Publications, Communications and students


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 Publications: 

Articles in Journals:

    • 17- A 4-dimensional model of ischemic stroke lesion metamorphosis from acute to final infarct volumeI. Rekik, S. Allassonniere, T. Carpenter and J. Wardlaw. Submitted.
    • 16- Bayesian Mixed Effect Atlas Estimation under Diffeomorphic constraint on the deformation model. S.Allassonnière, S.Durrleman and E.Kuhn. 
      SIAM Journal on Imaging Science., 8(3), 1367–1395.  (pdf)
    • 15- Convergent stochastic Expectation Maximization algorithm with efficient sampling in high dimension. Application to deformable template model estimation. S. Allassonniere and E. Kuhn. Journal of Computational Statistics & Data Analysis, Volume 91(C), 2015. 
    • 14- Using longitudinal metamorphosis to examine ischemic stroke lesion dynamics on perfusion- weighted and relation to final outcome on T2-w images. I. Rekik, S. Allassonniere, T. Carpenter and J. Wardlaw. NeuroImage Clinical, 5, 2014, pp 332-340. 
    • 13- Bayesian estimation of Probabilisitic atlas for tissue segmentation. H. Xu, B.Thirion and S. Allassonniere, IRBM Journal, 35(1), 2014, pp 27-32.
    • 12- Probabilistic Atlas and Geometric Variability Estimation to Drive Tissue Segmentation. H. Xu, B.Thirion and S. Allassonniere, Statistics in Medicine, 33(20), 2014, pp 3576–3599. 
    • 11- Statistical models for deformable templates in image and shape analysis. S. Allassonniere, J. Bigot, J.A. Glaunes, F. Maire and F.J.P. Richard. Annales mathématiques Blaise Pascal, vol 20(1), 2013.
    • 10- Spacio-temporal dynamic simulation of acute perfusion/diffusion ischemic stroke lesions evolution: a pilot study derived from longitudinal MR patient data. I. Rekik, S. Allassonniere, S. Durrleman, T. Carpenter and J. Wardlaw. Computational and Mathematical Methods in Medicine, vol 2013, doi:10.1155/2013/283593, 2013 (pdf).
    • 9- A Review of Medical Image Analysis Methods in MR/CT-imaged Acute-subacute Ischemic Stroke Lesion: Segmentation, Prediction and Insights into Dynamic Evolution Simulation Models. I. Rekik, S. Allassonniere, T. Carpenter and J. Wardlaw. NeuroImage Clinical Volume 1, Issue 1, (2012), (164-178) (pdf).
    • 8- Sparse Adaptive Parameterization of Variability in Image Ensembles. S. Durrleman, S. Allassonniere, S.Joshi. IJCV, 2012, (DOI) 10.1007/s11263-012-0556-1.
    • 7- Aircraft classification with a low resolution infrared sensor. S. Lefebvre, S. Allassonniere, J. Jakubowicz, T. Lasne, and E. Moulines. Machine Vision and Application Journal, 2013, Vol. 24(1), pp 175-186 (pdf).
    • 6- Tumor Growth Parameters Estimation and Source Localization From a Unique Time Point: Application to Low-grade Gliomas. I. Rekik, S. Allassonniere, H. Deslingette, O. Clatz, E. Geremia, N. Ayache.  Computer Vision and Image Understanding, 117(3), 2013, pp 238-249.
    • 5- A Stochastic Algorithm for Probabilistic Independent Component Analysis. S. Allassonnière, L. Younes.  Annals of Applied Statistics, 2012, Vol. 6, No. 1, 125-160 (.pdf)
    • 4- Bayesian Consistent Estimation in Deformable Models using Stochastic Algorithms: Applications to Medical ImagesS. Allassonnière, E. Kuhn, A. Trouvé. Journal de la Société Française de Statistiques. Vol. 151(1) p. 1-16, 2010.
    • 3- Stochastic Algorithm For Parameter Estimation For Dense Deformable Template Mixture Model. S. Allassonnière, E. Kuhn.  ESAIM-PS 2010, Vol 14, p. 382_408. (.pdf)
    • 2- Construction of Bayesian deformable models via stochastic approximation algorithm: A convergence study.  S. Allassonnière, E. Kuhn, A. Trouvé. Bernoulli Journal, Vol 16(3), p.641-678, 2010. (pdf)
    • 1- Toward a coherent statistical framework for dense deformable template estimation. S. Allassonnière, Y. Amit, A. Trouvé. Volume 69, part 1 (2007), pages 3-29, of the Journal of the Royal Statistical Society, Series B.  (pdf)
        

    PhD and HDR dissertations:

    • HDR manuscript: Statistical analysis of Deformable Template Models for medical image understanding. (pdf)
    • PhD Dissertation: Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy. S.Allassonnière. (pdf)

    Conference Articles:

    • Learning spatiotemporal trajectories from manifold-valued longitudinal data. J.J Schiratti, S. Allassonnière, O. Colliot, S. Durrleman. NIPS 2015.

    • Innovation-based sparse estimation of functional connectivity from multivariate autoregressive models. F. Deloche, F. De Vico Fallani, S. Allassonnière. Proc. SPIE 9597, Wavelets and Sparsity XVI, 95971I (August 24, 2015); doi:10.1117/12.2189640; Conference Volume 9597

    •  Mixed-effects model for the spatiotemporal analysis of longitudinal manifold-valued data. J-B.  Schiratti, S. Allassonnière, O. Colliot, S. Durrleman. MFCA 2015

    • Estimating the Template in the Total Space with the Fréchet Mean on Quotient Spaces may have a Bias: a Case Study on Vector Spaces Quotiented by the Group of Translations. L. Devilliers, S. Allassonnière, X. Pennec.MFCA 2015.

    • A mixed effect model with time reparametrization for longitudinal univariate manifold valued data}. \textsc{J.B. Schiratti, S. Allassonni\`ere, O. Colliot, S. Durrleman}. Information Processing in Medical Imaging (IPMI) 2015

    • Bayesian Estimation of Probabilistic Atlas for Anatomically-Informed Functional MRI Group Analyses. H. Xu, B. Thirion and S. Allassonniere. MICCAI, Nagoya, 2013

    • A 4D Patient-specific metamorphosis-based method to model ischemic stroke lesion evo- lution from acute diffusion-weighted to final T2-defined outcome. I. Rekik, S. Allas- sonnie`re, T. Carpenter and J. Wardlaw. International Stroke Conference, Honolulu, 2013. 
    • 4D spatio-temporal perfusion-diffusion Evolution scenarios estimation in Acute-subacute ischemic stroke. 

      I. Rekik, S. Allassonniere, S. Durrleman, T.K. Carpenter, J.M. Wardlaw, ISMRM, Melbroune, 2012.
    • Dynamic Patient-specific Modeling of Ischemic Stroke Lesion Evolution: From Presentation to Final Damage using Diffusion, Perfusion and T2 MR imaging, I. Rekik, S. Allassonniere, S. Durrleman, T.K. Carpenter, J.M. Wardlaw, ESC, Lisbon, 2012.
    • Mathematical Image Processing Algorithms in determining Stroke Tissue Status and Pre- dicting its Fate: Systematic Review reveals Untapped Potentials. I. Rekik, S. Allas- sonnie`re, T. Carpenter and J. Wardlaw.. European Stroke Conference, Hamburg 2011. 
    • Detection and classification of poorly known aircraft with a low-resolution infrared sensor. S. Lefebvre, S. Allassonnière, G. Durand, J. Jakubowicz, E. Moulines, A. Roblin. Proc. of SPIE volume 8050 (2011).
    • Detecting long distance conditional correlations between anatomical regions using Gaussian Graphical Models

      .
      S. Allassonnière, P.Jolivet, C.Giraud. Mathematical Fundation of Computational Anatomy
       (MFCA) workshop of the MICCAI 2011 conference. (pdf)
    • Consistent Atlas Estimation on BME Template Model: Applications to 3D Biomedical Images. S. Allassonnière, E. Kuhn, J. T. Ratnanather, A. TrouvéProbabilistic Models for Medical Image Analysis (PMMIA) worshop of the MICCAI 2009 conference. (pdf)
    •  MAP Estimation of Statistical Deformable Template Via Nonlinear Mixed Effect Models~:
      Deterministic and Stochastic Approaches.
      S.Allassonnière, E.Kuhn, A.Trouvé. Mathematical Foundations of Computational Anatomy (MFCA) workshop of MICCAI 2008 conference. (pdf)
    • Generative Model and consistent estimation algorithms for non-rigid deformable models. S.Allassonnière, E.Kuhn, Y.Amit, A.Trouvé. ICASSP conference, 2006 in Toulouse, France  (pdf)
    • Geodesic Shooting and Diffeomorphic Matching Via Textured Meshes. S.Allassonnière, A.Trouvé, L.Younes. EMMCVPR 2005, St Augustine, Florida, USA. (pdf)

    Grants:
    • PEPS Egalité (PI)
    • MMoVNI : Digiteo project (PI)
    • ANR_HM-TC (PI : Olivier Colliot)
    • ANR IRMGroup (PI : Stéphane Mallat)

    Students:

    • Master students
      • Pierre Jolivet (M1)
      • Islem Rekik (M2)
      • James Newling (M1)
    • PhD students
      • Jean-Baptiste Schirratti (01/09/2013-)
      • Islem Rekik (09/2010-31/03/2014)
      • Hao XU (03/2011-30/03/2014)

     

    Several Presentations and Seminars:

     
    • Seminar at the Institut National de Recherche Agronomique (INRA)  in Toulouse (November 2013)
    • Seminar at the University Paris Dauphine (November 2013)
    • Seminar at the CIMI thematic trimester on image processing (May 2013)
    • Presentation of the AMALA sampler at the conference Méthodes Mathématiques pour l'Image (Orléans, June 2012)
    • Presentation of the AMALA sampler at the BigMC seminar (January 2012)
    • Mini-course on  Computational Anatomy at the Forum des jeunes mathématiciennes (November 2011)
    • Seminar at the Institut des mathématiques in Toulouse for the Statistics and Imaging meeting (June 2011)
    • Presentation of current work at the annual Shape meeting, Imperial College London (May 2011)
    • Tutorial on Computational Anatomy at the KTH university in Stockholm (October 2010)
    • Image lunch seminar at the Scientific Computing and Imaging Institute (University of Utah September 2010)
    • Organization of the mini-symposium on Statistics for medical Image Analysis, part of the IMA conference on Imaging Science (April 2010)
    • Poster presentation at the  Probabilistic Models for Medical Image Analysis (PMMIA) worshop of the MICCAI 2009 conference. (pmmiabis.pdf)
    • Presentation at the Summer School Mathematics in Brain Imaging   in the Institute of Pure and Applied Mathematics (UCLA)  Generative Models and Stochastic Algorithms for Population Average Estimation and Image Analysis."(07/15/08).
    •  Seminar at the Applied Mathematics and Statistics department in Johns Hopkins University (03/04/08) :  Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy.
    • Seminar Siemens Corporate Research (04/02/08) :  Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy.
    • Seminar in University of Maryland Baltimore County (UMBC),  Department of Mathematics and Statistics (16/11/07) :  Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy.
    • Presentation in the New Researcher Session of the SAMSI Summer 2007 Program on the Geometry and Statistics of Shape Spaces (July 7-13, 2007) : Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy
    • Thesis defense, University Paris 13 (07/04/07)  : Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy.
    • Seminar in LATP University of Provense, Marseille (12/01/06)  Toward a coherent statistical framework for dense deformable template estimation.
    • Presentation in the colloquim of Centre de Mathematiques et leurs Applications, Cachan, France, (05/18/06)  : Toward a coherent statistical framework for dense deformable template estimation.
    • Presentation in the ICASSP conference, Toulouse (05/16/06) : Generative Model and consistent estimation algorithms for non-rigid deformable models.
    • Poster session in the workshop in IMA on Shape Spaces (02-06/04/06) : Generative Model and consistent estimation algorithms for non-rigid deformation model.
    • Presentation in the ENST for the "groupe de travail" ISIS and MSPC (09/06/05) : Geodesic Shooting and Diffeomorphic Matching Via Textured Meshes.
    • Presentation in the LAGA probability and statistics seminar (13/04/05): Large Deformations and Triangulation for Image Matching Problems.
    • Presentation in the Center for Imaging Science in Johns Hopkins University (Baltimore) (15/03/05): Large Deformations and Triangulation for Image Matching Problems. 


    Conferences: 


    • MICCAI 2009. London. Sept 20th to Sept 24th.
    • MICCAI 2008. New York City. Sept 6th to Sept 10th.
    • Summer School in UCLA: Mathematics in Brain Imaging (2008)
    • SAMSI Summer 2007 Program on the Geometry and Statistics of Shape Spaces (July 7-13, 2007)
    • Workshop in Paris Dauphine University on Mathematics and Image Analysis ( 2004 and 2006)
    • IMA workshop on Shape Spaces (Apr 2006)
    • International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2006)
    • Energy Minimisation Methods for Computer Vision and Pattern Recognition (EMMCVPR 2005)  
    • Summer School in UCLA: Mathematics in Brain Imaging (2004)