A library of cortical morphology analysis tools to study development, aging and genetics of cerebral cortex

Neuroinformatics

Volumn 10, Issue 1, 2012, Pages 81-96

  Kochunov, Peter ^a,b   Rogers, William ^a   Mangin, Jean Francois ^c   Lancaster, Jack ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^b SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

^c DIF   (France)

Author keywords

BrainVisa; Cortical analysis tools; Gray matter thickness; Object based morphometry; Sulcal span

Indexed keywords

AGING; ARTICLE; BRAIN CORTEX; COMPUTER PROGRAM; HISTOLOGY; HUMAN; IMAGE PROCESSING; METABOLISM; METHODOLOGY; NEUROIMAGING; NUCLEAR MAGNETIC RESONANCE IMAGING; PRENATAL DEVELOPMENT;

AGING; CEREBRAL CORTEX; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING; NEUROIMAGING; SOFTWARE;

EID: 84859383386     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-011-9127-9     Document Type: Article

References (93)

1. Amunts K. Jancke L. Mohlberg H. Steinmetz H. & Zilles K. (2000). Interhemispheric asymmetry of the human motor cortex related to handedness and gender. Neuropsychologia 38 304-312.
2. Ashburner J. & Friston K. (2000). Voxel-based morphometry-the methods. NeuroImage 11 805-821.
3. Barker D. J. (2004). The developmental origins of well-being. Philosophical Transactions of the Royal Society of London. Series B Biological Sciences 359 1359-1366.
4. Bonnici H. M. William T. Moorhead J. Stanfield A. C. Harris J. M. Owens D. G. et al. (2007). Pre-frontal lobe gyrification index in schizophrenia mental retardation and comorbid groups: an automated study. NeuroImage 35 648-654. (Pubitemid 46420425)
5. Brown T. T. Kuperman J. M. Erhart M. White N. S. Roddey J. C. Shankaranarayanan A. et al. (2010). Prospective motion correction of high-resolution magnetic resonance imaging data in children. NeuroImage 53 139-145.
6. Cachia A. Mangin J. F. Riviere D. Papadopoulos-Orfanos D. Kherif F. Bloch I. et al. (2003). A generic framework for the parcellation of the cortical surface into gyri using geodesic Voronoi diagrams. Medical Image Analysis 7 403-416. (Pubitemid 37322306)
7. Cachia A. Paillere-Martinot M. L. Galinowski A. Januel D. de Beaurepaire R. Bellivier F. et al. (2008). Cortical folding abnormalities in schizophrenia patients with resistant auditory hallucinations. NeuroImage 39 927-935.
8. Cheverud J. M. Falk D. Vannier M. Konigsberg L. Helmkamp R. C. & Hildebolt C. (1990). Heritability of brain size and surface features in rhesus macaques (Macaca mulatta). Journal of Heredity 81 51-57. (Pubitemid 20182440)
9. Coulon O. Clouchoux C. Operto G. Dauchot K. Sirigu A. & Anton J.-L. (2006). Cortical localization via surface parameterization: a sulcus-based approach. NeuroImage 31(Suppl. 1) S46.
10. Coyle T. R. Kochunov P. Patel R. D. Nery F. G. Lancaster J. L. Mangin J. F. et al. (2006). Cortical sulci and bipolar disorder. Neuroreport 17 1739-1742. (Pubitemid 44621575)
11. Cruchaga C. Fernandez-Seara M. A. Seijo-Martinez M. Samaranch L. Lorenzo E. Hinrichs A. et al. (2009). Cortical atrophy and language network reorganization associated with a novel progranulin mutation. Cerebral Cortex 19 1751-1760.
12. Cykowski M. D. Coulon O. Kochunov P. V. Amunts K. Lancaster J. L. Laird A. R. et al. (2007). The central sulcus: an observerindependent characterization of sulcal landmarks and depth asymmetry. Cerebral Cortex.
13. Cykowski M. D. Coulon O. Kochunov P. V. Amunts K. Lancaster J. L. Laird A. R. et al. (2008). The central sulcus: an observerindependent characterization of sulcal landmarks and depth asymmetry. Cerebral Cortex 18 1999-2009.
14. Fischl B. & Dale A. M. (2000). Measuring the thickness of the human cerebral cortex from magnetic resonance images. Proceedings of the National Academy of Sciences of the United States of America 97 11050-11055.
15. Freedman M. Knoefel J. Maeser M. & Levine H. (1984). Computerized axial tomography in aging. In M. Albert (Ed.) Clinical neurology of aging (pp. 139-148). New York: Oxford University Press.
16. Gaser C. Luders E. Thompson P. M. Lee A. D. Dutton R. A. Geaga J. A. et al. (2006). Increased local gyrification mapped in Williams syndrome. NeuroImage 33 46-54. (Pubitemid 44397584)
17. Glahn D. C. Thompson P. M. & Blangero J. (2007). Neuroimaging endophenotypes: strategies for finding genes influencing brain structure and function. Human Brain Mapping 28 488-501. (Pubitemid 46849366)
18. Good C. D. Scahill R. I. Fox N. C. Ashburner J. Friston K. J. Chan D. et al. (2002). Automatic differentiation of anatomical patterns in the human brain: validation with studies of degenerative dementias. NeuroImage 17 29-46.
19. Grossman R. Hoffman C. Mardor Y. & Biegon A. (2006). Quantitative MRI measurements of human fetal brain development in utero. NeuroImage 33 463-470. (Pubitemid 44485563)
20. Habas P. A. Kim K. Corbett-Detig J. M. Rousseau F. Glenn O. A. Barkovich A. J. et al. (2010). A spatiotemporal atlas of MR intensity tissue probability and shape of the fetal brain with application to segmentation. NeuroImage 53 460-470.
21. Hu H. H. Guo W. Y. Chen H. Y. Wang P. S. Hung C. I. Hsieh J. C. et al. (2009). Morphological regionalization using fetal magnetic resonance images of normal developing brains. European Journal of Neuroscience 29 1560-1567.
22. Hulshoff Pol H. E. Schnack H. G. Posthuma D. Mandl R. C. Baare W. F. van Oel C. et al. (2006). Genetic contributions to human brain morphology and intelligence. Journal of Neuroscience 26 10235-10242. (Pubitemid 44527417)
23. Hutsler J. J. Lee D. G. & Porter K. K. (2005). Comparative analysis of cortical layering and supragranular layer enlargement in rodent carnivore and primate species. Brain Research 1052 71-81. (Pubitemid 41121952)
24. Huttenlocher P. R. & Dabholkar A. S. (1997). Regional differences in synaptogenesis in human cerebral cortex. The Journal of Comparative Neurology 387 167-178. (Pubitemid 27430343)
25. Im K. Lee J. M. Seo S. W. Hyung Kim S. Kim S. I. & Na D. L. (2008). Sulcal morphology changes and their relationship with cortical thickness and gyral white matter volume in mild cognitive impairment and Alzheimer's disease. NeuroImage 43 103-113.
26. Janssen J. Reig S. Aleman Y. Schnack H. Udias J. M. Parellada M. et al. (2009). Gyral and sulcal cortical thinning in adolescents with first episode early-onset psychosis. Biological Psychiatry 66 1047-1054.
27. Jouvent E. Mangin J. F. Porcher R. Viswanathan A. O'Sullivan M. Guichard J. P. et al. (2008). Cortical changes in cerebral small vessel diseases: a 3D MRI study of cortical morphology in CADASIL. Brain 131 2201-2208.
28. Klein A. Andersson J. Ardekani B. A. Ashburner J. Avants B. Chiang M. C. et al. (2009). Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. NeuroImage 46 786-802.
29. Kochunov P. & Duff Davis M. (2009). Development of structural MR brain imaging protocols to study genetics and maturation. Methods 50 136-146.
30. Kochunov P. Lancaster J. Thompson P. Boyer A. Hardies J. & Fox P. (2000). Evaluation of octree regional spatial normalization method for regional anatomical matching. Human Brain Mapping 11 193-206.
31. Kochunov P. Mangin J. F. Coyle T. Lancaster J. Thompson P. Riviere D. et al. (2005). Age-related morphology trends of cortical sulci. Human Brain Mapping 26 210-220. (Pubitemid 41598319)
32. Kochunov P. Lancaster J. L. Glahn D. C. Purdy D. Laird A. R. Gao F. et al. (2006). Retrospective motion correction protocol for high-resolution anatomical MRI. Human Brain Mapping 27 957-962. (Pubitemid 44837498)
33. Kochunov P. Thompson P. M. Lancaster J. L. Bartzokis G. Smith S. Coyle T. et al. (2007). Relationship between white matter fractional anisotropy and other indices of cerebral health in normal aging: tract-based spatial statistics study of aging. NeuroImage 35 478-487. (Pubitemid 46420428)
34. Kochunov P. Thompson P. M. Coyle T. R. Lancaster J. L. Kochunov V. Royall D. et al. (2008). Relationship among neuroimaging indices of cerebral health during normal aging. Human Brain Mapping 29 36-45.
35. Kochunov P. Coyle T. Lancaster J. Robin D. A. Hardies J. Kochunov V. et al. (2009a). Processing speed is correlated with cerebral health markers in the frontal lobes as quantified by neuroimaging. NeuroImage 49 1190-1199.
36. Kochunov P. Glahn D. Fox P. T. Lancaster J. Saleem K. Shelledy W. et al. (2009b). Genetics of primary cerebral gyrification: heritability of length depth and area of primary sulci in an extended pedigree of Papio baboons. NeuroImage 15 1126-1132.
37. Kochunov P. Glahn D. Fox P. T. Lancaster J. Saleem K. Shelledy W. et al. (2009c). Genetics of primary cerebral gyrification: heritability of length depth and area of primary sulci in an extended pedigree of Papio baboons. Neuroimage. doi: 10.1016/j. neuroimage.2009.12.045.
38. Kochunov P. Glahn D. Winkler A. Duggirala R. Olvera R. Cole S. A. et al. (2009d). Analysis of genetic variability and whole genome linkage of whole-brain subcortical and ependymal hyperintense white matter volume. Stroke 40 3685-3690.
39. Kochunov P. Ramage A. E. Lancaster J. L. Robin D. A. Narayana S. Coyle T. et al. (2009e). Loss of cerebral white matter structural integrity tracks the gray matter metabolic decline in normal aging. NeuroImage 45 17-28.
40. Kochunov P. Robin D. Royall D. Lancaster J. Kochunov V. Coyle T. et al. (2009f). Can structural MRI cerebral health markers track cognitive trends in executive control function during normal maturation and adulthood? Human Brain Mapping 30 2581-2594.
41. Kochunov P. Castro C. Davis D. Dudley D. Brewer J. Zhang Y. et al. (2010a). Mapping primary gyrogenesis during fetal development in primate brains: high-resolution in utero structural MRI study of fetal brain development in pregnant baboons. Frontiers in Neurogenesis 4.
42. Kochunov P. Glahn D. Lancaster J. Winkler A. Kent J. Olvera R. et al. (2010b). Whole brain and regional hyperintense white matter volume and blood pressure: overlap of genetic loci produced by bivariate whole-genome linkage analyses. Stroke 41 2137-2142.
43. Kochunov P. Glahn D. C. Lancaster J. Winkler A. Karlsgodt K. Olvera R. L. et al. (2010c). Blood pressure and cerebral white matter share common genetic factors in Mexican Americans. Hypertension.
44. Kochunov P. Glahn D. Lancaster J. Thompson P. Kochunov V. Rogers B. et al. (2011). Fractional anisotropy of cerebral white matter and thickness of cortical gray matter across the lifespan. Neuroimage doi:10.1016/j.neuroimage. 2011.05.050.
45. Lancaster J. L. Fox P. T. Downs H. Nickerson D. S. Hander T. A. El Mallah M. et al. (1999). Global spatial normalization of human brain using convex hulls. Journal of Nuclear Medicine 40 942-955. (Pubitemid 29269213)
46. Lancaster J. L. Cykowski M. D. McKay D. R. Kochunov P. V. Fox P. T. Rogers W. et al. (2010). Anatomical global spatial normalization. Neuroinformatics 8 171-182.
47. Le Goualher G. Procyk E. Collins D. L. Venugopal R. Barillot C. & Evans A. C. (1999). Automated extraction and variability analysis of sulcal neuroanatomy. IEEE Transactions on Medical Imaging 18 206-217.
48. Le Goualher G. Argenti A. M. Duyme M. Baare W. F. Hulshoff Pol H. E. Boomsma D. I. et al. (2000). Statistical sulcal shape comparisons: application to the detection of genetic encoding of the central sulcus shape. NeuroImage 11 564-574. (Pubitemid 30346972)
49. Lerch J. P. & Evans A. C. (2005). Cortical thickness analysis examined through power analysis and a population simulation. NeuroImage 24 163-173. (Pubitemid 39611036)
50. Liu T. Wen W. Zhu W. Trollor J. Reppermund S. Crawford J. et al. (2010). The effects of age and sex on cortical sulci in the elderly. NeuroImage 51 19-27.
51. Liu T. Wen W. Zhu W. Kochan N. A. Trollor J. N. Reppermund S. et al. (2011). The relationship between cortical sulcal variability and cognitive performance in the elderly. NeuroImage 56 865-873.
52. Lohmann G. von Cramon D. Y. & Steinmetz H. (1999). Sulcal variability of twins. Cerebral Cortex 9 754-763. (Pubitemid 29514105)
53. Lohmann G. von Cramon D. Y. Colchester A. C. (2007). Deep Sulcal Landmarks Provide an Organizing Framework for Human Cortical Folding. Cerebral Cortex.
54. Luders E. Narr K. L. Thompson P. M. Rex D. E. Woods R. P. Deluca H. et al. (2006a). Gender effects on cortical thickness and the influence of scaling. Human Brain Mapping 27 314-324.
55. Luders E. Thompson P. M. Narr K. L. Toga A. W. Jancke L. & Gaser C. (2006b). A curvature-based approach to estimate local gyrification on the cortical surface. NeuroImage 29 1224-1230. (Pubitemid 43184185)
56. Magnotta V. A. Andreasen N. C. Schultz S. K. Harris G. Cizadlo T. Heckel D. et al. (1999). Quantitative in vivo measurement of gyrification in the human brain: changes associated with aging. Cerebral Cortex 9 151-160. (Pubitemid 29174196)
57. Mangin J. F. Frouin V. Bloch I. Régis J. & López-Krahe J. (1995). From 3D magnetic resonance images to structural representations of the cortex topography using topology preserving deformations. Journal of Mathematical Imaging and Vision 5 297-318.
58. Mangin J. F. Frouin V. Régis J. Bloch I. Belin P. & Samson Y. (1996). Towards better management of cortical anatomy in multimodal multi-individual brain studies. Physica Medica 12 103-107. (Pubitemid 126676002)
59. Mangin J. F. Riviere D. Cachia A. Papadopoulos-Orfanos D. Collins D. L. Evans A. C. et al. (2003). Object-based strategy for morphometry of the cerebral cortex. Information Processing in Medical Imaging 18 160-171.
60. Mangin J. F. Rivière D. Coulon O. Poupon C. Cachia A. Cointepas Y. et al. (2004a). Coordinate-based versus structural approaches to brain image analysis. Artificial Intelligence in Medicine 30 77-97.
61. Mangin J. F. Riviere D. Cachia A. Duchesnay E. Cointepas Y. Papadopoulos-Orfanos D. et al. (2004b). Object-based morphometry of the cerebral cortex. IEEE Transactions on Medical Imaging 23 968-982.
62. Nopoulos P. Flaum M. O'Leary D. & Andreasen N. C. (2000). Sexual dimorphism in the human brain: evaluation of tissue volume tissue composition and surface anatomy using magnetic resonance imaging. Psychiatry Research 98 1-13. (Pubitemid 30119884)
63. Ono M. Kubik S. & Abernathey C. (1990). Atlas of the Cerebral Sulci. New York: Thieme Medical Publishers.
64. Pfefferbaum A. Sullivan E. V. Jernigan T. L. Zipursky R. B. Rosenbloom M. J. Yesavage J. A. et al. (1990). A quantitative analysis of CT and cognitive measures in normal aging and Alzheimer's disease. Psychiatry Research 35 115-136.
65. Pillay P. & Manger P. R. (2007). Order-specific quantitative patterns of cortical gyrification. European Journal of Neuroscience 25 2705-2712. (Pubitemid 46888839)
66. Rajagopalan V. Scott J. Habas P. A. Kim K. Rousseau F. Glenn O. A. et al. (2010). Measures for characterizing directionality specific volume changes in TBM of brain growth. Medical Image Computing and Computer-Assisted Intervention 13 339-346.
67. Raz N. Gunning F. M. Head D. Dupuis J. H. McQuain J. Briggs S. D. et al. (1997). Selective aging of the human cerebral cortex observed in vivo: differential vulnerability of the prefrontal gray matter. Cerebral Cortex 7 268-282. (Pubitemid 27184486)
68. Raz N. Gunning-Dixon F. M. Head D. Dupuis J. H. & Acker J. D. (1998). Neuroanatomical correlates of cognitive aging: evidence from structural magnetic resonance imaging. Neuropsychology 12 95-114. (Pubitemid 28070401)
69. Richman D. Stewart R. Hutchinson J. & Caviness V. S. Jr. (1975). Mechanical model of brain convolutional development. Science 189 18-21.
70. Rivière D. Mangin J. F. Papadopoulos-Orfanos D. Martinez J. M. Frouin V. & Régis J. (2002). Automatic recognition of cortical sulci of the Human Brain using a congregation of neural networks. Medical Image Analysis 6 77-92. (Pubitemid 35282819)
71. Rogers J. Kochunov P. Lancaster J. Shelledy W. Glahn D. Blangero J. et al. (2007). Heritability of brain volume surface area and shape: an MRI study in an extended pedigree of baboons. Human Brain Mapping 28 576-583. (Pubitemid 46849373)
72. Rogers J. Kochunov P. Zilles K. Shelledy W. Lancaster J. Thompson P. et al. (2010). On the genetic architecture of cortical folding and brain volume in primates. NeuroImage 53 1103-1108.
73. Smart I. H. & McSherry G. M. (1986). Gyrus formation in the cerebral cortex in the ferret. I. Description of the external changes. Journal of Anatomy 146 141-152. (Pubitemid 16068562)
74. Smith S. M. Zhang Y. Jenkinson M. Chen J. Matthews P. M. Federico A. et al. (2002). Accurate robust and automated longitudinal and cross-sectional brain change analysis. Neuro- Image 17 479-489.
75. Smith S. Jenkinson M. Woolrich M. Beckmann C. Behrens T. Johansen-Berg H. et al. (2004a). Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage 23 208-219.
76. Smith S. M. Jenkinson M. Woolrich M. W. Beckmann C. F. Behrens T. E. Johansen-Berg H. et al. (2004b). Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage 23(Suppl 1) S208-219. (Pubitemid 39421720)
77. Sowell E. R. Peterson B. S. Kan E.,Woods R. P. Yoshii J. Bansal R. et al. (2007). Sex differences in cortical thickness mapped in 176 healthy individuals between 7 and 87 years of age. Cerebral Cortex 17 1550-1560.
78. Steiner I. Gomori J. M. & Melamed E. (1985). Progressive brain atrophy during normal aging in man: a quantitative computerized tomography study. Israel Journal of Medical Sciences 21 279-282. (Pubitemid 15055846)
79. Studholme C. Cardenas V. Blumenfeld R. Schuff N. Rosen H. J. Miller B. et al. (2004). Deformation tensor morphometry of semantic dementia with quantitative validation. NeuroImage 21 1387-1398. (Pubitemid 38450721)
80. Studholme C. Drapaca C. Iordanova B. & Cardenas V. (2006). Deformation-based mapping of volume change from serial brain MRI in the presence of local tissue contrast change. IEEE Transactions on Medical Imaging 25 626-639.
81. Thompson P. M. Schwartz C. Lin R. T. Khan A. A. & Toga A.W. (1996). Three-dimensional statistical analysis of sulcal variability in the human brain. Journal of Neuroscience 16 4261-4274. (Pubitemid 26192421)
82. Thompson P. M. Mega M. S. Woods R. P. Zoumalan C. I. Lindshield C. J. Blanton R. E. et al. (2001). Cortical change in Alzheimer's disease detected with a disease-specific populationbased brain atlas. Cerebral Cortex 11 1-16. (Pubitemid 32064172)
83. Thompson P. Cannon T. D. & Toga A. W. (2002). Mapping genetic influences on human brain structure. Annals of Medicine 34 523-536. (Pubitemid 36113810)
84. Thompson P. M. Hayashi K. M. De Zubicaray G. I. Janke A. L. Rose S. E. Semple J. et al. (2004). Mapping hippocampal and ventricular change in Alzheimer disease. NeuroImage 22 1754-1766. (Pubitemid 38962663)
85. Toro R. & Burnod Y. (2005). A morphogenetic model for the development of cortical convolutions. Cerebral Cortex 15 1900-1913. (Pubitemid 41628331)
86. Toro R. Perron M. Pike B. Richer L. Veillette S. Pausova Z. et al. (2008). Brain size and folding of the human cerebral cortex. Cerebral Cortex 18 2352-2357.
87. Van Essen D. C. (1997). A tension-based theory of morphogenesis and compact wiring in the central nervous system. Nature 385 313-318. (Pubitemid 27053095)
88. Van Essen D. C. Drury H. A. Dickson J. Harwell J. Hanlon D. & Anderson C. H. (2001). An integrated software suite for surface- based analyses of cerebral cortex. Journal of the American Medical Informatics Association 8 443-459. (Pubitemid 32847795)
89. Welker W. (1990). Why does cerebral cortex fissure and fold? A review of determinants of gyri and sulci. A review of determinants of gyri and sulci. In: Comparative structure and evolution of cerebral cortex Part II vol 8B New York.
90. Wey H. Y. Wang D. J. & Duong T. Q. (2010). Baseline CBF and BOLD CBF and CMRO(2) fMRI of visual and vibrotactile stimulations in baboons. Journal of Cerebral Blood Flow and Metabolism 31 715-724.
91. Winkler A. M. Kochunov P. Blangero J. Almasy L. Zilles K. Fox P. T. et al. (2009). Cortical thickness or grey matter volume? The importance of selecting the phenotype for imaging genetics studies. NeuroImage 15 1135-1146.
92. Zilles K. Armstrong E. Schleicher A. & Kretschmann H. J. (1988). The human pattern of gyrification in the cerebral cortex. Anatomy and Embryology (Berl) 179 173-179. (Pubitemid 19111637)
93. Zilles K. Armstrong E. Moser K. H. Schleicher A. & Stephan H. (1989). Gyrification in the cerebral cortex of primates. Brain Behavior and Evolution 34 143-150. (Pubitemid 20001940)