S. Allassonnì-ere, Y. Amit, A. S. Trouvé, E. Kuhn, and A. Trouvé, Towards a Coherent Statistical Framework for Dense Deformable Template Estimation Construction of Bayesian deformable models via stochastic approximation algorithm: a convergence study, Journal of the Royal Statistical Society. Series B (Statistical Methodology) Bernoulli, vol.69, issue.163, pp.641-678, 2007.

G. Auzias, O. Colliot, J. Glaunès, M. Perrot, J. Mangin et al., Diffeomorphic Brain Registration Under Exhaustive Sulcal Constraints, IEEE Transactions on Medical Imaging, vol.30, issue.6, pp.1214-1227, 2011.
DOI : 10.1109/TMI.2011.2108665
URL : https://hal.archives-ouvertes.fr/hal-00793675

B. Avants and J. C. Gee, Geodesic estimation for large deformation anatomical shape averaging and interpolation, NeuroImage, vol.23, issue.5, pp.139-150, 2004.
DOI : 10.1016/j.neuroimage.2004.07.010

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: A practical and powerful approach to multiple testing, Journal of the Royal, vol.590, 1995.

M. Bossa, E. Zacur, and S. Olmos, Statistical analysis of relative pose information of subcortical nuclei: Application on ADNI data, NeuroImage, vol.55, issue.3, pp.999-1008, 2011.
DOI : 10.1016/j.neuroimage.2010.12.078

J. Cates, P. T. Fletcher, M. Styner, H. C. Hazlett, and R. Whitaker, Particle-Based Shape Analysis of Multi-object Complexes, Medical Image Computing and Computer-Assisted Intervention MICCAI 2008. No. 5241 in Lecture 595 Notes in Computer Science, pp.477-485, 2008.
DOI : 10.1007/978-3-540-85988-8_57

B. Charlier, N. Charon, and A. Trouv, The Fshape Framework for the Variability Analysis of Functional Shapes, Foundations of Computational Mathematics, vol.5, issue.1, 2014.
DOI : 10.1007/s10208-015-9288-2
URL : https://hal.archives-ouvertes.fr/hal-00981805

N. Charon and A. Trouvé, The Varifold Representation of Nonoriented Shapes for Diffeomorphic Registration, SIAM Journal on Imaging Sciences, vol.6, issue.4, pp.2547-2580, 2013.
DOI : 10.1137/130918885

C. Cury, J. Glauns, M. Chupin, and O. Colliot, Analysis of anatomical variability using diffeomorphic iterative centroid in patients with Alzheimer's disease, Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, vol.56, issue.4, pp.1-9, 2015.
DOI : 10.1016/j.neuroimage.2004.07.023

R. Davies, C. Twining, T. Cootes, and C. Taylor, Building 3-D Statistical Shape Models by Direct Optimization, IEEE Transactions on Medical Imaging, vol.29, issue.4, pp.961-981, 2010.
DOI : 10.1109/TMI.2009.2035048

M. Descoteaux, E. Angelino, S. Fitzgibbons, and R. Deriche, Regularized, fast, and robust analytical Q-ball imaging, Magnetic Resonance in Medicine, vol.17, issue.3, pp.58-497, 2007.
DOI : 10.1002/mrm.21277

S. Durrleman, Statistical models of currents for measuring the variability of anatomical curves, surfaces and their evolution, 2010.
URL : https://hal.archives-ouvertes.fr/tel-00631382

S. Durrleman, P. Fillard, X. Pennec, A. Trouvé, and N. Ayache, Registration, atlas estimation and variability analysis of white matter fiber bundles modeled as currents, NeuroImage, vol.55, issue.3, pp.1073-1090, 2011.
DOI : 10.1016/j.neuroimage.2010.11.056
URL : https://hal.archives-ouvertes.fr/hal-00816044

S. Durrleman, X. Pennec, A. Trouvé, and N. Ayache, Statistical models of sets of curves and surfaces based on currents, Medical Image Analysis, vol.13, issue.5, pp.793-808, 2009.
DOI : 10.1016/j.media.2009.07.007
URL : https://hal.archives-ouvertes.fr/hal-00816051

S. Durrleman, M. Prastawa, N. Charon, J. R. Korenberg, S. Joshi et al., Morphometry of anatomical shape complexes with dense deformations and sparse parameters, NeuroImage, vol.101, pp.35-49, 2014.
DOI : 10.1016/j.neuroimage.2014.06.043
URL : https://hal.archives-ouvertes.fr/hal-01015771

S. Durrleman, M. Prastawa, G. Gerig, and S. Joshi, Optimal Data-Driven Sparse Parameterization of Diffeomorphisms for Population Anal- 615 ysis, Information Processing in Medical Imaging. No. 6801 in Lecture Notes in Computer Science, pp.123-134, 2011.

L. L. Folgoc, H. Delingette, A. Criminisi, and N. Ayache, Sparse Bayesian Registration, Medical Image Computing and Computer-Assisted Intervention MICCAI 2014. No. 8673 in Lecture Notes in Computer Science, pp.235-242, 2014.
DOI : 10.1007/978-3-319-10404-1_30
URL : https://hal.archives-ouvertes.fr/hal-01006605

E. Gerardin, G. Chtelat, M. Chupin, R. Cuingnet, B. Desgranges et al., Multidimensional classification of hippocampal shape features discriminates Alzheimer's disease and mild cognitive impairment from normal aging, NeuroImage, vol.47, issue.4, pp.1476-1486, 2009.
DOI : 10.1016/j.neuroimage.2009.05.036

J. Glaunès, Transport par diffomorphismes de points, de mesures et de courants pour la comparaison de formes et l'anatomie numrique, 2005.

P. Golland, W. E. Grimson, M. E. Shenton, R. Kikinis, and . Feb, Detection and analysis of statistical differences in anatomical shape, Medical Image Analysis, vol.9, issue.1, pp.69-86, 2005.
DOI : 10.1016/j.media.2004.07.003

V. Gorbunova, S. Durrleman, P. Lo, X. Pennec, and M. De-bruijne, Lung CT registration combining intensity, curves and surfaces, 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp.340-343, 2010.
DOI : 10.1109/ISBI.2010.5490341
URL : https://hal.archives-ouvertes.fr/inria-00616166

K. Gorczowski, M. Styner, J. Y. Jeong, J. Marron, J. Piven et al., Multi-Object Analysis of Volume, Pose, and Shape Using Statistical Discrimination, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.32, issue.4, pp.652-661, 2010.
DOI : 10.1109/TPAMI.2009.92

P. Gori, O. Colliot, Y. Worbe, L. Marrakchi-kacem, S. Lecomte et al., Bayesian Atlas Estimation for the Variability Analysis of Shape Complexes, Medical Image Computing and Computer-Assisted Intervention MICCAI 2013. No. 8149 in Lecture Notes in Computer Science, pp.267-274, 2013.
DOI : 10.1007/978-3-642-40811-3_34
URL : https://hal.archives-ouvertes.fr/hal-01188791

G. Fouquier, A. B. Durrleman, S. Yelnik, J. Fernndez-vidal, S. Bardinet et al., Iconic-Geometric Nonlinear Registration of a Basal Ganglia Atlas for Deep Brain Stimulation Planning, 2nd International MICCAI Workshop on Deep Brain Stimulation Methodological Challenges, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01108191

B. Gris, S. Durrleman, and A. Trouvé, A Sub-Riemannian Modular Approach for Diffeomorphic Deformations, Proceedings of the 2nd SEE Conference on Geometric Science of Information, p.22, 2015.
DOI : 10.1007/978-3-319-25040-3_5
URL : https://hal.archives-ouvertes.fr/hal-01191540

L. K. Ha, J. Krüger, P. T. Fletcher, S. Joshi, and C. T. Silva, Fast Parallel Unbiased Diffeomorphic Atlas Construction on Multi-Graphics Processing Units, Proceedings of the 9th Eurographics Conference on Parallel Graphics and Visualization. EG PGV'09, pp.41-48, 2009.

H. Hufnagel, X. Pennec, J. Ehrhardt, N. Ayache, and H. Handels, Computation of a Probabilistic Statistical Shape Model in a Maximum-a-posteriori Framework, Methods of Information in Medicine, vol.48, issue.4, pp.314-319, 2009.
DOI : 10.3414/ME9228
URL : https://hal.archives-ouvertes.fr/inria-00616088

S. Kurtek, E. Klassen, Z. Ding, S. W. Jacobson, J. B. Jacobson et al., Parameterization-Invariant Shape Comparisons of Anatomical Surfaces, IEEE Transactions on Medical Imaging, vol.30, issue.3, pp.849-858, 2011.
DOI : 10.1109/TMI.2010.2099130

H. Lombaert and J. Peyrat, Joint Statistics on Cardiac Shape and Fiber Architecture, Medical Image Computing and Computer-Assisted Intervention MICCAI 2013. No. 8150 in Lecture Notes in Computer Science, 2013.
DOI : 10.1007/978-3-642-40763-5_61

J. Ma, M. I. Miller, A. Trouvé, and L. Younes, Bayesian template estimation in computational anatomy, NeuroImage, vol.42, issue.1, pp.252-261, 2008.
DOI : 10.1016/j.neuroimage.2008.03.056

J. Ma, M. I. Miller, and L. Younes, A Bayesian Generative Model for Surface Template Estimation, International Journal of Biomedical Imaging, vol.23, issue.1, 2010.
DOI : 10.1007/BF02432002
URL : http://doi.org/10.1155/2010/974957

T. Mansi, I. Voigt, B. Leonardi, X. Pennec, S. Durrleman et al., A Statistical Model for Quantification and Prediction of Cardiac Remodelling: Application to Tetralogy of Fallot, IEEE Transactions on Medical Imaging, vol.30, issue.9, pp.1605-1616, 2011.
DOI : 10.1109/TMI.2011.2135375
URL : https://hal.archives-ouvertes.fr/inria-00616185

Y. E. Nesterov, A method for solving the convex programming problem with convergence rate $O(1/k?2$), Dokl. Akad. Nauk SSSR, vol.269, issue.655, pp.543-547, 1983.

M. Niethammer, M. Reuter, F. Wolter, S. Bouix, N. Peinecke et al., Global Medical Shape Analysis Using the Laplace-Beltrami Spectrum, Med Image Comput Comput Assist Interv, vol.10, issue.2, pp.850-857, 2007.
DOI : 10.1007/978-3-540-75757-3_103

O. Donnell, L. J. Westin, C. Golby, and A. J. , Tract-based morphometry for white matter group analysis, NeuroImage, vol.45, issue.3, pp.832-844, 2009.
DOI : 10.1016/j.neuroimage.2008.12.023

A. Palit, S. K. Bhudia, T. N. Arvanitis, G. A. Turley, M. A. Williams et al., Computational modelling of left-ventricular diastolic mechanics: Effect of fibre orientation and right-ventricle topology, Journal of Biomechanics, vol.48, issue.4, pp.604-612, 2015.
DOI : 10.1016/j.jbiomech.2014.12.054

B. Patenaude, S. M. Smith, D. N. Kennedy, and M. Jenkinson, A Bayesian model of shape and appearance for subcortical brain segmentation, NeuroImage, vol.56, issue.3, pp.907-922, 2011.
DOI : 10.1016/j.neuroimage.2011.02.046

A. Qiu, T. Brown, B. Fischl, J. Ma, and M. Miller, Atlas Generation for Subcortical and Ventricular Structures With Its Applications in Shape Analysis, IEEE Transactions on Image Processing, vol.19, issue.6, pp.1539-1547, 2010.
DOI : 10.1109/TIP.2010.2042099

P. Risholm, F. Janoos, I. Norton, A. J. Golby, I. Wells et al., Bayesian characterization of uncertainty in intra-subject non-rigid registration, Medical Image Analysis, vol.17, issue.5, pp.538-555, 2013.
DOI : 10.1016/j.media.2013.03.002

P. Savadjiev, G. J. Strijkers, A. J. Bakermans, E. Piuze, S. W. Zucker et al., Heart wall myofibers are arranged in minimal surfaces to optimize organ function, Proceedings of the National Academy of Sciences, vol.109, issue.24, pp.9248-9253, 2012.
DOI : 10.1073/pnas.1120785109

V. Siless, J. Glaunès, P. Guevara, J. Mangin, C. Poupon et al., Medical Image Computing and Computer- Assisted Intervention -MICCAI, pp.57-65, 2012.

I. J. Simpson, J. A. Schnabel, A. R. Groves, J. L. Andersson, and M. W. Woolrich, Probabilistic inference of regularisation in non-rigid registration, NeuroImage, vol.59, issue.3, pp.2438-2451, 2012.
DOI : 10.1016/j.neuroimage.2011.09.002

S. Sommer, F. Lauze, M. Nielsen, and X. Pennec, Sparse Multi-Scale Diffeomorphic Registration: The Kernel Bundle Framework, Journal of Mathematical Imaging and Vision, vol.45, issue.1, Suppl.??1, pp.292-308, 2012.
DOI : 10.1007/s10851-012-0409-0
URL : https://hal.archives-ouvertes.fr/hal-00813868

M. S. Srivastava and H. Yanagihara, Testing the equality of several covariance matrices with fewer observations than the dimension, Journal of Multivariate Analysis, vol.101, issue.6, pp.1319-1329, 2010.
DOI : 10.1016/j.jmva.2009.12.010

M. Vaillant and J. Glaunès, Surface Matching via Currents, Information Processing in Medical Imaging. No. 3565 in Lecture Notes in Computer Science, pp.381-392, 2005.
DOI : 10.1007/11505730_32
URL : https://hal.archives-ouvertes.fr/hal-00263652

M. Vaillant, M. I. Miller, L. Younes, and A. Trouvé, Statistics on diffeomorphisms via tangent space representations, NeuroImage, vol.23, pp.161-169, 2004.
DOI : 10.1016/j.neuroimage.2004.07.023

D. Wassermann, M. Toews, M. Niethammer, I. Wells, and W. , Probabilistic Diffeomorphic Registration: Representing Uncertainty, Biomedical Image Registration. No. 8545 in Lecture Notes in Computer Science, pp.72-82, 2014.
DOI : 10.1007/978-3-319-08554-8_8
URL : https://hal.archives-ouvertes.fr/hal-01095091

Y. Worbe, L. Marrakchi-kacem, S. Lecomte, R. Valabregue, F. Poupon et al., Altered structural connectivity of cortico-striato-pallido-thalamic networks in Gilles de la Tourette syndrome, Brain, vol.138, issue.2, pp.472-482, 2015.
DOI : 10.1093/brain/awu311

M. Zhang, N. Singh, and P. T. Fletcher, Bayesian Estimation of Regularization and Atlas Building in Diffeomorphic Image Registration, Information Processing in Medical Imaging. No. 7917 in Lecture Notes in Computer Science, pp.37-48, 2013.
DOI : 10.1007/978-3-642-38868-2_4