Alexandre Routier

Research Engineer and PhD candidate

About me

I am currently a R&D Engineer and PhD candidate at the Brain & Spine Institute in Paris. I previoulsy obtained the Engineer degree from INSA Rouen and the Master's degree in Theoretical and Applied Mathematics from University of Rouen in 2012.

From 2012 to 2015, I was an engineer in the ARAMIS Lab, working on the CATI project on the topic of development of methods and software for neuroimaging data analysis including the Deformetrica software (morphometry and statistical learning).

My PhD project aims at developing and applying multimodal image analysis techniques (anatomical MRI, diffusion MRI, PET) to the study of primary progressive aphasia, a neurodegenerative disease affecting language abilities. These approaches aim at finding new biomarkers of the disease and understanding the links between brain alterations and language deficits. I am among the main contributors of the Clinica software platform (multimodal brain image analysis).

Work Experience

R&D Engineer and PhD Candidate (AP-HP, ICM)

2015 - Present
ARAMIS and FrontLab Teams, ICM, Pitié-Salpêtrière Hospital, Paris, France

Multimodal neuroimaging for characterization of primary progressive aphasias under the supervision of of Marc Teichmann and under the co-supervistion of Olivier Coliot and Marie-Odile Habert.

On top of my work as a PhD candidate, I use my experience in neuroimaging and computer science by working on various research projects.

Keywords:

  • Structural MRI
  • Diffusion MRI
  • PET Imaging
  • Statistics
  • Python
  • Project management

Research and Development Engineer (CATI Neuroimaging Platform)

Dec 2012 – Jun 2015
ARAMIS Team, ICM, Pitié-Salpêtrière Hospital, Paris, France

I was working on the topic of development of methods and software for neuroimaging data analysis including the Deformetrica software (morphometry and statistical learning).

Tasks:

  • Software maintenance, architecture, documentation
  • Software optimisation including profiling, GPU implementation with CUDA and replacement of the former linear algebra library VNL by Armadillo.
  • Evaluation of Deformetrica on computer-aided diagnosis of dementia based on structural MRI data with the MICCAI Challenge. We used morphometric descriptors of deep brain structures for the automatic classification of patients with Alzheimer's disease, subjects with mild cognitive impairments and healthy subjects.
  • Participation to research projects involving topics of neuroimaging (in particular structural MRI) and statistics.

Keywords:

  • C++
  • git
  • Neuroimaging
  • Structural MRI
  • Statistics
  • CMake
  • CUDA
  • ITK
  • VTK

Research Internship (Inria)

Jun 2012 – Nov 2012
M3DISIM Team (Formerly MACS), Palaiseau, France

Data assimilation for the personalization of dynamical mechanical models under the supervision of Alexandre Imperiale and Philippe Moireau.

Keywords:

  • Partial differential equation
  • Luenberger observer
  • Finite element method
  • Matlab
  • C
  • SVN

Research Internship (Inria)

May 2011 – Sep 2011
POEMS Team, ENSTA, Paris, France

Study of sampling methods in acoustic and elastic waveguides under the supervision of Laurent Bourgeois and Eric Lunéville.

Keywords:

  • Partial differential equation
  • Finite element methods
  • Matlab
  • Fortran
  • SVN

Publications

Journal Articles or Book Chapters

  • A. Routier, M.-O. Habert, A. Bertrand, A. Kas, M. Sundqvist, J. Mertz, P.-M. David, H. Bertin, S. Belliard, F. Pasquier, K. Bennys, O. Martinaud, F. Fretcharry-Bouyx, O. Moreaud, O. Godefroy, J. Pariente, M. Puel, P. Couratier, C. Boutoleau-Bretonniere, B. Laurent, R. Migliaccio, B. Dubois, O. Colliot, M. Teichmann. Structural, microstructural and metabolic alterations in Primary Progressive Aphasia variants. Frontiers in Neurology, 2018
  • C. Sanches, A. Routier, O. Colliot, M. Teichmann. The structure of the mental lexicon: what primary progressive aphasias reveal. Neuropsychologia, 2018
  • J. Samper-González, N. Burgos, S. Bottani, S. Fontanella, P. Lu, A. Marcoux, A. Routier, J. Guillon, M. Bacci, J. Wen, A. Bertrand, H. Bertin, M.-O. Habert, S. Durrleman, T. Evgeniou, O. Colliot. Reproducible evaluation of classification methods in Alzheimer's disease: framework and application to MRI and PET data. NeuroImage, 2018
  • I. Koval, J.-B. Schiratti, A. Routier, M. Bacci, O. Colliot, S. Allassonniere, S. Durrleman. Spatiotemporal propagation of the cortical atrophy during the course of Alzheimer’s Disease: Population and individual patterns. Frontiers in Neurology, 2018
  • A. Mendes, A. Bertrand, F. Lamari, O. Colliot, A. Routier, O. Godefroy, F. Etcharry-Bouyx, O. Moreaud, F. Pasquier, P. Couratier, K. Bennys, M. Vercelletto, O. Martinaud, B. Laurent, J. Pariente, M. Puel, S. Epelbaum, S. Belliard, T. Kaaouana, L. Fillon, M. Chupin, B. Dubois, M. Teichmann. Cerebral microbleeds and CSF Alzheimer biomarkers in primary progressive aphasias. Neurology, 2018
  • A. Bertrand, J. Wen, D. Rinaldi, M. Houot, S. Sayah, A. Camuzat, C. Fournier, S. Fontanella, A. Routier, P. Couratier, F. Pasquier, M.-O. Habert, D. Hannequin, O. Martinaud, P. Caroppo, R. Levy, B. Dubois, A. Brice, S. Durrleman, O. Colliot, I. Le Ber. Early Cognitive, Structural, and Microstructural Changes in Presymptomatic C9orf72 Carriers Younger Than 40 Years. JAMA neurology, 2018
  • P. Gori, O. Colliot, L. Marrakchi-Kacem, Y. Worbe, A. Routier, C. Poupon, A. Hartmann, N. Ayache, S. Durrleman. Double diffeomorphism: combining morphometry and structural connectivity analysis. IEEE Transactions on Medical Imaging, 2018
  • A. Bône, M. Louis, A. Routier, J. Samper-González, M. Bacci, B. Charlier, O. Colliot, S. Durrleman. Prediction of the progression of subcortical brain structures in Alzheimer’s disease from baseline. MICCAI Workshop on Mathematical Foundations of Computational Anatomy, 2017
  • T. Jacquemont, F. De Vico Fallani, A. Bertrand, S. Epelbaum, A. Routier, B. Dubois, H. Hampel, S. Durrleman, O. Colliot. Amyloidosis and neurodegeneration result in distinct structural connectivity patterns in mild cognitive impairment. Neurobiology of aging, 2017
  • P. Caroppo, M.-O. Habert, S. Durrleman, A. Funkiewiez, V. Perlbarg, V. Hahn, H. Bertin, M. Gaubert, A. Routier D. Hannequin, V. Deramecourt, F. Pasquier, S. Rivaud-Pechoux, M. Vercelletto, G. Edouart, R. Valabregue, P. Lejeune, M. Didic, J.-C. Corvol, H. Benali, S. Lehericy, B. Dubois, O. Colliot, A. Brice, I. Le Ber. Lateral Temporal Lobe: An Early Imaging Marker of the Presymptomatic GRN Disease? Journal of Alzheimer's Disease, 2015
  • E.E. Bron et al. Standardized evaluation of algorithms for computer-aided diagnosis of dementia based on structural MRI: the CADDementia challenge. NeuroImage, 2015

Peer-reviewed Conference Articles

  • I. Koval, J.-B. Schiratti, A. Routier, M. Bacci, O. Colliot, S. Allassonnière, S. Durrleman. Statistical learning of spatiotemporal patterns from longitudinal manifold-valued networks. MICCAI, 2017
  • C. Cury, M. Lorenzi, D. Cash, N. David, J. Nicholas, A. Routier, J. Rohrer, S. Ourselin, S. Durrleman, M. Modat. Spatio-temporal shape analysis of cross-sectional data for detection of early changes in neurodegenerative disease. International Workshop on Spectral and Shape Analysis in Medical Imaging, 2016
  • J.-B. Schiratti, S. Allassonniere, A. Routier, O. Colliot, S. Durrleman. A mixed-effects model with time reparametrization for longitudinal univariate manifold-valued data. IPMI 2015
  • P. Gori, O. Colliot, L. Marrakchi-Kacem, Y. Worbe, A. Routier, C. Poupon, A. Hartmann, N. Ayache, S. Durrleman. Joint Morphometry of Fiber Tracts and Gray Matter Structures Using Double Diffeomorphisms. IPMI, 2015
  • A. Routier, P. Gori, A.B. Graciano Fouquier, S. Lecomte, O. Colliot, S. Durrleman. Evaluation of morphometric descriptors of deep brain structures for the automatic classification of patients with Alzheimer’s disease. MICCAI Challenge on Computer-Aided Diagnosis of Dementia based on structural MRI data (CADDementia), 2014 Paper Presentation
  • A. Imperiale, A. Routier, S. Durrleman, P. Moireau. Improving efficiency of data assimilation procedure for a biomechanical heart model by representing surfaces as currents. International Conference on Functional Imaging and Modeling of the Heart, 2013

Abstracts

  • A. Routier, M.-O. Habert, A. Bertrand, A. Kas, P.-M. David, H. Bertin, O. Godefroy, F. Etcharry-Bouyx, O. Moreaud, F. Pasquier, P. Couratier, K. Bennys, C. Boutoleau Bretoniere, O. Martinaud, B. Laurent, J. Pariente, M. Puel, S. Belliard, R. Migliaccio, B. Dubois, O. Colliot, M. Teichmann. Structural, microstructural and metabolic alterations in Primary Progressive Aphasia variants OHBM, 2018
  • A. Routier, J. Guillon, N. Burgos, J. Samper-González, J. Wen, S. Fontanella, S. Bottani, T. Jacquemont, A. Marcoux, P. Gori, P. Lu, T. Moreau, M. Bacci, S. Durrleman, O. Colliot Clinica: an open source software platform for reproducible clinical neuroscience studies. OHBM, 2018
  • A. Routier, M. Prastawa, B. Charlier, C. Doucet, J. Glaunès, S. Durrleman. Deformetrica: a software for statistical analysis of anatomical shapes. OHBM, 2015

Skills & Tools

Programming

  • Python
  • C++
  • Bash
  • Zsh
  • C
  • Matlab

Neuroimaging

  • ANTs
  • FreeSurfer
  • FSL
  • MRtrix3
  • Nipype
  • SPM

Education

  • PhD Candidate
    Pierre and Marie Curie University, Paris
    2015 - Present
  • MSc in Theoretical and Applied Mathematics
    University of Rouen
    2011 - 2012
  • Engineer's degree in Applied Mathematics and Computer Science
    National Institute for Applied Sciences, Rouen
    2007 - 2012

Projects

  • Clinica
    Clinica is a software platform for clinical research studies involving patients with neurological and psychiatric diseases and the acquistion of multimodal data (neuroimaging, clinical and cognitive evaluations, genetics...), most often with longitudinal follow-up.
  • Deformetrica
    Deformetrica is a software for the statistical analysis of 2D and 3D shape data. It essentially computes deformations of the 2D or 3D ambient space, which, in turn, warp any object embedded in this space, whether this object is a curve, a surface, a structured or unstructured set of points, or any combination of them.

Language

  • French (Native)
  • English (Professional)
  • German (Academic)

Interests

  • Reading (Books, Comics)
  • Music (Guitar, Ukulele)
  • Sport (Running, Swimming)