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Ninon Burgos

56
Documents
Identifiants chercheurs

Présentation

[Ninon Burgos](https://ninonburgos.com/) is a CNRS researcher at the [Paris Brain Institute](http://icm-institute.org/) in the [ARAMIS Lab](http://www.aramislab.fr/). She completed her PhD at University College London in the [Centre for Medical Image Computing](http://www.ucl.ac.uk/medical-image-computing). She received an MSc in Biomedical Engineering from Imperial College London and an Engineering degree from a French Graduate School in Electrical Engineering and Computer Science (ENSEA). Her research currently focuses on the development of computational imaging tools to improve the understanding and diagnosis of neurological diseases.

Publications

"olivier-colliot"
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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
Journal of Machine Learning for Biomedical Imaging, 2024, Special Issue for Generative Models, 2, pp.611. ⟨10.59275/j.melba.2024-b87a⟩
Article dans une revue hal-04315738v2
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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
Medical Image Analysis, 2024, 93, pp.103073. ⟨10.1016/j.media.2023.103073⟩
Article dans une revue hal-03910451v2
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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
BMC Medical Imaging, 2024, 24 (1), pp.67. ⟨10.1186/s12880-024-01242-3⟩
Article dans une revue hal-03497645v2
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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 Stroer
Medical Image Analysis, 2023, 89, pp.102903
Article dans une revue hal-03656136v2
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Automatic quality control of brain T1-weighted magnetic resonance images for a clinical data warehouse

Simona Bottani , Ninon Burgos , Aurélien Maire , Adam Wild , Sébastian Ströer
Medical Image Analysis, 2022, 75, ⟨10.1016/j.media.2021.102219⟩
Article dans une revue hal-03154792v4
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ClinicaDL: an open-source deep learning software for reproducible neuroimaging processing

Elina Thibeau-Sutre , Mauricio Diaz , Ravi Hassanaly , Alexandre M Routier , Didier Dormont
Computer Methods and Programs in Biomedicine, 2022, 220, pp.106818. ⟨10.1016/j.cmpb.2022.106818⟩
Article dans une revue hal-03351976v2
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Reproducible evaluation of diffusion MRI features for automatic classification of patients with Alzheimer's disease

Junhao Wen , Jorge Samper-González , Simona Bottani , Alexandre Routier , Ninon Burgos
Neuroinformatics, 2021, 19 (1), pp.57-78. ⟨10.1007/s12021-020-09469-5⟩
Article dans une revue hal-02566361v2
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Anomaly detection for the individual analysis of brain PET images

Ninon Burgos , Jorge M. Cardoso , Jorge Samper-González , Marie-Odile Habert , Stanley Durrleman​
Journal of Medical Imaging, 2021, 8 (02), pp.024003. ⟨10.1117/1.JMI.8.2.024003⟩
Article dans une revue hal-03193306v1
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Deep learning for brain disorders: from data processing to disease treatment

Ninon Burgos , Simona Bottani , Johann Faouzi , Elina Thibeau-Sutre , Olivier Colliot
Briefings in Bioinformatics, 2021, 22 (2), pp.1560-1576. ⟨10.1093/bib/bbaa310⟩
Article dans une revue hal-03070554v1
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Clinica: an open source software platform for reproducible clinical neuroscience studies

Alexandre Routier , Ninon Burgos , Mauricio Diaz , Michael Bacci , Simona Bottani
Frontiers in Neuroinformatics, 2021, 15, pp.689675. ⟨10.3389/fninf.2021.689675⟩
Article dans une revue hal-02308126v4
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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
Medical Image Analysis, 2021, 67, pp.101848. ⟨10.1016/j.media.2020.101848⟩
Article dans une revue hal-02337815v2
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AD Course Map charts Alzheimer’s disease progression

Igor Koval , Alexandre Bône , Maxime Louis , Thomas Lartigue , Simona Bottani
Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-87434-1⟩
Article dans une revue hal-01964821v3
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Machine learning for classification and prediction of brain diseases: recent advances and upcoming challenges

Ninon Burgos , Olivier Colliot
Current Opinion in Neurology, 2020, 33 (4), pp.439-450. ⟨10.1097/WCO.0000000000000838⟩
Article dans une revue hal-02902586v1
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Convolutional Neural Networks for Classification of Alzheimer's Disease: Overview and Reproducible Evaluation

Junhao Wen , Elina Thibeau-Sutre , Mauricio Diaz-Melo , Jorge Samper-González , Alexandre Routier
Medical Image Analysis, 2020, 63, pp.101694. ⟨10.1016/j.media.2020.101694⟩
Article dans une revue hal-02562504v2
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Ensemble Learning of Convolutional Neural Network, Support Vector Machine, and Best Linear Unbiased Predictor for Brain Age Prediction: ARAMIS Contribution to the Predictive Analytics Competition 2019 Challenge

Baptiste Couvy-Duchesne , Johann Faouzi , Benoît Martin , Elina Thibeau-Sutre , Adam Wild
Frontiers in Psychiatry, 2020, 11, ⟨10.3389/fpsyt.2020.593336⟩
Article dans une revue hal-03136463v1
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Tribute to Anne Bertrand (1978–2018): Neuroradiologist, scientist, teacher and friend

Didier Dormont , Noam Ben-Eliezer , Ninon Burgos , Olivier Colliot , Fabrizio de Vico Fallani
Journal de Neuroradiologie / Journal of Neuroradiology, 2019, 46 (2), pp.155-159. ⟨10.1016/j.neurad.2019.01.001⟩
Article dans une revue hal-02265305v1
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An Automated Pipeline for the Analysis of PET Data on the Cortical Surface

Arnaud Marcoux , Ninon Burgos , Anne Bertrand , Marc Teichmann , Alexandre Routier
Frontiers in Neuroinformatics, 2018, 12, ⟨10.3389/fninf.2018.00094⟩
Article dans une revue hal-01950933v1
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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
NeuroImage, 2018, 183, pp.504-521. ⟨10.1016/j.neuroimage.2018.08.042⟩
Article dans une revue hal-01858384v2
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Recent advances in the open-source ClinicaDL software for reproducible neuroimaging with deep learning

Ravi Hassanaly , Camille Brianceau , Mauricio Diaz , Sophie Loizillon , Elina Thibeau-Sutre
SPIE Medical Imaging, Feb 2024, San Diego, United States
Communication dans un congrès hal-04419141v1
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Generating PET-derived maps of myelin content from clinical MRI using curricular discriminator training in generative adversarial networks

Théodore Soulier , Mariem Hamzaoui , Milena Sales Pitombeira , Daniele De Paula Faria , Arya Yazdan-Panah
SPIE Medical Imaging, Feb 2024, San Diego, United States
Communication dans un congrès hal-04362506v1
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Semi-supervised Domain Adaptation for Automatic Quality Control of FLAIR MRIs in a Clinical Data Warehouse

Sophie Loizillon , Olivier Colliot , Lydia Chougar , Sebastian Stroer , Yannick Jacob
DART 2023 - 5th MICCAI Workshop on Domain Adaptation and Representation Transfer, Oct 2023, Vancouver (BC), Canada. pp.84-93, ⟨10.1007/978-3-031-45857-6_9⟩
Communication dans un congrès hal-04273997v1
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Unsupervised anomaly detection in 3D brain FDG PET: A benchmark of 17 VAE-based approaches

Ravi Hassanaly , Camille Brianceau , Olivier Colliot , Ninon Burgos
Deep Generative Models workshop at the 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023), Oct 2023, Vancouver, Canada
Communication dans un congrès hal-04185304v1
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From Nipype to Pydra: a Clinica story

Ghislain Vaillant , Nicolas Gensollen , Matthieu Joulot , Omar El-Rifai , Mauricio Diaz
OHBM 2023 - Annual meeting of the Organization for Human Brain Mapping, Jul 2023, Montreal, Canada
Communication dans un congrès hal-04278898v1
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How can data augmentation improve attribution maps for disease subtype explainability?

Elina Thibeau-Sutre , Jelmer M Wolterink , Olivier Colliot , Ninon Burgos
SPIE Medical Imaging, Feb 2023, San Diego, United States
Communication dans un congrès hal-03966737v1
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Simulation-based evaluation framework for deep learning unsupervised anomaly detection on brain FDG PET

Ravi Hassanaly , Simona Bottani , Benoît Sauty , Olivier Colliot , Ninon Burgos
SPIE Medical Imaging, Feb 2023, San Diego, United States
Communication dans un congrès hal-03835015v2
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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
SPIE Medical Imaging 2022: Image Processing, Feb 2022, San Diego, United States. pp.576-582, ⟨10.1117/12.2608565⟩
Communication dans un congrès hal-03478798v1
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ClinicaDL: an open-source deep learning software for reproducible neuroimaging processing

Elina Thibeau-Sutre , Mauricio Diaz , Ravi Hassanaly , Olivier Colliot , Ninon Burgos
OHBM 2022 - Annual meeting of the Organization for Human Brain Mapping, Jun 2022, Glasgow, United Kingdom
Communication dans un congrès hal-04279014v1
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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 - International Symposium on Biomedical Imaging, Mar 2022, Kolkata, India. ⟨10.1109/ISBI52829.2022.9761504⟩
Communication dans un congrès hal-03542213v1
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Advances in the Clinica software platform for clinical neuroimaging studies

Omar El Rifai , Mauricio Diaz Melo , Ravi Hassanaly , Matthieu Joulot , Alexandre M Routier
OHBM 2022 - Annual meeting of the Organization for Human Brain Mapping, Jun 2022, Glasgow, United Kingdom
Communication dans un congrès hal-03728243v1
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Clinica: an open-source software platform for reproducible clinical neuroscience studies

Omar El-Rifai , Mauricio Diaz Melo , Ravi Hassanaly , Matthieu Joulot , Alexandre M Routier
MRI Together 2021 - A global workshop on Open Science and Reproducible MR Research, Dec 2021, Online, France
Communication dans un congrès hal-03513920v1
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New longitudinal and deep learning pipelines in the Clinica software platform

Alexandre Routier , Arnaud Marcoux , Mauricio Diaz Melo , Jorge Samper-González , Adam Wild
OHBM 2020 - Annual meeting of the Organization for Human Brain Mapping, Jun 2020, Montreal / Virtual, Canada
Communication dans un congrès hal-02549242v1
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Visualization approach to assess the robustness of neural networks for medical image classification

Elina Thibeau-Sutre , Olivier Colliot , Didier Dormont , Ninon Burgos
SPIE Medical Imaging 2020, Feb 2020, Houston, United States. ⟨10.1117/12.2548952⟩
Communication dans un congrès hal-02370532v3
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Deciphering the progression of PET alterations using surface-based spatiotemporal modeling

Igor Koval , Arnaud Marcoux , Ninon Burgos , Stéphanie Allassonnière , Olivier Colliot
OHBM 2019 - Annual meeting of the Organization for Human Brain Mapping, Jun 2019, Rome, Italy
Communication dans un congrès hal-02134909v1
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Beware of feature selection bias! Example on Alzheimer's disease classification from diffusion MRI

Junhao Wen​ , Jorge Samper-González​ , Alexandre M Routier , Simona Bottani​ , Stanley Durrleman​
2019 OHBM Annual Meeting - Organization for Human Brain Mapping, Jun 2019, Rome, Italy
Communication dans un congrès hal-02105134v2
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Reproducible evaluation of methods for predicting progression to Alzheimer's disease from clinical and neuroimaging data

Jorge Samper-Gonzalez , Ninon Burgos , Simona Bottani , Marie-Odile Habert , Theodoros Evgeniou
SPIE Medical Imaging 2019, Feb 2019, San Diego, United States. ⟨10.1117/12.2512430⟩
Communication dans un congrès hal-02025880v2
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Prediction of future cognitive scores and dementia onset in Mild Cognitive Impairment patients

Manon Ansart , Ninon Burgos , Olivier Colliot , Didier Dormont , Stanley Durrleman
OHBM 2019 - Organization for Human Brain Mapping Conference, Jun 2019, Rome, Italy
Communication dans un congrès hal-02098427v2
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Predicting progression to Alzheimer’s disease from clinical and imaging data: a reproducible study

Jorge Samper-Gonzalez , Ninon Burgos , Simona Bottani , Marie-Odile Habert , Theodoros Evgeniou
OHBM 2019 - Organization for Human Brain Mapping Annual Meeting 2019, Jun 2019, Rome, Italy
Communication dans un congrès hal-02142315v1
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New advances in the Clinica software platform for clinical neuroimaging studies

Alexandre Routier , Arnaud Marcoux , Mauricio Diaz Melo , Jérémy Guillon , Jorge Samper-González
OHBM 2019 - Annual Meeting on Organization for Human Brain Mapping, Jun 2019, Roma, Italy. ⟨10.1016/j.neuroimage.2011.09.015⟩
Communication dans un congrès hal-02132147v2
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How serious is data leakage in deep learning studies on Alzheimer's disease classification?

Junhao Wen​ , Elina Thibeau--Sutre​ , Jorge Samper-González​ , Alexandre M Routier , Simona Bottani​
2019 OHBM Annual meeting - Organization for Human Brain Mapping, Jun 2019, Rome, Italy
Communication dans un congrès hal-02105133v2
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Clinica: an open source software platform for reproducible clinical neuroscience studies

Alexandre Routier , Jérémy Guillon , Ninon Burgos , Jorge Samper-Gonzalez , Junhao Wen
Annual meeting of the Organization for Human Brain Mapping - OHBM 2018, Jun 2018, Singapore, Singapore
Communication dans un congrès hal-01760658v1
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A pipeline for the analysis of 18F-FDG PET data on the cortical surface and its evaluation on ADNI

Arnaud Marcoux , Ninon Burgos , Anne Bertrand , Alexandre Routier , Junhao Wen
Annual meeting of the Organization for Human Brain Mapping - OHBM 2018, Jun 2018, Singapour, Singapore
Communication dans un congrès hal-01757646v1
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Using diffusion MRI for classification and prediction of Alzheimer's Disease: a reproducible study

Junhao Wen , Jorge Samper-Gonzalez , Simona Bottani , Alexandre Routier , Ninon Burgos
AAIC 2018 - Alzheimer's Association International Conference, Jul 2018, Chicago, United States
Communication dans un congrès hal-01758167v2
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Reproducible evaluation of Alzheimer's Disease classification from MRI and PET data

Jorge Samper-Gonzalez , Simona Bottani , Ninon Burgos , Sabrina Fontanella , Pascal Lu
Annual meeting of the Organization for Human Brain Mapping - OHBM 2018, Jun 2018, Singapour, Singapore
Communication dans un congrès hal-01761666v1
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Comparison of DTI Features for the Classification of Alzheimer's Disease: A Reproducible Study

Junhao Wen , Jorge Samper-Gonzalez , Simona Bottani , Alexandre Routier , Ninon Burgos
OHBM 2018 - Organization for Human Brain Mapping Annual Meeting, Jun 2018, Singapour, Singapore
Communication dans un congrès hal-01758206v3
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Three simple ideas for predicting progression to Alzheimer's disease

Jorge Samper-Gonzalez , Ninon Burgos , Simona Bottani , Marie-Odile Habert , Theodoros Evgeniou
8th International Workshop on Pattern Recognition in Neuroimaging, Jun 2018, Singapour, Singapore
Communication dans un congrès hal-01891996v1
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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
Computational Methods for Molecular Imaging - [MICCAI 2017 Satellite Workshop], Sep 2017, Quebec City, Canada
Communication dans un congrès hal-01567343v1
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Diagnosis of Alzheimer’s Disease Through Identification of Abnormality Patterns in FDG PET Data

Ninon Burgos , Jorge Samper-González , Anne Bertrand , Marie-Odile Habert , Sébastien Ourselin
30th Annual Congress of the European Association of Nuclear Medicine (EANM), Oct 2017, Vienna, Austria. pp.253 - 254, ⟨10.1007/s00259-017-3822-1⟩
Communication dans un congrès hal-01632509v1
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Yet Another ADNI Machine Learning Paper? Paving The Way Towards Fully-reproducible Research on Classification of Alzheimer's Disease

Jorge Samper-Gonzalez , Ninon Burgos , Sabrina Fontanella , Hugo Bertin , Marie-Odile Habert
Machine Learning in Medical Imaging 2017, Sep 2017, Quebec City, Canada. pp.8
Communication dans un congrès hal-01578479v1
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Early Diagnosis of Alzheimer’s Disease Using Subject-Specific Models of FDG-PET Data

Ninon Burgos , Jorge Samper-González , Jorge M. Cardoso , Stanley Durrleman , Sébastien Ourselin
AAIC 2017 - Alzheimer's Association International Conference, Jul 2017, London, United Kingdom. pp.1-2, ⟨10.1016/j.jalz.2017.06.1618⟩
Communication dans un congrès hal-01621383v1