Perelman School of Medicine at the University of Pennsylvania

Section for Biomedical Image Analysis (SBIA)

participating with CBICA

Nicolas Honnorat, Ph.D.


Research Associate

Section of Biomedical Image Analysis
Center for Biomedical Image Computing & Analytics
Department of Radiology
Perelman School of Medicine
University of Pennsylvania

Richards Medical Research Laboratories, Floor 7
3700 Hamilton Walk
Philadelphia, PA 19104
fax: (001) 215.573.1811
email: Nicolas.Honnorat@uphs.upenn.edu

Personal webpage

Educational Background

Ph.D. in Applied Mathematics                               Ecole Centrale de Paris (Paris, France)
M.Sc. in Applied Mathematics/Computer Vision  Ecole Centrale de Paris (Paris, France)
Engineering Degree                                              Ecole Centrale de Paris (Paris, France)

Research Summary

My current researches focus on the development of novel mathematical tools for analyzing resting-state functional MRI, in neurodevelopment and aging.

Publications

Journals

 

  • Honnorat N, Dong A, Meisenzahl-Lechner E, Koutsouleris N, Davatzikos C. Neuroanatomical Heterogeneity of Schizophrenia Revealed by Semi-supervised Machine Learning Methods. Schizophrenia Research In press
  • Honnorat N, Satterthwaite TD, Gur RE, Gur RC, Davatzikos C. sGraSP: A graph-based method for the derivation of subject-specific functional parcellations of the brain. Journal of neuroscience methods 2017 277:1-20
  • Dong A, Toledo JB, Honnorat N, Doshi J, Varol E, Sotiras A, Wolk D, Trojanowski JQ, Davatzikos C. Heterogeneity of neuroanatomical patterns in prodromal Alzheimer's disease: links to cognition, progression and biomarkers. Brain 2017 140(3):735-747
  • Eavani H., Habes M., An Y., Hsieh M.-K., Honnorat N, Erus G., Doshi J., Ferrucci L., Beason-Held L.L., Resnick S.M., Davatzikos C. Mapping the heterogeneity of neuroanatomy and functional connectivity deviation from typical brain aging: a pattern analysis and machine learning study. Alzheimer's and Dementia July 2017 13(7):P1464
  • *Gross P, *Honnorat N, *Varol E, Wallner M, Trappanese DM, Sharp TE, Starosta T, Duran JM, Koller S, Davatzikos C, Houser SR. Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images. Scientific reports 2016 6:23431*These authors contributed equally to this work.
  • Dong A, Honnorat N, Gaonkar B, Davatzikos C. CHIMERA: Clustering of Heterogeneous Disease Effects via Distribution Matching of Imaging Patterns. IEEE transactions on medical imaging (TMI) 2016 35(2):612-21
  • Sotiras A, Gaonkar B, Eavani H, Honnorat N, Varol E, Dong A, Davatzikos C. Chapter 10, Machine learning as a means toward precision diagnostics and prognostics. in Machine Learning and Medical Imaging. pp:299-334.
  • Honnorat N, Eavani H, Satterthwaite TD, Gur RE, Gur RC, Davatzikos C. GraSP: geodesic Graph-based Segmentation with
  • Le Borgne H, Honnorat N. Fast shared boosting for large-scale concept detection. Multimedia Tools and Applications 2012 60(2):389-402

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Conferences

Sahoo D, Honnorat N, Davatzikos C. GPU accelerated extraction of sparse Granger causality patterns. IEEE International Symposium on Biomedical Imaging (ISBI) 2018 Washington, D.C. (oral presentation)

Honnorat N, Davatzikos C. Extrapolated nonnegative decompositions for the analysis of functional connectivity. SPIE Medical Imaging 2018 Houston(oral presentation)

Honnorat N, Davatzikos C. High resolution robust and smooth precision matrices to capture functional connectivity. SPIE Medical Imaging 2018 Houston poster

Honnorat N, Parker D, Tunc B, Davatzikos C, Verma R. Subject-specific Structural Parcellations Based on Randomized AB-divergences. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 poster

Honnorat N, Davatzikos C. Riccati-regularized Precision Matrices for Neuroimaging. Information Processing in Medical Imaging (IPMI) 2017 275-86(oral presentation, top 15%)

Yang Z, Gu S, Honnorat N, Oathes D, Bruce S, Shinohara T, Aselcioglu I, Cook PA, Linn KA, Satterthwaite TD, Bassett DS, Sheline YI. Intrinsic functional organization and network roles in MDD and PTSD change with Cognitive Behavioral Therapy (CBT). 56th Annual meeting of the American College of Neuropsychopharmacology (ACNP) 2017 Palm Springs

Peifer M, Honnorat N, Davatzikos C. Randomized voxel based morphometry for the study of cortical myelin group differences. Organization for Human Brain Mapping (OHBM) 2017 Vancouver

Sahoo D, Honnorat N, Davatzikos C. GPU accelerated extraction of sparse Granger causality patterns. Organization for Human Brain Mapping (OHBM) 2017 Vancouver

Honnorat N, Davatzikos C. Functional Stability of the Human Connectome Project Parcellation. Organization for Human Brain Mapping (OHBM) 2017 Vancouver poster

Honnorat N, Satterthwaite T, Gur RC, Gur RE, Davatzikos C. Relations between local cortical geometry and functional homogeneity: a replication study. Organization for Human Brain Mapping (OHBM) 2017 Vancouver poster

Honnorat N, Davatzikos C. Characterization of the patterns of healthy cortical myelination 16th Annual Biomedical Postdoc Research Symposium 2017 Philadelphia poster

Eavani H, Honnorat N, An Y, Hsieh M, Erus G, Doshi J, Ferrucci L, Beason-Held L, Resnick S, Davatzikos C. Discovering heterogeneous patterns of advanced brain aging: a BLSA study. Organization for Human Brain Mapping (OHBM) 2016 Geneva (oral presentation, top 1%) poster

Honnorat N, Satterthwaite T, Gur RE, Gur RC, Davatzikos C. Reproducible and Efficient Computation of Functional Partial Correlations for the Entire Brain. Organization for Human Brain Mapping (OHBM) 2016 Geneva poster

Honnorat N, Eavani H, Satterthwaite T, Gur R, Gur R, Davatzikos C. Subject-specific Parcellations Detect Reduced Local Functional Coherence during Neuro Development. Organization for Human Brain Mapping (OHBM) 2015 Honolulu poster

Honnorat N, Satterthwaite T, Vandekar S, Shinohara R, Gur R, Gur R, Davatzikos C. Correlation and Spatial Coherence of Functional Homogeneity, Cortical Curvature and Thickness. Organization for Human Brain Mapping (OHBM) 2015 Honolulu poster

Honnorat N, Eavani H, Satterthwaite T, Gur RE, Gur RC, Davatzikos C. Discrete functional parcellation of the cortex with clustering methods and MRF. Fourth Biennial Conference on Resting State-Brain Connectivity 2014 MIT, Boston poster

Honnorat N, Eavani H, Satterthwaite T, Gur RE, Gur RC, Davatzikos C. Functional Parcellation of the Cortex from rs-fMRI with Graph-based Methods and shape priors. Organization for Human Brain Mapping (OHBM) 2014 Hamburg(oral presentation, top 1%) poster

Honnorat N, Vaillant R, Paragios N. Graph-based Guide-wire Segmentation through Fusion of Contrast-enhanced and fluoroscopic Images. IEEE International Symposium on Biomedical Imaging (ISBI) 2012 948-51(oral presentation, top 20%)

Honnorat N, Vaillant R, Paragios N. Graph-based geometric-iconic guide-wire tracking. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2011 14(Pt 1):9-16

Honnorat N, Vaillant R, Duncan JS, Paragios N. Curvilinear structures extraction in cluttered bioimaging data with discrete optimization methods. IEEE International Symposium on Biomedical Imaging (ISBI) 2011 1353-1357

Honnorat N, Vaillant R, Paragios N. Guide-wire extraction through perceptual organization of local segments in fluoroscopic images. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2010 13(Pt 3):440-8

Honnorat N, Vaillant R, Paragios N. Robust guidewire segmentation through boosting, clustering and linear programming. IEEE International Symposium on Biomedical Imaging (ISBI) 2010 924-927

Le Borgne H, Honnorat N. Fast shared boosting for large-scale concept detection. International Workshop on Content Based Multimedia Indexing (CBMI). 2010 1-6 (best paper award)

Honnorat N, Le Borgne H. Accélérer le boosting avec partage de caractéristiques. Proceedings of CORESA 2009. 2009 203-8

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Theses

  • Honnorat N, "Curvilinear Structures Segmentation and Tracking in Interventional Imaging", 2013

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Software

  • GraSP