Bibliography

Major publications by the team in recent years

1C. Ciofolo, C. Barillot.

Atlas-based segmentation of 3D cerebral structures with competitive level sets and fuzzy control, in: Medical Image Analysis, 2009, vol. 13, n^o 3, p. 456–470.
2P. Coupé, P. Hellier, C. Kervrann, C. Barillot.

NonLocal Means-based Speckle Filtering for Ultrasound Images, in: IEEE Transactions on Image Processing, 2009.
3P. Coupé, P. Yger, S. Prima, P. Hellier, C. Kervrann, C. Barillot.

An Optimized Blockwise Non Local Means Denoising Filter for 3D Magnetic Resonance Images, in: IEEE Transactions on Medical Imaging, April 2008, vol. 27, n^o 4, p. 425-441.

http://hal.inria.fr/inria-00332014/en/
4C. De Guibert, C. Maumet, J.-C. Ferré, P. Jannin, A. Biraben, C. Allaire, C. Barillot, E. Le Rumeur.

FMRI language mapping in children: A panel of language tasks using visual and auditory stimulation without reading or metalinguistic requirements, in: NeuroImage, February 2010, vol. 51, n^o 2, p. 897–909.

http://www.hal.inserm.fr/inserm-00461666/en/
5C. Haegelen, D. García-Lorenzo, F. Le Jeune, J. Peron, B. Gibaud, L. Riffaud, G. Brassier, C. Barillot, M. Verin, X. Morandi.

SPECT and PET analysis of subthalamic stimulation in Parkinson's disease: analysis using a manual segmentation, in: J Neurol, 2010, vol. 257, n^o 3, p. 375-82.
6P. Jannin, X. Morandi.

Surgical models for computer-assisted neurosurgery, in: Neuroimage, 2007, vol. 37, n^o 3, p. 783–91.
7F. Lalys, C. Haegelen, J.-C. Ferré, O. El-Ganaoui, P. Jannin.

Construction and assessment of a 3T MRI brain template, in: Neuroimage, 2010, vol. 49, n^o 1, p. 345-354. [ DOI : 10.1016/j.neuroimage.2009.08.007 ]

http://www.hal.inserm.fr/inserm-00546487/en/
8A. Mechouche, X. Morandi, C. Golbreich, B. Gibaud.

A Hybrid System Using Symbolic and Numeric Knowledge for the Semantic Annotation of Sulco-Gyral Anatomy in Brain MRI Images, in: IEEE Transactions on Medical Imaging, August 2009, vol. 28, n^o 8, p. 1165–1178.
9F. Rousseau, P. Hellier, C. Barillot.

A Novel Temporal Calibration Method for 3-D Ultrasound, in: IEEE Transactions on Medical Imaging, August 2006, vol. 25, n^o 8, p. 1108–1112.

http://hal.inria.fr/inria-00001215/en/
10L. Temal, M. Dojat, G. Kassel, B. Gibaud.

Towards an ontology for sharing medical images and regions of interest in neuroimaging, in: J Biomed Inform, 2008, vol. 41, n^o 5, p. 766–778.

http://www.hal.inserm.fr/inserm-00344293/en/

Publications of the year

Doctoral Dissertations and Habilitation Theses

11F. Lalys.

Automatic recognition of low-level and high-level surgical tasks in the Operating Room from video images, Université Rennes 1, May 2012.

http://hal.inria.fr/tel-00695648
12L. Riffaud.

Enregistrement des procédures chirurgicales crâniennes et rachidiennes, et analyse des " workflows " pour l'étude du processus chirurgical, Université Rennes 1, June 2012.

http://hal.inria.fr/tel-00737144

Articles in International Peer-Reviewed Journals

13A. Balzeau, D. Grimaud-Hervé, F. Détroit, R. Holloway, B. Combès, S. Prima.

First description of the Cro-Magnon 1 endocast and study of brain variation and evolution in anatomically modern Homo sapiens, in: Bulletins et mémoires de la Société d'anthropologie de Paris, 2012, p. 1–18.

http://dx.doi.org/10.1007/s13219-012-0069-z
14S. Chen, P. Hellier, M. Marchal, J.-Y. Gauvrit, R. Carpentier, X. Morandi, D. L. Collins.

An anthropomorphic polyvinyl alcohol brain phantom based on Colin27 for use in multimodal imaging, in: Medical Physics, January 2012, vol. 39, n^o 1, p. 554-561. [ DOI : 10.1118/1.3673069 ]

http://hal.inria.fr/hal-00766567
15O. Commowick, A. Akhondi-Asl, S. Warfield.

Estimating A Reference Standard Segmentation with Spatially Varying Performance Parameters: Local MAP STAPLE, in: IEEE Transactions on Medical Imaging, August 2012, vol. 31, n^o 8, p. 1593-1606. [ DOI : 10.1109/TMI.2012.2197406 ]

http://hal.inria.fr/inserm-00697775
16J.-C. Ferré, J. Petr, E. Bannier, C. Barillot, J.-Y. Gauvrit.

Improving quality of arterial spin labeling MR imaging at 3 Tesla with a 32-channel coil and parallel imaging., in: Journal of Magnetic Resonance Imaging, May 2012, vol. 35, n^o 5, p. 1233-9. [ DOI : 10.1002/jmri.23586 ]

http://hal.inria.fr/inserm-00723540
17G. Forestier, F. Lalys, L. Riffaud, B. Trelhu, P. Jannin.

Classification of surgical processes using dynamic time warping., in: Journal of Biomedical Informatics, January 2012, vol. 45, p. 255-264. [ DOI : 10.1016/j.jbi.2011.11.002 ]

http://hal.inria.fr/inserm-00669624
18J.-C. Gentric, J.-C. Ferré, H. Raoult, F. Eugène, J.-Y. Gauvrit.

Endovascular treatment of inferior petrosal sinus dural arteriovenous fistula via percutaneous puncture of the superior ophthalmic vein., in: Journal de Neuroradiologie / Journal of Neuroradiology, May 2012, epub ahead of print. [ DOI : 10.1016/j.neurad.2012.03.009 ]

http://hal.inria.fr/inserm-00722523
19C. Person, V. Louis-Dorr, S. Poussier, O. Commowick, G. Malandain, L. Maillard, D. Wolf, N. Gilet, V. Roch, G. Karcher, P.-Y. Marie.

Voxel-based quantitative analysis of brain images from F-18 Fluorodeoxyglucose Positron Emission Tomography with a Block-Matching algorithm for spatial normalization, in: Clinical Nuclear Medicine, 2012, vol. 37, n^o 3, p. 268-273. [ DOI : 10.1097/RLU.0b013e3182443b2d ]

http://hal.inria.fr/hal-00651731
20J. Petr, J.-C. Ferré, H. Raoult, E. Bannier, J.-Y. Gauvrit, C. Barillot.

Template-based approach for detecting motor task activation-related hyperperfusion in pulsed ASL data, in: Human Brain Mapping, 2012, (to appear).
21H. Raoult, J.-C. Ferré, J. Petr, E. Bannier, A. Stamm, C. Barillot, J.-Y. Gauvrit.

Functional arterial spin labeling: Optimal sequence duration for motor activation mapping in clinical practice., in: Journal of Magnetic Resonance Imaging, August 2012, epub ahead of print. [ DOI : 10.1002/jmri.23782 ]

http://hal.inria.fr/inserm-00727889
22R. Seizeur, N. Wiest-Daesslé, S. Prima, C. Maumet, J.-C. Ferré, X. Morandi.

Corticospinal tractography with morphological, functional and diffusion tensor MRI: a comparative study of four deterministic algorithms used in clinical routine., in: Surg Radiol Anat, October 2012, vol. 34, n^o 8, p. 709-19. [ DOI : 10.1007/s00276-012-0951-x ]

http://hal.inria.fr/inserm-00766622
23R. Suarez, O. Commowick, S. Prabhu, S. Warfield.

Automated delineation of white matter fiber tracts with a multiple region-of-interest approach., in: NeuroImage, February 2012, vol. 59, n^o 4, p. 3690-3700. [ DOI : 10.1016/j.neuroimage.2011.11.043 ]

http://hal.inria.fr/inserm-00657707

International Conferences with Proceedings

24E. Bannier, C. Maumet, A. Pasnicu, J.-C. Ferré, E. Pasqualini, A. Biraben, J.-Y. Gauvrit, C. Barillot.

Voxel Based Analysis of 3D Double Inversion Recovery for the detection of cortical abnormalities in drug resistant epilepsy, in: International Society for Magnetic Resonance in Medicine 20th Annual Meeting & Exhibition (ISMRM 2012), Melbourne, Australia, May 2012, 3244 p.

http://hal.inria.fr/inserm-00686834
25F. Cao, O. Commowick, E. Bannier, J.-C. Ferré, G. Edan, C. Barillot.

MRI Estimation of T1 Relaxation Time Using a Constrained Optimization Algorithm, in: MBIA 2012, Nice, France, P.-T. Yap, et al. (editors), October 2012, p. 203-214.

http://hal.inria.fr/inserm-00723849
26O. Commowick, A. Stamm.

Non-Local Robust Detection of DTI White Matter Differences with Small Databases, in: 15th International Conference on Medical Image Computing and Computer Assisted Intervention, Nice, France, LNCS, October 2012, vol. 7512, p. 476-484. [ DOI : 10.1007/978-3-642-33454-2_59 ]

http://hal.inria.fr/inserm-00716094
27O. Commowick, N. Wiest-Daesslé, S. Prima.

Automated diffeomorphic registration of anatomical structures with rigid parts: Application to dynamic cervical MRI, in: 15th International Conference on Medical Image Computing and Computer Assisted Intervention, Nice, France, LNCS, October 2012, vol. 7511, p. 163-170. [ DOI : 10.1007/978-3-642-33418-4_21 ]

http://hal.inria.fr/inserm-00716106
28O. Commowick, N. Wiest-Daesslé, S. Prima.

Block-Matching Strategies for Rigid Registration of Multimodal Medical Images, in: 9th IEEE International Symposium on Biomedical Imaging (ISBI'2012), Barcelona, Spain, May 2012, p. 700-703. [ DOI : 10.1109/ISBI.2012.6235644 ]

http://hal.inria.fr/inserm-00681610
29I. Corouge, A. Esquevin, F. Lejeune, J.-C. Ferré, E. Bannier, C. Merck, S. Belliard, C. Barillot, J.-Y. Gauvrit.

Arterial Spin Labeling at 3T in semantic dementia: perfusion abnormalities detection and comparison with FDG-PET, in: MICCAI 2012 Workshop on Novel Biomarkers for Alzheimer's Disease and Related Disorders, Nice, France, L. Wang, S. Ourselin (editors), September 2012, p. 32-40.

http://hal.inria.fr/inserm-00730431
30A. Crimi, O. Commowick, G. Edan, C. Barillot.

Multiple Sclerosis Lesions Evolution in Patients with Clinically Isolated Syndrome, in: SPIE Medical Imaging: Image Processing, Orlando, FL, SPIE, 2013.
31A. Esquevin, I. Corouge, E. Bannier, J.-C. Ferré, C. Merck, F. Lejeune, S. Belliard, C. Barillot, J.-Y. Gauvrit.

Arterial spin labeling at 3T in semantic dementia: Perfusion abnormalities detection, in: ISMRM scientific workshop. Perfusion MRI: Standardization, Beyond CBF & Everyday Clinical Applications, Netherlands, October 2012, 39 p.

http://www.hal.inserm.fr/inserm-00772291
32A. Martín, J. Garamendi, E. Schiavi.

MRI TV-Rician Denoising, in: International Conference on Bio-inspired Systems and Signal Processing, 2012, p. 15-24.
33C. Maumet, P. Maurel, E. Bannier, J.-C. Ferré, C. Barillot.

A contrario detection of focal brain perfusion abnormalities based on an Arterial Spin Labeling template, in: 9th IEEE International Symposium on Biomedical Imaging (ISBI'2012), Barcelona, Spain, May 2012, p. 1176-1179.

http://hal.inria.fr/inserm-00677106
34C. Maumet, P. Maurel, J.-C. Ferré, E. Bannier, C. Barillot.

Using negative signal in mono-TI pulsed arterial spin labeling to outline pathological increases in arterial transit times, in: ISMRM Scientific Workshop. Perfusion MRI: Standardization, Beyond CBF & Everyday Clinical Applications, Amsterdam, Netherlands, October 2012, 42 p.

http://hal.inria.fr/inserm-00767119
35C. Maumet, P. Maurel, J.-C. Ferré, C. Barillot.

A comprehensive framework for the detection of individual brain perfusion abnormalities using Arterial Spin Labeling, in: International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'12), Nice, France, October 2012, p. 542-549.

http://hal.inria.fr/inserm-00720593
36C. Maumet, P. Maurel, J.-C. Ferré, C. Barillot.

Automatic detection of perfusion abnormalities based on an Arterial Spin Labeling template, in: ISMRM scientific workshop. Perfusion MRI: Standardization, Beyond CBF & Everyday Clinical Applications, Netherlands, October 2012, 8 p.

http://hal.inria.fr/inserm-00767115
37C. Maumet, P. Maurel, J.-C. Ferré, C. Barillot.

Robust Cerebral Blood Flow Map Estimation in Arterial Spin Labeling, in: International Workshop on Multimodal Brain Image Analysis (MBIA'2012), held in conjunction with MICCAI 2012, Nice, France, October 2012, p. 215-224.

http://hal.inria.fr/inserm-00724974
38M. Mehri, F. Lalys, C. Maumet, C. Haegelen, P. Jannin.

Analysis of electrodes' placement and deformation in deep brain stimulation from medical images, in: SPIE medical imaging, San diego, CA, United States, February 2012, p. 8316-32.

http://hal.inria.fr/inserm-00669674
39S. Prima, O. Commowick.

Multimodal rigid-body registration of 3D brain images using bilateral symmetry, in: Medical Imaging 2013: Image Processing, Orlando, United States, February 2013, p. 1-8.

http://hal.inria.fr/inserm-00766642
40S. Prima, G. Subsol, J. Braga, J. F. Garamendi Bragado, B. Combès, J. Dumoncel, D. Falk.

Comparison of endocranial and ectocranial "symmetry planes" and application to the virtual reconstruction of hominid fossils, in: 82nd annual meeting of the American Association of Physical Anthropologists, United States, 2013, p. 1-1.

http://hal.inria.fr/inserm-00767670
41A. Stamm, O. Commowick, P. Perez, C. Barillot.

Multifiber Deterministic Streamline Tractography of the Corticospinal Tract Based on a New Diffusion Model: Part II, in: MICCAI 2012 DTI Tractography Challenge, Nice, France, October 2012, p. 12-20.

http://hal.inria.fr/inserm-00725366
43A. Stamm, P. Perez, C. Barillot.

A new multi-fiber model for low angular resolution diffusion MRI, in: Biomedical Imaging (ISBI), 2012 9th IEEE International Symposium on, 2012, p. 936-939.
44M. Taquet, B. Scherrer, O. Commowick, J. Peters, M. Sahin, B. Macq, S. Warfield.

Registration and Analysis of White Matter Group Differences with a Multi-Fiber Model, in: 15th International Conference on Medical Image Computing and Computer Assisted Intervention, Nice, France, LNCS, October 2012, vol. 7512, p. 313-320.

http://hal.inria.fr/inserm-00716110
45L. Yu, P. Maurel, C. Barillot, R. Gribonval.

Compressive Matched Filter for Cerebral Blood Flow Quantification with ASL: sampling diversity or repetition?, in: Miccai Workshop on Sparsity Techniques in Medical Imaging (STMI'12), Nice, France, October 2012, p. 0-0.

http://hal.inria.fr/hal-00762774

National Conferences with Proceeding

46G. Forestier, F. Lalys, L. Riffaud, B. Trelhu, P. Jannin.

Clustering de séquences d'activités pour l'étude de procédures neurochirurgicales, in: 12e Conférence Internationale Francophone sur l'Extraction et la Gestion des Connaissances, Bordeaux, France, February 2012, p. 489-494.

http://hal.inria.fr/inserm-00670007

Scientific Books (or Scientific Book chapters)

47A. Martín, J. Garamendi, E. Schiavi.

Two Efficient Primal-Dual Algorithms for MRI Rician Denoising, in: Computational modelling of objects represented in images III: Fundamentals, Methods and Applications, CRC Press, 2012, p. 290-297.

Internal Reports

48B. Combès, S. Prima.

A new efficient EM-ICP algorithm for non-linear registration of 3D point sets, Inria, January 2012, n^o RR-7853.

http://hal.inria.fr/hal-00656388

References in notes

49A. Abadie, B. Combès, C. Haegelen, S. Prima.

CLARCS, a C++ Library for Automated Registration and Comparison of Surfaces: Medical Applications, in: MICCAI Workshop on Mesh Processing in Medical Image Analysis (MeshMed'2011), Toronto, Canada, September 2011, p. 117-126.

http://hal.inria.fr/inria-00626270/en
50B. Combès, C. Garraud, X. Morandi, S. Prima, P. Hellier.

MRI-free neuronavigation for transcranial magnetic stimulation in severe depression, in: MICCAI Workshop on Mesh Processing in Medical Image Analysis (MeshMed'2011), Canada, September 2011, p. 29-38.

http://hal.inria.fr/inserm-00633573/en
51B. Combès, S. Prima.

New algorithms to map asymmetries of 3D surfaces, in: 11th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'2008), New-York, États-Unis, 2008, vol. 11 (Pt 1), p. 17-25. [ DOI : 10.1007/978-3-540-85988-8_3 ]

http://hal.inria.fr/inria-00331762
52I. Corouge, C. Barillot.

Use of a probabilistic shape model for non-linear registration of 3D scattered data, in: IEEE Int. Conf. on Image Processing, ICIP'2001, Thessaloniki, Greece, IEEE Press, 2001, p. 149-152.
53I. Corouge, M. Dojat, C. Barillot.

Statistical shape modeling of low level visual area borders, in: Medical Image Analysis, 2004, vol. 8, n^o 3, p. 353-360. [ DOI : 10.1016/j.media.2004.06.023 ]

http://authors.elsevier.com/sd/article/S1361841504000350
54I. Corouge, P. Hellier, B. Gibaud, C. Barillot.

Inter-individual functional mapping: a non linear local approach, in: Neuroimage, 2003, vol. 19, n^o 4, p. 1337–1348.

http://dx.doi.org/10.1016/S1053-8119(03)00158-7
55P. Hellier, J. Ashburner, I. Corouge, C. Barillot, K. Friston.

Inter subject registration of functional and anatomical data using SPM, in: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2002, Tokyo, R. Kikinis, R. Ellis, T. Dohi (editors), Lecture Notes in Computer Sciences, Springer-Verlag, Tokyo, 2002, vol. LNCS-2489, p. 590-587.

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