M. Chupin, A. Hammers, R.S.N. Liu, J. Burdett, O. Colliot, E. Bardinet, J.S. Duncan, L. Garnero, L. Lemieux, Fast and fully automatic segmentation of the hippocampus and the amygdala driven by hybrid anatomic and probabilistic constraints: method and validation on controls and patients with hippocampal atrophy, NeuroImage, 46(3):749-61, 2009

O. Colliot, G. Chételat, M. Chupin, B. Desgranges, B. Magnin, H. Benali, B. Dubois, L. Garnero, F. Eustache, S. Lehéricy, Discrimination between Alzheimer disease, mild cognitive impairment and normal aging by using automated segmentation of the hippocampus, Radiology, 248, pp 194-201, 2008

E. Gerardin, G. Chételat, M. Chupin, R. Cuingnet, B. Desgranges, H.-S. Kim, M. Niethammer, B. Dubois, L. Garnero, S. Lehéricy, F. Eustache, O. Colliot, The ADNI, Multidimensional classification of hippocampal shape features discriminates Alzheimer’s disease and mild cognitive impairment from normal aging, NeuroImage, 47 (4), 1476-86, 2009

M. Chupin, E. Gérardin, R. Cuingnet, C. Boutet, L. Lemieux,  S. Lehéricy, H. Benali, L. Garnero, O. Colliot, The ADNI, Fully automatic hipocampus segmentation and classification in Alzheimer’s disease and mild cognitive impairment applied on data from ADNI. Hippocampus. 19(6):579-87, 2009

B. Dubois, M. Chupin, H. Hampel, S. Lista, E. Cavedo, B. Croisille, G.L. Tisserand, J. Touchon, A. Bonafé, P.J. Ousset, A. Ait Ameur, O. Rouaud, F. Ricolfi, A. Vighetto, F. Pasquier, C. Delmaire, M. Ceccaldi, N. Girard, C. Dufouil, S. Lehéricy, I. Tonelli, F. Duveau, O. Colliot, L. Garnero, M. Sarazin, D. Dormont, Hippocampus Study Group, Donepezil decreases annual rate of hippocampal atrophy in suspected prodromal Alzheimer’s disease, Alzheimers and Dementia, 2015

Atrophy from fold opening

J.-F. Mangin, E. Jouvent, and A. Cachia. In vivo measurement of cortical morphology: means and meanings. Current Opinion in Neurology, 23(4):359-67, 2010.

E. Jouvent, J.-F. Mangin, R. Porcher, A. Viswanathan, M. O’Sullivan, J.-P. Guichard, M. Dichgans, M.-G. Bousser, and H. Chabriat. Cortical changes in cerebral small vessel diseases: a 3D MRI study of cortical morphology in CADASIL, Brain, 131(8):2201-8, 2008

P. Kochunov, J.-F. Mangin, T.R. Coyle, J.L. Lancaster, P.M. Thompson, D. Rivière, Y. Cointepas, J. Régis, A. Schlosser, D.R. Royall, K. Zilles, J. Mazziotta, A.W. Toga, and P. T. Fox. Age-related morphology trends of cortical sulci. Hum Brain Mapp., 26(3):210-220, 2005

White Matter Hyperintensity

T. Samaille, L. Fillon, R. Cuingnet, E. Jouvent, H. Chabriat, D. Dormont, O. Colliot, M. Chupin, Contrast-based fully automatic segmentation of white matter hyperintensities: method and validation. PLoS One. 7(11):e48953, 2012

Diffusion MRI

P. Guevara, C. Poupon, D. Rivière, Y. Cointepas, M. Descoteaux, B. Thirion, and J-F. Mangin. Robust clustering of massive tractography datasets. Neuroimage, 54(3):1975-1993, 2011

P. Fillard, M. Descoteaux, A. Goh, S. Gouttard, B. Jeurissen, J. Malcolm, A. Ramirez-Manzanares, M. Reisert, K. Sakaie, F. Tensaouti, T. Yo, J.-F. Mangin, C. Poupon. Quantitative evaluation of 10 tractography algorithms on a realistic diffusion MR phantom. Neuroimage. 2011, in press

L. Marrakchi-Kacem, C. Delmaire, A. Tucholka, P. Roca, P. Guevara, F. Poupon, J. Yelnik, A. Durr, J.-F. Mangin, S. Lehericy, and C. Poupon. Analysis of the striato-thalamo-cortical connectivity on the cortical surface to infer biomarkers of Huntington’s disease.. In MICCAI, volume 13, pages 217-224, 2010

C. Poupon, C. A. Clark, V. Frouin, J. Régis, I. Bloch, D. Le Bihan, and J.-F. Mangin. Regularization of Diffusion-based direction maps for the tracking of brain white matter fascicles. Neuroimage, 12(2):184-195, 2000

C. Poupon , A. Roche, J. Dubois, J.-F. Mangin, F. Poupon, F. Real-time MR diffusion tensor and Q-ball imaging using Kalman filtering. Medical Image Analysis. 2008, 12(5):527-534. Best Paper Elsevier Award

Resting state fMRI

G. Varoquaux, S. Sadaghiani, Ph. Pinel, A. Kleinschmidt, J.-B. Poline, and B. Thirion. A group model for stable multi-subject ICA on fMRI datasets. Neuroimage, 2010, 51(1):288-99

Bellec P, Rosa-Neto P, Lyttelton OC, Benali H, Evans AC. Multi-level bootstrap analysis of stable clusters in resting-state fMRI. Neuroimage. 2010 Jul 1;51(3):1126-39

Li X, Coyle D, Maguire L, McGinnity T, Benali H. A model selection method for nonlinear system identification based fMRI effective connectivity analysis. IEEE Trans Med Imaging. 2011 

Bellec P, Perlbarg V, Jbabdi S, Pélégrini-Issac M, Anton JL, Doyon J, Benali H. Identification of large-scale networks in the brain using fMRI. Neuroimage. 2006 Feb 15;29(4):1231-43

G. Marrelec;P. Bellec;H. Duffau;M. Pélégrini-Issac;A. Krainik;S. Lehéricy;J. Doyon;H. Benali, Regions, systems, and the brain: hierarchical measures of functional integration in fMRI. Medical Image Analysis, 2008, 12(4):484-496

Nuclear Medicine

Habert MO, Horn JF, Sarazin M, Lotterie JA, Puel M, Onen F, Zanca M, Portet F, Touchon J, Verny M, Mahieux F, Giron A, Fertil B, Dubois B. Brain perfusion SPECT with an automated quantitative tool can identify prodromal Alzheimer’s disease among patients with mild cognitive impairment. Neurobiol Aging. 2011 Jan;32(1):15-23

Machine learning for biomarkers

R. Cuingnet, E. Gerardin, J. Tessieras, G. Auzias, S. Lehéricy, M.-O. Habert, M. Chupin, H. Benali, O. Colliot, The ADNI, Automatic classification of patients with Alzheimer’s disease from structural MRI: a comparison of ten methods using the ADNI database. NeuroImage, in press

B. Magnin, L. Mesrob, S. Kinkingnéhun, M. Pellegrini-Issac, O. Colliot, M. Sarazin, B. Dubois, S. Lehéricy, H. Benali, Support vector machine based classification of Alzheimer’s disease from whole-brain anatomical MRI, Neuroradiology, 51(2):73-83, 2009

E. Duchesnay, A. Cachia, A. Roche, D. Rivière, Y. Cointepas, D. Papadopoulos-Orfanos, M. Zilbovicius, J.-L. Martinot, and J.-F. Mangin. Classification from cortical folding patterns. IEEE Trans. Med. Imag., 26(4):553-565, 2007

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