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Data-driven models for Progression Of Neurological Disease

Deliverables

Paper: data-driven subtype analysis

Providing fundamental new knowledge on dementia subtypes.

Paper: simulation framework

Dissemination of our framework.

Website and Mailing List

Communication (internal and external) of results, and for online meetings.

Paper: basic models of ageing

Getting a reference point (normal ageing) for sporadic neurological diseases.

Paper: basic models of prion disease

Multimodal models of changes in prion disease.

Paper: basic models of dementia

Developing disease understanding.

Paper: unified modelling framework

Dissemination of our unified modelling framework.

Paper: Bayesian spatio-temporal models

A new formulation of these models.

Paper: network propagation models

How such models fit into the framework.

Paper: enhanced models

Advancing models for features and robustness.

Paper: refined EBM

Update to the event-based model of disease progression.

Paper: basic MS models

Multimodal models of changes in MS.

Open source software tool

This will have primary Impact within the research community, but will be developed with clinical usage in mind.

Paper: Bayesian scalar trajectory models

A new formulation of these models.

Publications

Longitudinal study of neonatal brain tissue volumes in preterm infants and their ability to predict neurodevelopmental outcome

Author(s): L. Gui, S. Loukas, F. Lazeyras, P.S. Hüppi, D.E. Meskaldji, C. Borradori Tolsa
Published in: NeuroImage, Issue 185, 2019, Page(s) 728-741, ISSN 1053-8119
DOI: 10.1016/j.neuroimage.2018.06.034

A spatio-temporal reference model of the aging brain

Author(s): W. Huizinga, D.H.J. Poot, M.W. Vernooij, G.V. Roshchupkin, E.E. Bron, M.A. Ikram, D. Rueckert, W.J. Niessen, S. Klein
Published in: NeuroImage, Issue 169, 2018, Page(s) 11-22, ISSN 1053-8119
DOI: 10.1016/j.neuroimage.2017.10.040

Trajectories of imaging markers in brain aging: the Rotterdam Study

Author(s): Elisabeth J. Vinke, Marius de Groot, Vikram Venkatraghavan, Stefan Klein, Wiro J. Niessen, M. Arfan Ikram, Meike W. Vernooij
Published in: Neurobiology of Aging, Issue 71, 2018, Page(s) 32-40, ISSN 0197-4580
DOI: 10.1016/j.neurobiolaging.2018.07.001

Spatiotemporal Propagation of the Cortical Atrophy: Population and Individual Patterns

Author(s): Igor Koval, Jean-Baptiste Schiratti, Alexandre Routier, Michael Bacci, Olivier Colliot, Stéphanie Allassonnière, Stanley Durrleman
Published in: Frontiers in Neurology, Issue 9, 2018, ISSN 1664-2295
DOI: 10.3389/fneur.2018.00235

Progression of regional grey matter atrophy in multiple sclerosis

Author(s): Arman Eshaghi, Razvan V Marinescu, Alexandra L Young, Nicholas C Firth, Ferran Prados, M Jorge Cardoso, Carmen Tur, Floriana De Angelis, Niamh Cawley, Wallace J Brownlee, Nicola De Stefano, M Laura Stromillo, Marco Battaglini, Serena Ruggieri, Claudio Gasperini, Massimo Filippi, Maria A Rocca, Alex Rovira, Jaume Sastre-Garriga, Jeroen J G Geurts, Hugo Vrenken, Viktor Wottschel, Cyra E Leurs, Berna
Published in: Brain, Issue 141/6, 2018, Page(s) 1665-1677, ISSN 0006-8950
DOI: 10.1093/brain/awy088

Early Cognitive, Structural, and Microstructural Changes in Presymptomatic C9orf72 Carriers Younger Than 40 Years

Author(s): Anne Bertrand, Junhao Wen, Daisy Rinaldi, Marion Houot, Sabrina Sayah, Agnès Camuzat, Clémence Fournier, Sabrina Fontanella, Alexandre Routier, Philippe Couratier, Florence Pasquier, Marie-Odile Habert, Didier Hannequin, Olivier Martinaud, Paola Caroppo, Richard Levy, Bruno Dubois, Alexis Brice, Stanley Durrleman, Olivier Colliot, Isabelle Le Ber
Published in: JAMA Neurology, Issue 75/2, 2018, Page(s) 236, ISSN 2168-6149
DOI: 10.1001/jamaneurol.2017.4266

Disease progression timeline estimation for Alzheimer's disease using discriminative event based modeling

Author(s): Vikram Venkatraghavan, Esther E. Bron, Wiro J. Niessen, Stefan Klein
Published in: NeuroImage, Issue 186, 2019, Page(s) 518-532, ISSN 1053-8119
DOI: 10.1016/j.neuroimage.2018.11.024

Data-driven models of dominantly-inherited Alzheimer’s disease progression

Author(s): Neil P Oxtoby, Alexandra L Young, David M Cash, Tammie L S Benzinger, Anne M Fagan, John C Morris, Randall J Bateman, Nick C Fox, Jonathan M Schott, Daniel C Alexander
Published in: Brain, Issue 141/5, 2018, Page(s) 1529-1544, ISSN 0006-8950
DOI: 10.1093/brain/awy050

Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference

Author(s): Alexandra L Young, Razvan V Marinescu, Neil P Oxtoby, Martina Bocchetta, Keir Yong, Nicholas C Firth, David M Cash, David L Thomas, Katrina M Dick, Jorge Cardoso, John van Swieten, Barbara Borroni, Daniela Galimberti, Mario Masellis, Maria Carmela Tartaglia, James B Rowe, Caroline Graff, Fabrizio Tagliavini, Giovanni B Frisoni, Robert Laforce, Elizabeth Finger, Alexandre de Mendonça, Sandro Sorbi
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-05892-0

Probabilistic disease progression modeling to characterize diagnostic uncertainty: Application to staging and prediction in Alzheimer's disease

Author(s): Marco Lorenzi, Maurizio Filippone, Giovanni B. Frisoni, Daniel C. Alexander, Sebastien Ourselin
Published in: NeuroImage, Issue 190, 2019, Page(s) 56-68, ISSN 1053-8119
DOI: 10.1016/j.neuroimage.2017.08.059

Data-Driven Sequence of Changes to Anatomical Brain Connectivity in Sporadic Alzheimer’s Disease

Author(s): Neil P. Oxtoby, Sara Garbarino, Nicholas C. Firth, Jason D. Warren, Jonathan M. Schott, Daniel C. Alexander
Published in: Frontiers in Neurology, Issue 8, 2017, ISSN 1664-2295
DOI: 10.3389/fneur.2017.00580

Reproducible evaluation of classification methods in Alzheimer's disease: Framework and application to MRI and PET data

Author(s): 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
Published in: NeuroImage, Issue 183, 2018, Page(s) 504-521, ISSN 1053-8119
DOI: 10.1016/j.neuroimage.2018.08.042

DIVE: A spatiotemporal progression model of brain pathology in neurodegenerative disorders

Author(s): Răzvan V. Marinescu, Arman Eshaghi, Marco Lorenzi, Alexandra L. Young, Neil P. Oxtoby, Sara Garbarino, Sebastian J. Crutch, Daniel C. Alexander
Published in: NeuroImage, Issue 192, 2019, Page(s) 166-177, ISSN 1053-8119
DOI: 10.1016/j.neuroimage.2019.02.053

Automatic normative quantification of brain tissue volume to support the diagnosis of dementia: A clinical evaluation of diagnostic accuracy

Author(s): Meike W. Vernooij, Bas Jasperse, Rebecca Steketee, Marcel Koek, Henri Vrooman, M. Arfan Ikram, Janne Papma, Aad van der Lugt, Marion Smits, Wiro J. Niessen
Published in: NeuroImage: Clinical, Issue 20, 2018, Page(s) 374-379, ISSN 2213-1582
DOI: 10.1016/j.nicl.2018.08.004

Predicting Global Cognitive Decline in the General Population Using the Disease State Index

Author(s): Lotte G. M. Cremers, Wyke Huizinga, Wiro J. Niessen, Gabriel P. Krestin, Dirk H. J. Poot, M. Arfan Ikram, Jyrki Lötjönen, Stefan Klein, Meike W. Vernooij
Published in: Frontiers in Aging Neuroscience, Issue 11, 2020, ISSN 1663-4365
DOI: 10.3389/fnagi.2019.00379

Multi-study validation of data-driven disease progression models to characterize evolution of biomarkers in Alzheimer's disease

Author(s): Damiano Archetti, Silvia Ingala, Vikram Venkatraghavan, Viktor Wottschel, Alexandra L. Young, Maura Bellio, Esther E. Bron, Stefan Klein, Frederik Barkhof, Daniel C. Alexander, Neil P. Oxtoby, Giovanni B. Frisoni, Alberto Redolfi
Published in: NeuroImage: Clinical, Issue 24, 2019, Page(s) 101954, ISSN 2213-1582
DOI: 10.1016/j.nicl.2019.101954

Differences in topological progression profile among neurodegenerative diseases from imaging data

Author(s): Sara Garbarino, Marco Lorenzi, Neil P Oxtoby, Elisabeth J Vinke, Razvan V Marinescu, Arman Eshaghi, M Arfan Ikram, Wiro J Niessen, Olga Ciccarelli, Frederik Barkhof, Jonathan M Schott, Meike W Vernooij, Daniel C Alexander
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
DOI: 10.7554/elife.49298

Normative brain volumetry derived from different reference populations: impact on single-subject diagnostic assessment in dementia

Author(s): Elisabeth J. Vinke, Wyke Huizinga, Martin Bergtholdt, Hieab H. Adams, Rebecca M.E. Steketee, Janne M. Papma, Frank J. de Jong, Wiro J. Niessen, M. Arfan Ikram, Fabian Wenzel, Meike W. Vernooij
Published in: Neurobiology of Aging, Issue 84, 2019, Page(s) 9-16, ISSN 0197-4580
DOI: 10.1016/j.neurobiolaging.2019.07.008

SVM recursive feature elimination analyses of structural brain MRI predicts near-term relapses in patients with clinically isolated syndromes suggestive of multiple sclerosis

Author(s): Viktor Wottschel, Declan T. Chard, Christian Enzinger, Massimo Filippi, Jette L. Frederiksen, Claudio Gasperini, Antonio Giorgio, Maria A. Rocca, Alex Rovira, Nicola De Stefano, Mar Tintoré, Daniel C. Alexander, Frederik Barkhof, Olga Ciccarelli
Published in: NeuroImage: Clinical, Issue 24, 2019, Page(s) 102011, ISSN 2213-1582
DOI: 10.1016/j.nicl.2019.102011

Music in premature infants enhances high-level cognitive brain networks

Author(s): Lara Lordier, Djalel-Eddine Meskaldji, Frédéric Grouiller, Marie P. Pittet, Andreas Vollenweider, Lana Vasung, Cristina Borradori-Tolsa, François Lazeyras, Didier Grandjean, Dimitri Van De Ville, Petra S. Hüppi
Published in: Proceedings of the National Academy of Sciences, 2019, Page(s) 201817536, ISSN 0027-8424
DOI: 10.1073/pnas.1817536116

Spatio-Temporal Shape Analysis of Cross-Sectional Data for Detection of Early Changes in Neurodegenerative Disease

Author(s): Claire Cury, Marco Lorenzi, David Cash, Jennifer M. Nicholas, Alexandre Routier, Jonathan Rohrer, Sebastien Ourselin, Stanley Durrleman, Marc Modat
Published in: Springer, 2016, Page(s) 63-75, ISSN 0018-1560
DOI: 10.1007/978-3-319-51237-2_6

Imaging plus X


Published in: ISSN 1350-7540
DOI: 10.1097/WCO.0000000000000460

Statistical Learning of Spatiotemporal Patterns from Longitudinal Manifold-Valued Networks

Author(s): I. Koval, J.-B. Schiratti, A. Routier, M. Bacci, O. Colliot, S. Allassonnière, S. Durrleman
Published in: Medical Image Computing and Computer Assisted Intervention − MICCAI 2017, Issue 10433, 2017, Page(s) 451-459
DOI: 10.1007/978-3-319-66182-7_52

Deformetrica 4: An Open-Source Software for Statistical Shape Analysis

Author(s): Alexandre Bône, Maxime Louis, Benoît Martin, Stanley Durrleman
Published in: Shape in Medical Imaging - International Workshop, ShapeMI 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 20, 2018, Proceedings, Issue 11167, 2018, Page(s) 3-13
DOI: 10.1007/978-3-030-04747-4_1

A Vertex Clustering Model for Disease Progression: Application to Cortical Thickness Images

Author(s): Răzvan Valentin Marinescu, Arman Eshaghi, Marco Lorenzi, Alexandra L. Young, Neil P. Oxtoby, Sara Garbarino, Timothy J. Shakespeare, Sebastian J. Crutch, Daniel C. Alexander
Published in: Information Processing in Medical Imaging, Issue 10265, 2017, Page(s) 134-145
DOI: 10.1007/978-3-319-59050-9_11

Prediction of Amyloidosis from Neuropsychological and MRI Data for Cost Effective Inclusion of Pre-symptomatic Subjects in Clinical Trials

Author(s): Manon Ansart, Stéphane Epelbaum, Geoffroy Gagliardi, Olivier Colliot, Didier Dormont, Bruno Dubois, Harald Hampel, Stanley Durrleman
Published in: Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support, Issue 10553, 2017, Page(s) 357-364
DOI: 10.1007/978-3-319-67558-9_41

Prediction of the Progression of Subcortical Brain Structures in Alzheimer’s Disease from Baseline

Author(s): Alexandre Bône, Maxime Louis, Alexandre Routier, Jorge Samper, Michael Bacci, Benjamin Charlier, Olivier Colliot, Stanley Durrleman
Published in: Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics, Issue 10551, 2017, Page(s) 101-113
DOI: 10.1007/978-3-319-67675-3_10

A Discriminative Event Based Model for Alzheimer’s Disease Progression Modeling

Author(s): Vikram Venkatraghavan, Esther E. Bron, Wiro J. Niessen, Stefan Klein
Published in: Information Processing in Medical Imaging, Issue 10265, 2017, Page(s) 121-133
DOI: 10.1007/978-3-319-59050-9_10

TADPOLE Challenge: Accurate Alzheimer’s Disease Prediction Through Crowdsourced Forecasting of Future Data

Author(s): Răzvan V. Marinescu, Neil P. Oxtoby, Alexandra L. Young, Esther E. Bron, Arthur W. Toga, Michael W. Weiner, Frederik Barkhof, Nick C. Fox, Polina Golland, Stefan Klein, Daniel C. Alexander
Published in: Predictive Intelligence in Medicine - Second International Workshop, PRIME 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 13, 2019, Proceedings, Issue 11843, 2019, Page(s) 1-10
DOI: 10.1007/978-3-030-32281-6_1

Event-Based Modeling with High-Dimensional Imaging Biomarkers for Estimating Spatial Progression of Dementia

Author(s): Vikram Venkatraghavan, Florian Dubost, Esther E. Bron, Wiro J. Niessen, Marleen de Bruijne, Stefan Klein
Published in: Information Processing in Medical Imaging - 26th International Conference, IPMI 2019, Hong Kong, China, June 2–7, 2019, Proceedings, Issue 11492, 2019, Page(s) 169-180
DOI: 10.1007/978-3-030-20351-1_13

Riemannian Geometry Learning for Disease Progression Modelling

Author(s): Maxime Louis, Raphaël Couronné, Igor Koval, Benjamin Charlier, Stanley Durrleman
Published in: Information Processing in Medical Imaging - 26th International Conference, IPMI 2019, Hong Kong, China, June 2–7, 2019, Proceedings, Issue 11492, 2019, Page(s) 542-553
DOI: 10.1007/978-3-030-20351-1_42

Simulating Alzheimer's disease progression with personalised digital brain models

Author(s): Igor Koval, Alexandre Bône, Maxime Louis, Simona Bottani, Arnaud Marcoux, Jorge Samper-Gonzalez, Ninon Burgos, Benjamin Charlier, Anne Bertrand, Stéphane Epelbaum, Olivier Colliot, Stéphanie Allassonnière, Stanley Durrleman
Published in: 2018

Learning Distributions of Shape Trajectories from Longitudinal Datasets: A Hierarchical Model on a Manifold of Diffeomorphisms

Author(s): Alexandre Bone, Olivier Colliot, Stanley Durrleman
Published in: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2018, Page(s) 9271-9280
DOI: 10.1109/cvpr.2018.00966

Reproducible evaluation of methods for predicting progression to Alzheimer's disease from clinical and neuroimaging data

Author(s): Jorge Samper-Gonzalez, Ninon Burgos, Simona Bottani, Marie-Odile Habert, Theodoros Evgeniou, Stephane Epelbaum, Olivier Colliot
Published in: Medical Imaging 2019: Image Processing, 2019, Page(s) 30
DOI: 10.1117/12.2512430

Auto-encoding meshes of any topology with the current-splatting and exponentiation layers

Author(s): Alexandre Bône, Olivier Colliot, Stanley Durrleman
Published in: 2019

Hierarchical modeling of Alzheimer’s disease progression from a large longitudinal MRI data set

Author(s): Alexandre Bône, Benoît Martin, Maxime Louis, Olivier Colliot, Stanley Durrleman
Published in: 2019

Predicting the Progression of Mild Cognitive Impairment Using Machine Learning: A Systematic and Quantitative Review

Author(s): Manon Ansart, Stéphane Epelbaum, Giulia Bassignana, Alexandre Bône, Simona Bottani, Tiziana Cattai, Raphael Couronne, Johann Faouzi, Igor Koval, Maxime Louis, et al.
Published in: 2019

Learning the spatiotemporal variability in longitudinal shape data sets

Author(s): Alexandre Bône, Olivier Colliot, Stanley Durrleman
Published in: 2019

Simulation of virtual cohorts increases predictive accuracy of cognitive decline in MCI subjects

Author(s): Igor Koval, Stéphanie Allassonnière, Stanley Durrleman
Published in: 2019

Disease Progression Modeling and Prediction through Random Effect Gaussian Processes and Time Transformation

Author(s): Marco Lorenzi, Maurizio Filippone, Daniel C. Alexander, Sebastien Ourselin
Published in: 2016

Prediction of the progression of subcortical brain structures in Alzheimer's disease from baseline

Author(s): Alexandre Bône, Maxime Louis, Alexandre Routier, Jorge Samper, Michael Bacci, Benjamin Charlier, Olivier Colliot, Stanley Durrleman
Published in: 2017

Datasets

Additional file 1: of MRI predictors of amyloid pathology: results from the EMIF-AD Multimodal Biomarker Discovery study

Author(s): Kate, Mara Ten,Redolfi, Alberto,Peira, Enrico,Bos, Isabelle,Vos, Stephanie,Vandenberghe, Rik,Gabel, Silvy,Schaeverbeke, Jolien,Scheltens, Philip,Blin, Olivier,Richardson, Jill,Bordet, Regis,Wallin, Anders,Eckerstrom, Carl,JosĂŠ Molinuevo,Engelborghs, Sebastiaan,Broeckhoven, Christine Van,Martinez-Lage, Pablo,Popp, Julius,Tsolaki, Magdalini,Verhey, Frans,Baird, Alison,Legido-Quigley, Cristina,Bertram, Lars,Dobricic, Valerija,Zetterberg, Henrik,Lovestone, Simon,Streffer, Johannes,Bianchetti, Silvia,Novak, Gerald,Revillard, Jerome,Gordon, Mark,Zhiyong Xie,Wottschel, Viktor,Frisoni, Giovanni,Visser, Pieter,Barkhof, Frederik
Published in: Figshare

Additional file 2: of MRI predictors of amyloid pathology: results from the EMIF-AD Multimodal Biomarker Discovery study

Author(s): Kate, Mara Ten,Redolfi, Alberto,Peira, Enrico,Bos, Isabelle,Vos, Stephanie,Vandenberghe, Rik,Gabel, Silvy,Schaeverbeke, Jolien,Scheltens, Philip,Blin, Olivier,Richardson, Jill,Bordet, Regis,Wallin, Anders,Eckerstrom, Carl,JosĂŠ Molinuevo,Engelborghs, Sebastiaan,Broeckhoven, Christine Van,Martinez-Lage, Pablo,Popp, Julius,Tsolaki, Magdalini,Verhey, Frans,Baird, Alison,Legido-Quigley, Cristina,Bertram, Lars,Dobricic, Valerija,Zetterberg, Henrik,Lovestone, Simon,Streffer, Johannes,Bianchetti, Silvia,Novak, Gerald,Revillard, Jerome,Gordon, Mark,Zhiyong Xie,Wottschel, Viktor,Frisoni, Giovanni,Visser, Pieter,Barkhof, Frederik
Published in: Figshare

MRI predictors of amyloid pathology: results from the EMIF-AD Multimodal Biomarker Discovery study

Author(s): Mara Ten Kate,Alberto Redolfi,Enrico Peira,Isabelle Bos,Stephanie Vos,Rik Vandenberghe,Silvy Gabel,Jolien Schaeverbeke,Philip Scheltens,Olivier Blin,Jill Richardson,Regis Bordet,Anders Wallin,Carl Eckerstrom,José Molinuevo,Sebastiaan Engelborghs,Christine Van Broeckhoven,Pablo Martinez-Lage,Julius Popp,Magdalini Tsolaki,Frans Verhey,Alison Baird,Cristina Legido-Quigley,Lars Bertram,Valerija Dobricic,Henrik Zetterberg,Simon Lovestone,Johannes Streffer,Silvia Bianchetti,Gerald Novak,Jerome Revillard,Mark Gordon,Zhiyong Xie,Viktor Wottschel,Giovanni Frisoni,Pieter Visser,Frederik Barkhof
Published in: Figshare