C. Arthofer, P. S. Morgan, and A. Pitiot, Hierarchical Multi-Atlas Segmentation Using Label-Specific Embeddings, Target-Specific Templates and 1165 Patch Refinement, International Workshop on Patch-based Techniques in Medical Imaging, pp.84-91, 2016.
DOI : 10.1007/978-3-319-47118-1_11

C. Askeland, O. V. Solberg, J. B. Beate, I. Reinertsen, G. A. Tangen et al., CustusX: an open-source research platform for image-guided therapy, International Journal of Computer Assisted Radiology and Surgery, vol.41, issue.4, pp.505-519, 2015.
DOI : 10.1118/1.4866884

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819973

U. Ayachit, The ParaView Guide: A Parallel Visualization Application Kitware, 2015.
DOI : 10.1201/b12985-23

O. M. Benkarim, G. Piella, M. A. Gonzalez-ballester, and G. Sanroma, Enhanced Probabilistic Label Fusion by Estimating Label Confidences Through Discriminative Learning, Medical Image Computing and Computer- Assisted Intervention -MICCAI 2016, pp.1175-505, 2016.
DOI : 10.1109/TMI.2004.828354

P. J. Besl and N. D. Mckay, A method for registration of 3-D shapes, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.14, issue.2, pp.239-1180, 1992.
DOI : 10.1109/34.121791

A. Bilger, J. Dequidt, C. Duriez, and S. Cotin, Biomechanical simulation of electrode migration for deep brain stimulation. Medical Image Computing and Computer-Assisted Intervention -MICCAI, pp.339-346, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00685737

M. Bucki, O. Palombi, M. Bailet, and Y. Payan, Doppler Ultrasound, 1185.
URL : https://hal.archives-ouvertes.fr/hal-00706803

A. D. Castellano-smith, W. R. Crum, D. L. Hill, N. A. Thacker, and P. A. Bromiley, Biomechanical simulation of atrophy in MR images, Medical Imaging 2003: Image Processing, pp.481-490, 1190.
DOI : 10.1117/12.480412

S. Chatelin, J. Vappou, S. Roth, J. S. Raul, and R. Willinger, Towards child versus adult brain mechanical properties, Journal of the mechanical 1195 behavior of biomedical materials, pp.166-173, 2012.
DOI : 10.1016/j.jmbbm.2011.09.013

I. Chen, A. M. Coffey, S. Ding, P. Dumpuri, B. M. Dawant et al., Intraoperative Brain Shift Compensation: Accounting for Dural Septa, IEEE Transactions on Biomedical Engineering, vol.58, issue.3, pp.499-508, 2011.
DOI : 10.1109/TBME.2010.2093896

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864010

N. Ayache and S. K. Warfield, Robust Nonrigid Registration to Capture Brain Shift From Intraoperative MRI, IEEE Transactions on Medical Imaging, vol.24, pp.1417-1427, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00615963

L. W. Clements, J. A. Collins, J. A. Weis, A. L. Simpson, L. B. Adams et al., Evaluation of model-based deformation correction in image-guided liver surgery via tracked intraoperative ultrasound, Journal of Medical Imaging, vol.3, issue.1, p.15003, 2016.
DOI : 10.1117/1.JMI.3.1.015003

H. Courtecuisse, J. Allard, C. Duriez, and S. Cotin, Preconditioner-Based Contact Response and Application to Cataract Surgery, International Conference on Medical Image Computing and Computer-Assisted Interven- 1215 tion, pp.315-322, 2011.
DOI : 10.1007/978-3-540-70521-5_17

URL : https://hal.archives-ouvertes.fr/hal-00685593

D. Lorenzo, C. Papademetris, X. Staib, L. H. Vives, K. P. Spencer et al., Volumetric Intraoperative Brain Deformation Compensation: Model Development and Phantom Validation, IEEE Transactions on Medical Imaging, vol.31, issue.8, pp.1607-1619, 2012.
DOI : 10.1109/TMI.2012.2197407

J. Dequidt, E. Coevoet, L. Thines, and C. Duriez, Vascular neurosurgery simulation with bimanual haptic feedback, 12th Workshop on Virtual Reality Interaction and Physical Simulation, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01226256

P. Dumpuri, R. C. Thompson, T. K. Sinha, and M. I. Miga, Automated brain shift correction using a pre-computed deformation atlas, Medical Imaging 2006: Visualization, Image-Guided Procedures, and Display, pp.61411-61411, 1225.
DOI : 10.1117/12.652350

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.3602

C. Duriez, F. Dubois, A. Kheddar, and C. Andriot, Realistic haptic rendering of interacting deformable objects in virtual environments, IEEE Transactions on Visualization and Computer Graphics, vol.12, issue.1, pp.36-47, 2006.
DOI : 10.1109/TVCG.2006.13

URL : https://hal.archives-ouvertes.fr/hal-00269404

R. Kikinis and N. Chrisochoides, Evaluation of Brain MRI Alignment with the Robust Hausdorff Distance Measures, 2008.

C. A. Felippa and B. Haugen, A unified formulation of small-strain corotational finite elements: I. Theory, Computer Methods in Applied Mechanics and Engineering, vol.194, issue.21-24, pp.2285-2335, 2005.
DOI : 10.1016/j.cma.2004.07.035

M. Ferrant, A. Nabavi, B. Macq, P. M. Black, F. A. Jolesz et al., Serial registration of intraoperative MR images of the brain, Medical Image Analysis, vol.6, issue.4, pp.337-359, 2002.
DOI : 10.1016/S1361-8415(02)00060-9

B. Fuerst, W. Wein, M. Müller, and N. Navab, Automatic ultrasound???MRI registration for neurosurgery using the 2D and 3D LC2 Metric, Medical Image Analysis, vol.18, issue.8, pp.1312-1319, 2014.
DOI : 10.1016/j.media.2014.04.008

R. R. Garlapati, A. Mostayed, G. R. Joldes, A. Wittek, B. Doyle et al., Towards measuring neuroimage misalignment, Computers in Biology and Medicine, vol.64, pp.12-23, 2015.
DOI : 10.1016/j.compbiomed.2015.06.003

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742413

R. R. Garlapati, A. Roy, G. R. Joldes, A. Wittek, A. Mostayed et al., More accurate neuronavigation data provided by biomechanical modeling instead of rigid registration, Journal of Neurosurgery, vol.120, issue.6, pp.1477-1483, 2014.
DOI : 10.3171/2013.12.JNS131165

I. J. Gerard, M. Kersten-oertel, K. Petrecca, D. Sirhan, J. A. Hall et al., Brain shift in neuronavigation of brain tumors: A review, Medical Image Analysis, vol.35, pp.403-420, 2017.
DOI : 10.1016/j.media.2016.08.007

P. Hastreiter, C. Rezk-salama, G. Soza, M. Bauer, G. Greiner et al., Strategies for brain shift evaluation, Medical Image Analysis, vol.8, issue.4, pp.447-464, 2004.
DOI : 10.1016/j.media.2004.02.001

D. L. Hill, C. R. Maurer-jr, R. J. Maciunas, J. A. Barwise, M. J. Fitzpatrick et al., Measurement of Intraoperative Brain Surface Deformation under a Craniotomy, Neurosurgery, vol.43, issue.3, pp.514-526, 1998.
DOI : 10.1097/00006123-199809000-00066

J. Hu, X. Jin, J. B. Lee, L. Zhang, V. Chaudary et al., Intraoperative brain shift prediction using a 3D inhomogeneous patient-specific finite element model, Journal of Neurosurgery, vol.106, issue.1, pp.164-169, 2007.
DOI : 10.3171/jns.2007.106.1.164

S. Ji, Z. Wu, A. Hartov, D. W. Roberts, and K. D. Paulsen, Mutualinformation-based image to patient re-registration using intraoperative ultrasound in image-guided neurosurgery, Medical physics, p.35, 2008.
DOI : 10.1118/1.2977728

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673587

G. R. Joldes, A. Wittek, and K. Miller, Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, Medical Image Analysis, vol.13, issue.6, p.1275, 2009.
DOI : 10.1016/j.media.2008.12.001

G. R. Joldes, A. Wittek, and K. Miller, Real-time nonlinear finite element computations on GPU ??? Application to neurosurgical simulation, Computer Methods in Applied Mechanics and Engineering, vol.199, issue.49-52, pp.3305-3314, 2010.
DOI : 10.1016/j.cma.2010.06.037

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3003932

T. Kaster, I. Sack, and A. Samani, Measurement of the hyperelastic properties of ex vivo brain tissue slices, Journal of Biomechanics, vol.44, issue.6, pp.1158-1163, 2011.
DOI : 10.1016/j.jbiomech.2011.01.019

S. A. Kruse, M. A. Dresner, P. J. Rossman, J. P. Felmlee, C. R. Jack et al., Palpation of the Brain Using Magnetic Resonance Elastography, International Society for Magnetic Resonance in Medicine, pp.1285-258, 1999.

S. A. Kruse, G. H. Rose, K. J. Glaser, A. Manduca, J. P. Felmlee et al., Magnetic resonance elastography of the brain, NeuroImage, vol.39, issue.1, pp.231-237, 2008.
DOI : 10.1016/j.neuroimage.2007.08.030

M. Li, A. Wittek, and K. Miller, Efficient Inverse Isoparametric Mapping Algorithm for Whole-Body Computed Tomography Registration Using Deformations Predicted by Nonlinear Finite Element Modeling, Journal of Biomechanical Engineering, vol.136, issue.8, p.84503, 2014.
DOI : 10.1115/1.4027667

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991307

P. J. Mccracken, A. Manduca, J. P. Felmlee, and R. L. Ehman, Mechanical transient-based magnetic resonance elastography, Magnetic Resonance 1295 in Medicine, pp.628-639, 2005.
DOI : 10.1016/S0140-6736(86)90837-8

L. Mercier, V. Fonov, C. Haegelen, D. Maestro, R. F. Petrecca et al., Comparing two approaches to rigid registration of three-dimensional ultrasound and magnetic resonance images for neurosurgery, International Journal of Computer Assisted Radiology and Surgery, vol.62, issue.3 Suppl 1, pp.125-136, 2012.
DOI : 10.1227/01.neu.0000317377.15196.45

M. I. Miga, K. Sun, I. Chen, L. W. Clements, T. S. Pheiffer et al., Clinical evaluation of a model-updated image-guidance approach to brain shift compensation: experience in 16 cases, International Journal of Computer Assisted Radiology and Surgery, vol.61, issue.6, pp.1467-1474, 2015.
DOI : 10.1109/TBME.2014.2308299

K. Miller and K. Chinzei, Mechanical properties of brain tissue in tension, Journal of Biomechanics, vol.35, issue.4, pp.483-490, 2002.
DOI : 10.1016/S0021-9290(01)00234-2

K. Miller, A. Horton, G. R. Joldes, and A. Wittek, Beyond finite elements: A comprehensive, patient-specific neurosurgical simulation utilizing a meshless method, Journal of Biomechanics, vol.45, issue.15, pp.2698-2701, 2012.
DOI : 10.1016/j.jbiomech.2012.07.031

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871993

K. Miller, G. R. Joldes, D. Lance, and A. Wittek, Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering, vol.33, issue.4, pp.121-134, 2007.
DOI : 10.1002/cnm.887

K. Miller and J. Lu, On the prospect of patient-specific biomechanics without patient-specific properties of tissues, Journal of the Mechanical Behavior of Biomedical Materials, vol.27, pp.154-166, 2013.
DOI : 10.1016/j.jmbbm.2013.01.013

A. Mohammadi, A. Ahmadian, D. Azar, A. , D. Sheykh et al., Estimation of intraoperative brain shift by combination of stereovision and doppler ultrasound: phantom and animal model study, International Journal of Computer Assisted Radiology and Surgery, vol.189, issue.5, pp.1753-1764, 2015.
DOI : 10.2214/AJR.06.1247

F. Morin, M. Chabanas, H. Courtecuisse, and Y. Payan, Biomechanical Modeling of Brain Soft Tissues for Medical Applications, Biomechanics of Living Organs: Hyperelastic Laws for Finite Element Modeling, 2017.
DOI : 10.1016/B978-0-12-804009-6.00006-7

F. Morin, H. Courtecuisse, M. Chabanas, and Y. Payan, Rest shape computation for highly deformable model of brain, Computer Methods in Biomechanics and Biomedical Engineering, vol.18, issue.sup1, 2006.
DOI : 10.1016/j.jfluidstructs.2011.08.002

URL : https://hal.archives-ouvertes.fr/hal-01217673

A. Mostayed, R. R. Garlapati, G. R. Joldes, A. Wittek, A. Roy et al., Biomechanical Model as a Registration Tool for Image-Guided Neurosurgery: Evaluation Against BSpline Registration, Annals of Biomedical Engineering, vol.26, issue.11, pp.2409-2425, 2013.
DOI : 10.1016/j.patrec.2004.09.022

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3939696

M. Müller, J. Dorsey, L. Mcmillan, R. Jagnow, and B. Cutler, Stable real-time deformations, Proceedings of the 2002 ACM SIGGRAPH/Eurographics symposium on Computer animation , SCA '02, pp.49-54, 2002.
DOI : 10.1145/545261.545269

A. Nabavi, P. M. Black, D. T. Gering, C. Westin, V. Mehta et al., Serial Intraoperative Magnetic Resonance Imaging of Brain Shift, Neurosurgery, vol.48, pp.787-798, 2001.

S. Nakajima, H. Atsumi, R. Kikinis, T. M. Moriarty, D. C. Metcalf et al., Use of Cortical Surface Vessel Registration for Image-guided Neurosurgery, Neurosurgery, vol.40, issue.6, pp.1201-1210, 1997.
DOI : 10.1097/00006123-199706000-00018

M. Nesme, Y. Payan, and F. Faure, Efficient, physically plausible finite elements, Eurographics, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00394480

C. Nimsky, O. Ganslandt, S. Cerny, P. Hastreiter, G. Greiner et al., Quantification of, Visualization of, and Compensation for Brain Shift Using Intraoperative Magnetic Resonance Imaging, Neurosurgery, vol.47, issue.5, pp.1070-1080, 1345.
DOI : 10.1097/00006123-200011000-00008

C. Nimsky, O. Ganslandt, P. Hastreiter, and R. Fahlbush, Intraoperative compensation for brain shift, Surgical Neurology, vol.56, issue.6, pp.357-364, 2001.
DOI : 10.1016/S0090-3019(01)00628-0

K. D. Paulsen, M. I. Miga, F. E. Kennedy, J. Hoopes, A. Hartov et al., A computational model for tracking subsurface tissue deformation during stereotactic neurosurgery, IEEE Transactions on Biomedical Engineering, vol.46, issue.2, pp.213-225, 1999.
DOI : 10.1109/10.740884

V. M. Pereira, I. Smith-ockeloen, O. Brina, D. Babic, M. Breeuwer et al., Volumetric Measurements of Brain Shift Using Intraoperative Cone-Beam Computed Tomography, Operative Neurosurgery, vol.12, issue.1, pp.4-13, 2016.
DOI : 10.1227/NEU.0000000000000999

M. Prastawa, E. Bullit, and G. Gerig, Simulation of brain tumors in MR images for evaluation of segmentation efficacy, Medical Image Analysis, vol.13, issue.2, pp.1360-297, 2009.
DOI : 10.1016/j.media.2008.11.002

I. Reinertsen, M. Descoteaux, K. Siddiqi, and D. L. Collins, Validation of vessel-based registration for correction of brain shift, Medical Image Analysis, vol.11, issue.4, pp.374-388, 2007.
DOI : 10.1016/j.media.2007.04.002

I. Reinertsen, F. Lindseth, G. Unsgard, and D. L. Collins, Clinical validation of vessel-based registration for correction of brain-shift, Medical Image Analysis, vol.11, issue.6, pp.673-684, 2007.
DOI : 10.1016/j.media.2007.06.008

H. Rivaz and D. L. Collins, Deformable registration of preoperative MR, pre-resection ultrasound, and post-resection ultrasound images of neurosurgery, International Journal of Computer Assisted Radiology and Surgery, vol.21, issue.2, pp.1017-1028, 2015.
DOI : 10.1109/TMI.2010.2091966

D. W. Roberts, A. Hartov, F. E. Kennedy, M. I. Miga, and K. D. Paulsen, Intraoperative Brain Shift and Deformation: A Quantitative Analysis of Cortical Displacement in 28 Cases, Neurosurgery, vol.43, issue.4, pp.1375-749, 1998.
DOI : 10.1097/00006123-199810000-00010

I. Sack, B. Beierbach, J. Wuerfel, K. Dieter, U. Hamhaber et al., The impact of aging and gender on brain viscoelasticity, NeuroImage, vol.46, issue.3, pp.652-657, 2009.
DOI : 10.1016/j.neuroimage.2009.02.040

K. Sase, A. Fukuhara, T. Tsujita, and A. Konno, GPU-accelerated surgery simulation for opening a brain fissure, ROBOMECH Journal, vol.4, issue.1, pp.1-16, 2015.
DOI : 10.15676/ijeei.2012.4.1.2

URL : http://doi.org/10.1186/s40648-015-0040-0

P. Schiavone, F. Chassat, T. Boudou, E. Promayon, F. Valdivia et al., In vivo measurement of human brain elasticity using a light aspiration device, Medical Image Analysis, vol.13, issue.4, pp.673-678, 2009.
DOI : 10.1016/j.media.2009.04.001

URL : https://hal.archives-ouvertes.fr/hal-00374101

W. Schroeder, K. Martin, and B. Lorensen, The Visualization Toolkit Kitware, 2006.

M. Shakeri, E. Ferrante, S. Tsogkas, S. Lippe, S. Kadoury et al., Prior-Based Coregistration and Cosegmentation, Medical Image Computing and Computer-Assisted Intervention -MICCAI 2016, pp.1390-529, 2016.
DOI : 10.1109/TMI.2011.2163944

URL : https://hal.archives-ouvertes.fr/hal-01349189

S. M. Smith, Fast robust automated brain extraction, Human Brain Mapping, vol.20, issue.3, pp.143-155, 2002.
DOI : 10.1002/hbm.10062

H. Sun, K. E. Lunn, H. Farid, Z. Wu, D. W. Roberts et al., Stereopsis-Guided Brain Shift Compensation, IEEE Transac- 1395 tions on Medical Imaging, pp.1039-1052, 2005.

H. Sun, D. W. Roberts, H. Farid, Z. Wu, A. Hartov et al., Cortical Surface Tracking Using a Stereoscopic Operating Microscope, Operative Neurosurgery, vol.56, pp.86-97, 2005.
DOI : 10.1227/01.NEU.0000146263.98583.CC

M. I. Miga, Near Real-Time Computer Assisted Surgery for Brain Shift Correction Using Biomechanical Models, IEEE Journal of Translational Engineering in Health and Medicine, vol.2, pp.1-13, 2014.

A. A. Taha and A. Hanbury, Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool, BMC Medical Imaging, vol.1, issue.3, p.29, 2015.
DOI : 10.1002/jmri.22473

URL : http://doi.org/10.1186/s12880-015-0068-x

A. Tavner, T. D. Roy, K. Hor, M. Majimbi, G. R. Joldes et al., On the appropriateness of modelling brain parenchyma as a biphasic continuum, Journal of the Mechanical Behavior of Biomedical Materials, vol.61, pp.511-518, 2016.
DOI : 10.1016/j.jmbbm.2016.04.010

K. Uffmann, S. Maderwald, A. De-greiff, and M. E. Ladd, Determination 1410 of Gray and White Matter Elasticity with MR Elastography, Proc. Intl. Soc, 2004.

A. Valencia, B. Benjamin, and J. H. Ortega, Modeling of Brain Shift Phenomenon for Different Craniotomies and Solid Models, Journal of Applied Mathematics, vol.24, issue.5, 2012.
DOI : 10.1109/TMI.2005.856734

F. Serial and . Xfem-, Based Update of Preoperative Brain Images Using Intra- 1420 operative MRI, International Journal of Biomedical Imaging, p.872783, 2012.

M. Wan, Z. Liang, Q. Ke, L. Hong, I. Bitter et al., Automatic Centerline Extraction for Virtual Colonoscopy, IEEE Transactions on Medical Imaging, vol.21, pp.1450-1460, 2002.

A. Wittek, T. Hawkins, and K. Miller, On the unimportance of constitutive models in computing brain deformation for image-guided surgery, Biomechanics and Modeling in Mechanobiology, vol.5, issue.1, pp.77-84, 2009.
DOI : 10.1115/1.3426188

A. Wittek, K. Miller, R. Kikinis, and S. K. Warfield, Patient-specific model of brain deformation: Application to medical image registration, Journal of Biomechanics, vol.40, issue.4, pp.919-929, 2007.
DOI : 10.1016/j.jbiomech.2006.02.021

P. A. Yushkevich, J. Piven, C. Hazlett, H. Smith, R. Ho et al., User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability, NeuroImage, vol.31, issue.3, pp.31-1116, 2006.
DOI : 10.1016/j.neuroimage.2006.01.015

J. Y. Zhang, G. R. Joldes, A. Wittek, and K. Miller, Patient-specific computational biomechanics of the brain without segmentation and meshing, International Journal for Numerical Methods in Biomedical Engineering, vol.199, issue.49-52, pp.293-308, 1440.
DOI : 10.1016/j.cma.2010.06.037