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Olivier Colliot

Olivier Colliot - Research Director at CNRS - ARAMIS Lab at the Paris Brain Institute (CNRS/Inria/Inserm/Sorbonne Universite)
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Présentation

Research Director at [CNRS](http://www.cnrs.fr/) Head of the [ARAMIS Lab](http://www.aramislab.fr/), a joint team between [CNRS](http://www.cnrs.fr/), [Inria](http://www.inria.fr/), [Inserm](http://www.inserm.fr/) and [University Pierre and Marie Curie](http://www.upmc.fr/) at the [Paris Brain Institute (ICM)](http://www.icm-institute.org/), in co-direction with Stanley Durrleman. Homepage: <https://www.aramislab.fr/perso/colliot/> Email: olivier.colliot@cnrs.fr
Research Director at [CNRS](http://www.cnrs.fr/) Head of the [ARAMIS Lab](http://www.aramislab.fr/), a joint team between [CNRS](http://www.cnrs.fr/), [Inria](http://www.inria.fr/), [Inserm](http://www.inserm.fr/) and [University Pierre and Marie Curie](http://www.upmc.fr/) at the [Paris Brain Institute (ICM)](http://www.icm-institute.org/), in co-direction with Stanley Durrleman. Homepage: <https://www.aramislab.fr/perso/colliot/> Email: olivier.colliot@cnrs.fr

Domaines de recherche

Intelligence artificielle [cs.AI] Imagerie médicale Apprentissage [cs.LG] Traitement des images [eess.IV]

Publications

"ninon-burgos"
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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