:
ClinicaDL: An open-source deep learning software for reproducible neuroimaging processing. Comput. Methods Programs Biomed. 220: 106818 (2022) - [j13]Simona Bottani, Ninon Burgos, Aurélien Maire, Adam Wild, Sebastian Ströer, Didier Dormont, Olivier Colliot:
Automatic quality control of brain T1-weighted magnetic resonance images for a clinical data warehouse. Medical Image Anal. 75: 102219 (2022) - 2021
- [j12]Ninon Burgos, Simona Bottani, Johann Faouzi, Elina Thibeau-Sutre, Olivier Colliot:
Deep learning for brain disorders: from data processing to disease treatment. Briefings Bioinform. 22(2): 1560-1576 (2021) - [j11]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, Pascal Lu, Arnaud Marcoux, Tristan Moreau, Jorge Samper-González, Marc Teichmann, Elina Thibeau-Sutre, Ghislain Vaillant, Junhao Wen, Adam Wild, Marie Odile Habert, Stanley Durrleman, Olivier Colliot:
Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies. Frontiers Neuroinformatics 15: 689675 (2021) - [j10]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, Adam Wild, Ninon Burgos, Didier Dormont, Olivier Colliot, Stanley Durrleman:
Predicting the progression of mild cognitive impairment using machine learning: A systematic, quantitative and critical review. Medical Image Anal. 67: 101848 (2021) - [j9]Junhao Wen, Jorge Samper-González, Simona Bottani, Alexandre Routier, Ninon Burgos, Thomas Jacquemont, Sabrina Fontanella, Stanley Durrleman, Stéphane Epelbaum, Anne Bertrand, Olivier Colliot:
Reproducible Evaluation of Diffusion MRI Features for Automatic Classification of Patients with Alzheimer's Disease. Neuroinformatics 19(1): 57-78 (2021) - 2020
- [j8]Junhao Wen, Elina Thibeau-Sutre, Mauricio Diaz-Melo, Jorge Samper-González, Alexandre Routier, Simona Bottani, Didier Dormont, Stanley Durrleman, Ninon Burgos, Olivier Colliot:
Convolutional neural networks for classification of Alzheimer's disease: Overview and reproducible evaluation. Medical Image Anal. 63: 101694 (2020) - 2018
- [j7]Arnaud Marcoux, Ninon Burgos, Anne Bertrand, Marc Teichmann, Alexandre Routier, Junhao Wen, Jorge Samper-González, Simona Bottani, Stanley Durrleman, Marie Odile Habert, Olivier Colliot:
An Automated Pipeline for the Analysis of PET Data on the Cortical Surface. Frontiers Neuroinformatics 12: 94 (2018) - [j6]Jorge Samper-González, Ninon Burgos, Simona Bottani, Sabrina Fontanella, Pascal Lu, Arnaud Marcoux, Alexandre Routier, Jérémy Guillon, Michael Bacci, Junhao Wen, Anne Bertrand, Hugo Bertin, Marie Odile Habert, Stanley Durrleman, Theodoros Evgeniou, Olivier Colliot:
Reproducible evaluation of classification methods in Alzheimer's disease: Framework and application to MRI and PET data. NeuroImage 183: 504-521 (2018) - 2017
- [j5]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, Alexander Hammers, Didier Benoit, Søren Holm, Meher R. Juttukonda, Hongyu An, Jorge Cabello, Mathias Lukas, Stephan G. Nekolla, Sibylle Ziegler, Matthias Fenchel, Bjoern Jakoby, Michael E. Casey, Tammie L. S. Benzinger, Liselotte Højgaard, Adam Espe Hansen, Flemming Littrup Andersen:
A multi-centre evaluation of eleven clinically feasible brain PET/MRI attenuation correction techniques using a large cohort of patients. NeuroImage 147: 346-359 (2017) - [j4]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:
Direct Parametric Reconstruction With Joint Motion Estimation/Correction for Dynamic Brain PET Data. IEEE Trans. Medical Imaging 36(1): 203-213 (2017) - 2015
- [j3]Martin Kochan, Pankaj Daga, Ninon Burgos, Mark White, Manuel Jorge Cardoso, Laura Mancini, Gavin P. Winston, Andrew W. McEvoy, John S. Thornton, Tarek A. Yousry, John S. Duncan, Danail Stoyanov, Sébastien Ourselin:
Simulated field maps for susceptibility artefact correction in interventional MRI. Int. J. Comput. Assist. Radiol. Surg. 10(9): 1405-1416 (2015) - [j2]Maria A. Zuluaga, Ninon Burgos, Alex F. Mendelson, Andrew Mayall Taylor, Sébastien Ourselin:
Voxelwise atlas rating for computer assisted diagnosis: Application to congenital heart diseases of the great arteries. Medical Image Anal. 26(1): 185-194 (2015) - 2014
- [j1]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, Simon R. Arridge, Brian F. Hutton, Sébastien Ourselin:
Attenuation Correction Synthesis for Hybrid PET-MR Scanners: Application to Brain Studies. IEEE Trans. Medical Imaging 33(12): 2332-2341 (2014)
Conference and Workshop Papers
- 2024
- [c23]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, Michela Antonelli, Leon D. Mayer, Minu Dietlinde Tizabi, M. Jorge Cardoso, Amber L. Simpson, Paul F. Jäger, Annette Kopp-Schneider, Gaël Varoquaux, Olivier Colliot, Lena Maier-Hein:
Confidence Intervals Uncovered: Are We Ready for Real-World Medical Imaging AI? MICCAI (10) 2024: 124-132 - 2023
- [c22]Francesco Galati, Daniele Falcetta, Rosa Cortese, Barbara Casolla, Ferran Prados, Ninon Burgos, Maria A. Zuluaga:
A2V: A Semi-Supervised Domain Adaptation Framework for Brain Vessel Segmentation via Two-Phase Training Angiography-to-Venography Translation. BMVC 2023: 750-751 - [c21]Sophie Loizillon, Olivier Colliot, Lydia Chougar, Sebastian Ströer, Yannick Jacob, Aurélien Maire, Didier Dormont, Ninon Burgos:
Semi-supervised Domain Adaptation for Automatic Quality Control of FLAIR MRIs in a Clinical Data Warehouse. DART@MICCAI 2023: 84-93 - [c20]Ravi Hassanaly, Camille Brianceau, Olivier Colliot, Ninon Burgos:
Unsupervised Anomaly Detection in 3D Brain FDG PET: A Benchmark of 17 VAE-Based Approaches. DGM4MICCAI 2023: 110-120 - [c19]Ninon Burgos:
Exploiting hospital data warehouses: the challenges of image quality and heterogeneity (Conference Presentation). Medical Imaging: Image Processing 2023 - [c18]Ravi Hassanaly, Simona Bottani, Benoît Sauty, Olivier Colliot, Ninon Burgos:
Simulation based evaluation framework for deep learning unsupervised anomaly detection on brain FDG-PET. Medical Imaging: Image Processing 2023 - [c17]Sophie Loizillon, Simona Bottani, Aurélien Maire, Sebastian Ströer, Didier Dormont, Olivier Colliot, Ninon Burgos:
Transfer learning from synthetic to routine clinical data for motion artefact detection in brain T1-weighted MRI. Medical Imaging: Image Processing 2023 - [c16]Elina Thibeau-Sutre, Jelmer M. Wolterink, Olivier Colliot, Ninon Burgos:
How can data augmentation improve attribution maps for disease subtype explainability. Medical Imaging: Image Processing 2023 - 2022
- [c15]Elina Thibeau-Sutre, Baptiste Couvy-Duchesne, Didier Dormont, Olivier Colliot, Ninon Burgos:
MRI Field Strength Predicts Alzheimer's Disease: a Case Example of Bias in the ADNI Data Set. ISBI 2022: 1-4 - [c14]Simona Bottani, Elina Thibeau-Sutre, Aurélien Maire, Sebastian Ströer, Didier Dormont, Olivier Colliot, Ninon Burgos:
Homogenization of brain MRI from a clinical data warehouse using contrast-enhanced to non-contrast-enhanced image translation with U-Net derived models. Medical Imaging: Image Processing 2022 - 2020
- [c13]Elina Thibeau-Sutre, Olivier Colliot, Didier Dormont, Ninon Burgos:
Visualization approach to assess the robustness of neural networks for medical image classification. Medical Imaging: Image Processing 2020: 113131J - 2019
- [c12]Jorge Samper-González, Ninon Burgos, Simona Bottani, Marie Odile Habert, Theodoros Evgeniou, Stéphane Epelbaum, Olivier Colliot:
Reproducible evaluation of methods for predicting progression to Alzheimer's disease from clinical and neuroimaging data. Medical Imaging: Image Processing 2019: 109490V - 2017
- [c11]Ninon Burgos, Jorge Samper-González, Anne Bertrand, Marie Odile Habert, Sébastien Ourselin, Stanley Durrleman, M. Jorge Cardoso, Olivier Colliot:
Individual Analysis of Molecular Brain Imaging Data Through Automatic Identification of Abnormality Patterns. CMMI/RAMBO/SWITCH@MICCAI 2017: 13-22 - [c10]Jorge Samper-González, Ninon Burgos, Sabrina Fontanella, Hugo Bertin, Marie Odile Habert, Stanley Durrleman, Theodoros Evgeniou, Olivier Colliot:
Yet Another ADNI Machine Learning Paper? Paving the Way Towards Fully-Reproducible Research on Classification of Alzheimer's Disease. MLMI@MICCAI 2017: 53-60 - [c9]Catherine J. Scott, Jieqing Jiao, M. Jorge Cardoso, Andrew Melbourne, Enrico De Vita, David Thomas, Ninon Burgos, Pawel Markiewicz, Jonathan M. Schott, Brian F. Hutton, Sébastien Ourselin:
Short Acquisition Time PET Quantification Using MRI-Based Pharmacokinetic Parameter Synthesis. MICCAI (2) 2017: 737-744 - 2016
- [c8]Ninon Burgos, Filipa Guerreiro, Jamie McClelland, Simeon Nill, David Dearnaley, Nandita deSouza, Uwe Oelfke, Antje-Christin Knopf, Sébastien Ourselin, M. Jorge Cardoso:
Joint Segmentation and CT Synthesis for MRI-only Radiotherapy Treatment Planning. MICCAI (2) 2016: 547-555 - 2015
- [c7]Jieqing Jiao, Pawel Markiewicz, Ninon Burgos, David Atkinson, Brian F. Hutton, Simon R. Arridge, Sébastien Ourselin:
Detail-Preserving PET Reconstruction with Sparse Image Representation and Anatomical Priors. IPMI 2015: 540-551 - [c6]Maria A. Zuluaga, Ninon Burgos, Andrew Mayall Taylor, Sébastien Ourselin:
Multi-atlas synthesis for computer assisted diagnosis: Application to cardiovascular diseases. ISBI 2015: 290-293 - [c5]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:
Robust CT Synthesis for Radiotherapy Planning: Application to the Head and Neck Region. MICCAI (2) 2015: 476-484 - [c4]Ninon Burgos, Manuel Jorge Cardoso, Alex F. Mendelson, Jonathan M. Schott, David Atkinson, Simon R. Arridge, Brian F. Hutton, Sébastien Ourselin:
Subject-specific Models for the Analysis of Pathological FDG PET Data. MICCAI (2) 2015: 651-658 - 2014
- [c3]Martin Kochan, Pankaj Daga, Ninon Burgos, Mark White, Manuel Jorge Cardoso, Laura Mancini, Gavin Winston, Andrew W. McEvoy, John S. Thornton, Tarek A. Yousry, John S. Duncan, Danail Stoyanov, Sébastien Ourselin:
Simulated Field Maps: Toward Improved Susceptibility Artefact Correction in Interventional MRI. IPCAI 2014: 226-235 - [c2]Jieqing Jiao, Alexandre Bousse, Kris Thielemans, Pawel Markiewicz, Ninon Burgos, David Atkinson, Simon R. Arridge, Brian F. Hutton, Sébastien Ourselin:
Joint Parametric Reconstruction and Motion Correction Framework for Dynamic PET Data. MICCAI (1) 2014: 114-121 - 2013
- [c1]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:
Attenuation Correction Synthesis for Hybrid PET-MR Scanners. MICCAI (1) 2013: 147-154
Editorship
- 2021
- [e4]David Svoboda, Ninon Burgos, Jelmer M. Wolterink, Can Zhao:
Simulation and Synthesis in Medical Imaging - 6th International Workshop, SASHIMI 2021, Held in Conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Lecture Notes in Computer Science 12965, Springer 2021, ISBN 978-3-030-87591-6 [contents] - 2020
- [e3]Ninon Burgos, David Svoboda, Jelmer M. Wolterink, Can Zhao:
Simulation and Synthesis in Medical Imaging - 5th International Workshop, SASHIMI 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 4, 2020, Proceedings. Lecture Notes in Computer Science 12417, Springer 2020, ISBN 978-3-030-59519-7 [contents] - 2019
- [e2]Ninon Burgos, Ali Gooya, David Svoboda:
Simulation and Synthesis in Medical Imaging - 4th International Workshop, SASHIMI 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 13, 2019, Proceedings. Lecture Notes in Computer Science 11827, Springer 2019, ISBN 978-3-030-32777-4 [contents] - 2018
- [e1]Ali Gooya, Orcun Goksel, Ipek Oguz, Ninon Burgos:
Simulation and Synthesis in Medical Imaging - Third International Workshop, SASHIMI 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 16, 2018, Proceedings. Lecture Notes in Computer Science 11037, Springer 2018, ISBN 978-3-030-00535-1 [contents]
Informal and Other Publications
- 2024
- [i15]Ravi Hassanaly, Camille Brianceau, Maëlys Solal, Olivier Colliot, Ninon Burgos:
Evaluation of pseudo-healthy image reconstruction for anomaly detection with deep generative models: Application to brain FDG PET. CoRR abs/2401.16363 (2024) - [i14]Sophie Loizillon, Simona Bottani, Stéphane Mabille, Yannick Jacob, Aurélien Maire, Sebastian Ströer, Didier Dormont, Olivier Colliot, Ninon Burgos:
Automated MRI Quality Assessment of Brain T1-weighted MRI in Clinical Data Warehouses: A Transfer Learning Approach Relying on Artefact Simulation. CoRR abs/2406.12448 (2024) - 2023
- [i13]Guanghui Fu, Gabriel Jimenez, Sophie Loizillon, Lydia Chougar, Didier Dormont, Romain Valabrègue, Ninon Burgos, Stéphane Lehéricy, Daniel Racoceanu, Olivier Colliot:
Frequency Disentangled Learning for Segmentation of Midbrain Structures from Quantitative Susceptibility Mapping Data. CoRR abs/2302.12980 (2023) - [i12]Francesco Galati, Daniele Falcetta, Rosa Cortese, Barbara Casolla, Ferran Prados, Ninon Burgos, Maria A. Zuluaga:
A2V: A Semi-Supervised Domain Adaptation Framework for Brain Vessel Segmentation via Two-Phase Training Angiography-to-Venography Translation. CoRR abs/2309.06075 (2023) - [i11]Maëlys Solal, Ravi Hassanaly, Ninon Burgos:
Leveraging healthy population variability in deep learning unsupervised anomaly detection in brain FDG PET. CoRR abs/2311.12081 (2023) - 2022
- [i10]Elina Thibeau-Sutre, Sasha Collin, Ninon Burgos, Olivier Colliot:
Interpretability of Machine Learning Methods Applied to Neuroimaging. CoRR abs/2204.07005 (2022) - [i9]Olivier Colliot, Elina Thibeau-Sutre, Ninon Burgos:
Reproducibility in machine learning for medical imaging. CoRR abs/2209.05097 (2022) - [i8]Guanghui Fu, Gabriel Jimenez, Sophie Loizillon, Rosana El Jurdi, Lydia Chougar, Didier Dormont, Romain Valabrègue, Ninon Burgos, Stéphane Lehéricy, Daniel Racoceanu, Olivier Colliot:
Fourier Disentangled Multimodal Prior Knowledge Fusion for Red Nucleus Segmentation in Brain MRI. CoRR abs/2211.01353 (2022) - 2021
- [i7]Simona Bottani, Ninon Burgos, Aurélien Maire, Adam Wild, Sebastian Ströer, Didier Dormont, Olivier Colliot:
Automatic quality control of brain T1-weighted magnetic resonance images for a clinical data warehouse. CoRR abs/2104.08131 (2021) - [i6]Clément Chadebec, Elina Thibeau-Sutre, Ninon Burgos, Stéphanie Allassonnière:
Data Augmentation in High Dimensional Low Sample Size Setting Using a Geometry-Based Variational Autoencoder. CoRR abs/2105.00026 (2021) - 2019
- [i5]Junhao Wen, Elina Thibeau-Sutre, Jorge Samper-González, Alexandre Routier, Simona Bottani, Stanley Durrleman, Ninon Burgos, Olivier Colliot:
Convolutional Neural Networks for Classification of Alzheimer's Disease: Overview and Reproducible Evaluation. CoRR abs/1904.07773 (2019) - [i4]Elina Thibeau-Sutre, Olivier Colliot, Didier Dormont, Ninon Burgos:
Visualization approach to assess the robustness of neural networks for medical image classification. CoRR abs/1911.08264 (2019) - 2018
- [i3]Jorge Samper-González, Ninon Burgos, Simona Bottani, Sabrina Fontanella, Pascal Lu, Arnaud Marcoux, Alexandre Routier, Jérémy Guillon, Michael Bacci, Junhao Wen, Anne Bertrand, Hugo Bertin, Marie Odile Habert, Stanley Durrleman, Theodoros Evgeniou, Olivier Colliot, Alzheimer's Disease Neuroimaging Initiative:
Reproducible evaluation of classification methods in Alzheimer's disease: framework and application to MRI and PET data. CoRR abs/1808.06452 (2018) - [i2]Junhao Wen, Jorge Samper-González, Simona Bottani, Alexandre Routier, Ninon Burgos, Thomas Jacquemont, Sabrina Fontanella, Stanley Durrleman, Stéphane Epelbaum, Anne Bertrand, Olivier Colliot:
Reproducible evaluation of diffusion MRI features for automatic classification of patients with Alzheimers disease. CoRR abs/1812.11183 (2018) - 2017
- [i1]Jorge Samper-González, Ninon Burgos, Sabrina Fontanella, Hugo Bertin, Marie Odile Habert, Stanley Durrleman, Theodoros Evgeniou, Olivier Colliot:
Yet Another ADNI Machine Learning Paper? Paving The Way Towards Fully-reproducible Research on Classification of Alzheimer's Disease. CoRR abs/1709.07267 (2017)
Coauthor Index
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