The creation of a brain atlas for image guided neurosurgery using serial histological data

NeuroImage

Volumn 30, Issue 2, 2006, Pages 359-376

  Chakravarty, M Mallar ^a   Bertrand, Gilles ^a,b   Hodge, Charles P ^c   Sadikot, Abbas F ^a,b   Collins, D Louis ^a  

^a MCGILL UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c NONE

Author keywords

Basal ganglia; Brain atlas; Functional neurosurgery; Image guided neurosurgery; MRI; Neurosurgery; Registration; Segmentation; Thalamus

Indexed keywords

ALGORITHM; ARTICLE; AUTOPSY; BASAL GANGLION; BRAIN REGION; BRAIN SLICE; GEOMETRY; HISTOLOGY; HUMAN; IMAGE INTENSIFIER; NEUROIMAGING; NEUROSURGERY; NONLINEAR SYSTEM; NUCLEAR MAGNETIC RESONANCE IMAGING; PRIORITY JOURNAL; STAINING; THALAMUS; THREE DIMENSIONAL IMAGING;

ALGORITHMS; BASAL GANGLIA; BRAIN; DATA INTERPRETATION, STATISTICAL; DATABASES, FACTUAL; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; NEUROSURGICAL PROCEDURES; NONLINEAR DYNAMICS; SOFTWARE; STEREOTAXIC TECHNIQUES; THALAMUS;

EID: 33645127544     PISSN: 10538119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2005.09.041     Document Type: Article

References (62)

1. E. Afshar, E.S. Watkins, and J.C. Yap Stereotactic Atlas of the Human Brainstem and Cerebellar Nuclei 1978 Raven Press New York
2. J.D. Atkinson, D.L. Collins, G. Bertrand, T.M. Peters, G.B. Pike, and A.F. Sadikot Optimal location of thalamotomy lesions for tremor associated with Parkinson disease: a probablisitic analysis based on postoperative magnetic resonance imaging and integrated digital atlas J. Neurosurg. 96 5 2002 672 680 (October)
3. E. Bardinet, A.C.F Colchester, A. Roche, Y. Zhu, Y. He, S. Ourselin, B. Nailon, S.A. Hojjat, J. Ironside, S. Al-Sarraj, N. Ayache, and J. Wardlaw Registration of reconstructed post mortem optical data with MR scans of the same patient W. Niessen M. Viergever Fourth International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2003, Lecture Notes in Computer Science 2001 Springer Utrecht
4. T.E.J. Behrens, H. Johansen-Berg, M.W. Woolrich, S.M. Smith, C.A.M. Wheeler-Kingshott, P.A. Boulby, G.J. Barker, E.L. Sillery, K. Sheehan, O. Ciccarelli, A.J. Thompson, J.M. Brady, and P.M. Matthews Non-invasive mapping of connections between human thalamus and cortex using diffusion imaging Nat. Neurosci. 6 2003 750 757
5. G. Bertrand, A. Olivier, and C.J. Thompson The computerized brain atlas: its use in stereotaxic surgery Trans. Am. Neurol. Ass. 98 1973 233 237
6. F.L. Bookstein Principal warps: thin-plate splines and the decompostion of deformations IEEE Trans. Pattern Anal. Mach. Intell. 11 6 1989 567 585
7. G. Borgefors Distance transformations in arbitrary dimensions Comput. Vis. Graph. Image Process. 27 1984 321 345
8. U. Burgel, T. Schormann, A. Schleicher, and K. Zilles Mapping of histologically identified long fiber tracts in human cerebral hemispheres to the MRI volume of a reference brain: position and spatial variability of the optic radiation NeuroImage 10 5 1999 489 499
9. M.M. Chakravarty, G. Bertrand, M. Descoteaux, A.F. Sadikot, and D.L. Collins The creation of a brain atlas for image guided neurosurgery using serial histological data R.E. Ellis T.M. Peters Fifth International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2003, Lecture Notes in Computer Science, Montreal, Canada 2003 Springer 343 350 November
10. M.M. Chakravarty, A.F. Sadikot, J. Germann, G. Bertrand, and D.L. Collins Anatomical and electrophysiological validation of an atlas for neurosurgical planning J.S. Duncan G. Gerig Seventh International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 Lecture Notes in Computer Science, Palm Springs, USA, October vol. 2 2005 Springer 394 401
11. M.C. Cohn, P.A. Hudgins, S.K. Sheppard, P.A. Starr, and R.A.E. Bakay Pre- and postoperative evaluation of stereotactic pallidotomy Am. J. Neuroradiol. 19 6 1998 1075 1080 (June)
12. A.C.F. Colchester, S. Ourselin, Y. Zhu, E. Bardinet, Y. He, A. Roche, S. Al-Sarraj, J. Ironside, B. Nailon, J. Ironside, and N. Ayache 3-d reconstruction of macroscpic optical brain slice images Scott L. Delp Anthony M. Digoia Branislav Jarama Medical Image Computing and Computer Assisted Intervention (MICCAI), Lecture Notes in Computer Science, Pittsburgh, USA 2000 Springer 95 105 October
13. D.L. Collins, and A.C. Evans ANIMAL: validation and application of non-linear registration-based segmentation Int. J. Pattern Recogn. Artif. Intell. 1997 1271 1294 (December)
14. D.L. Collins, C.J. Holmes, T. Peters, and A.C. Evans Automatic 3-D model based neuroanatomical segmentation Hum. Brain Mapp. 3 1995 190 208
15. E. Cuny, D. Guehl, P. Burbard, C. Gross, V. Dousset, and A. Rougier Lack of agreement between direct magnetic resonance imaging and statistical determination of a subthalamic target: the role of electrophysiological guidance J. Neurosurg. 97 3 2002 591 597
16. J. Dauguet, J.F. Mangin, T. Delzescaux, and V. Frouin Robust inter-slice intensity normalization using histogram scale-space analysis C. Barillot D.R. Haynor P. Hellier Medical Image Computing and Computer Assisted Intervention (MICCAI), Lecture Notes in Computer Science, Saint-Malo, France 2004 Springer 242 249 September
17. T. Delzescaux, J. Dauguet, F. Condé, R. Maroy, and V. Frouin Using 3d non rigid ffd-based method to register post mortem 3d histological data and in vivo MRI of a baboon brain R.E. Ellis T.M. Peters Fifth International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2003, Lecture Notes in Computer Science, Montreal, Canada 2003 Springer November
18. S.C.L. Deoni, T.M. Peters, and B.K. Rutt High resolution T1 and T2 mapping of the brain in clinically acceptable time with DESPOT1 and DESPOT2 Magn. Reson. Med. 53 2005 237 241
19. R.O. Duda, P.E. Hart, and D.G. Stork Pattern Classification 2nd ed. 2000 John Wiley and Sons New York, USA
20. D.L. Foley, A. van Dam, S.K. Feiner, and J.K. Hughes Computer Graphics, Principles, and Practice 1990 Addison-Wesley Reading, MA
21. N. Fujita, H. Tanaka, M. Takanashi, N. Hirabuki, K. Abe, H. Yoshimura, and H. Nakamura Lateral geniculate nucleus: anatomic and functional identification by use of MR imaging Am. J. Neuroradiol. 22 7 2001 1719 1726
22. K.A. Ganser, H. Dickhaus, R. Metzner, and C.R. Wirtz A deformable digital brain atlas system according to Talairach and Tournoux Med. Image. Anal. 8 1 2004 3 22
23. P. Gloor The Temporal Lobe and The Limbic System 1997 Oxford Univ. Press New York
24. R.E. Gross, W.J. Lombardi, A.E. Lang, J. Duff, W.D. Hutchinson, J.A. Saint-Cyr, R.R. Tasker, and A.M. Lozano Relationship of lesion location to clinical outcome following microelectrode-guided pallidotomy for Parkinson's disease Brain 122 3 1999 405 416
25. T. Hirai, and E.G. Jones A new parcellation of the human thalamus on the basis of histochemical staining Brain Res. Brain Res. Rev. 14 1 1989 1 34
26. C.J. Holmes, R. Hoge, L. Collins, R. Woods, A.W. Toga, and A.C. Evans Enhancement of MR images using registration for signal averaging J. Comput. Assist. Tomogr. 22 2 1998
27. H. Johansen-Berg, T.E.J. Behrens, E. Sillery, O. Ciccarelli, A.J. Thompson, S.M. Smith, and P.M. Matthews Functional-anatomical validation and individual of diffusion tractography-based segmentation of the human thalamus Cereb. Cortex 15 1 2005 31 39
28. C. Kenwright, É. Bardinet, S.A. Hojjat, G. Malandain, N. Ayache, and A.C.F. Colchester 2-d to 3-d refinement of post mortem optical and MRI co-registration Fifth International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2003, Lecture Notes in Computer Science, Montreal, Canada 2003 Springer November
29. B. Kim, J.L. Boes, K.A. Frey, and C.R. Meyer Mutual information for automated unwarping of rat brain autoradiographs NeuroImage 5 1 1997 31 40
30. F.A. Lenz, S.L. Normand, H.C. Kwan, D. Andrews, L.H. Rowland, M.W. Jones, M. Seike, Y.C. Lin, R.R. Tasker, J.O. Dostrovsky, and Y.E. Lenz Statistical prediction of the optimal site for thalamotomy in parkinsonian tremor Mov. Disord. 10 3 1995 318 328
31. W.J. Lombardi, R.E. Gross, L.L. Trepanier, A.E. Lang, A.M. Lozano, and J.A. Saint-Cyr Relationship of lesion location to cognitive outcome following microelectrode-guided pallidotomy for Parkinson's disease: support for the existence of cognitive circuits in the human pallidum Brain 123 4 2000 746 758
32. W.E. Lorensen, and H.E. Cline Marching cubes: a resolution 3d surface reconstruction algorithm Comput. Graph. 21 4 1987 163 169
33. MacDonald, D., 1998. A Method for Identifying Geometrically Simple Surfaces from Three Dimensional Images. PhD thesis, McGill University.
34. G. Malandain, and E. Bardinet Intensity compensation within series of images Fifth International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2003, Lecture Notes in Computer Science, Montreal, Canada 2003 Springer November
35. G. Malandain, E. Bardinet, K. Nelissen, and W. Vanduffel Fusion of autoradiographs with an MR volume using 2-D and 3-D linear transformations NeuroImage 23 1 2004 111 127
36. M.S. Mega, S.S. Chen, P.M. Thompson, R.P. Woods, T.J. Karaca, H.V. Vinters, G.W. Small, and A.W. Toga Mapping histology to metabolism: coregistration of stained whole-brain sections to premortem PET in Alzheimer's disease NeuroImage 5 2 1997 147 153
37. W.L. Nowinski, A. Fang, B.T. Nguyen, J.K. Raphel, L. Jagannathan, and R. Raghavan Multiple brain atlas database and atlas based neuroimaging system Comput. Aided Surg. 2 1997 42 66
38. G.L. Nowinski, W.L. Yang, T.T. Yeo, R.N. Bryan, and G.A. Yeo Computer aided stereotactic functional neurosurgery enhanced by the use of the multiple brain atlas database IEEE Trans. Med. Imaging 19 1 2000 62 69 (January)
39. M. Ono, S. Kubik, and C.D. Abernathy Atlas of the Cerebral Sulcii 1990 Georg Thieme Verlag/Thieme Medical Publishers Stuttgart, Germany
40. Otsuki, T., Jokura, H., Takahashi, K., Ishikawa, S., Yoshimoto, T., Kimura, M., Yoshida, R., Miyazawa, T., (1994). Sterotactic gamma-thalamotomy with a computerized brain atlas: Technical case report. Neurosurgery, 35 (4), 764-768 (October).
41. S. Ourselin, A. Roche, S. Prima, and N. Ayache Block matching: a general framework to improve robustness of rigid registration of medical images S.L. Delp A.M. DiGoia B. Jaramaz Third International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI'2000, volume 1935 of Lecture Notes in Computer Science, Pittsburgh, USA 2000 Springer 557 566 October
42. S. Ourselin, E. Bardinet, D. Dormont, G. Malandain, A. Roche, N. Ayache, D. Tandé, K. Parain, and J. Yelnik Fusion of histological sections and MR images: towards the construction of an atlas of the human basal ganglia W. Niessen M. Viergever Medical Image Computing and Computer-Assisted Intervention (MICCAI), Utrecht, Netherlands 2001 743 751 October
43. S. Prima, N. Ayache, T. Barrick, and N. Roberts Maximum likelihood estimation of the bias field in MR brain images: investigating different modelings of the imaging process W.J. Niessen M.A. Viergever Fourth International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI'2001, volume 2208 of Lecture Notes in Computer Science, Utrecht, Netherlands 2001 Springer 811 819 (October)
44. J. Rademacher, U. Burgel, S. Geyer, T. Schormann, A. Schleicher, H.J. Freund, and K. Zilles Variability and asymmetry in the human precentral motor system. A cytoarchitectonic and myeloarchitectonic brain mapping Brain 124 2001 2232 2258
45. S. Robbins, A.C. Evans, D.L. Collins, and S. Whitesides Tuning and comparing spatial normalization methods R.E. Ellis T.M. Peters Fifth International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2003, Lecture Notes in Computer Science, Montreal, Canada 2003 Springer November
46. P.J. Rousseeuw, and A.M. Leroy Robust Regression and Outlier Detection Wiley Ser. Probab. Math. Stat. 1987
47. M. Samuel, E. Caputo, D.J. Brooks, A. Schrag, T. Scaravilli, N.M. Branston, J.C Rothwell, C.D. Marsden, D.G.T. Thomas, A.J. Lees, and N.P. Quinn A study of medial pallidotomy for Parkinson's disease: clinical outcome, MRI location and complications Brain 121 1998 59 75
48. G. Schaltenbrand, and W. Bailey Atlas of Stereotaxy of the Human Brain 1959 Georg Thieme Verlag Stuttgart, Germany
49. G. Schaltenbrand, and W. Wahren Atlas for Stereotaxy of the Human Brain 1977 Georg Thieme Verlag Stuttgart, Germany
50. H.N. Schnitzlein, and F.R. Murtagh Imaging anatomy of the head and spine A Photographic Color Atlas of MRI, CT, Gross, and Microscopic Anatomy in Axial, Coronal, and Sagittal Planes 2nd ed. 1980 Urban and Schwarzenberg Baltimore
51. T. Schormann, and K. Zilles Limitations of the principal-axes theory IEEE Trans. Med. Imaging 16 6 1997 942 947 (January)
52. T. Schormann, and K. Zilles Three-dimensional linear and nonlinear transformations: an integration of light microscopical and MRI data Hum. Brain Mapp. 6 1998 339 347
53. R. Sibson Studies in the robustness of multidimensional scaling: procrustes statistics J.R. Stat. Soc. 40 1978 234 238
54. P. St-Jean, A.F. Sadikot, L. Collins, D. Clonda, R. Kasrai, A.C. Evans, and T.M. Peters Automated atlas integration and interactive three-dimensional visualization tools for planning and guidance in functional neurosurgery IEEE Trans. Med. Imaging (TMI) 17 5 1998 672 680
55. P.A. Starr, J.L. Vitek, M. DeLong, and R.A. Bakay Magnetic resonance imaging-based steretactic localization of the globus pallidus and subthalamic nucleus Neurosurgery 44 2 1999 303 314
56. J. Talairach, and P. Tournoux Co-Planar Stereotaxic Atlas of the Human Brain 1988 Georg Thieme Verlag Stuttgart, Germany
57. J. Talairach, and P. Tournoux Referentially Oriented Cerebral MRI Anatomy. Atlas of Stereotaxic Anatomical Correlations for Gray and White Matter 1993 Georg Thieme Verlag Stuttgart, Germany
58. P.M. Thompson, and A.W. Toga A surface-based technique for warping three dimensional images of the brain IEEE Trans. Med. Imaging 15 1996
59. A.W. Toga, A. Goldkorn, K. Ambach, K. Chao, B.C. Quinn, and P. Yao Postmortem cryosectioning as an anatomic reference for human brain mapping Comput. Med. Imaging Graph. 21 2 1997 131 141
60. J.M. Van Buren, and R.C. Borke Variations and Connections of the Human Thalamus 1972 Springer-Verlag New York
61. A.J. Watkins A Stereotaxic Atlas of the Human Thalamus and Adjacent Structures. A Variability Study 1969 Williams and Watkins Baltimore
62. M. Xu, and W.L. Nowinski Talairach-Tournoux brain atlas registration using a metalforming principle-based finite element method Med. Image Anal. 5 4 2001 271 279