Skip to main content

Advertisement

Log in

Computational biology for visualization of brain structure

  • Original Article
  • Published:
Anatomy and Embryology Aims and scope Submit manuscript

Abstract

The complexity and variability of human brain (as well as other species) across subjects is so great that reliance on maps and atlases is essential to effectively manipulate, analyze and interpret brain data. Central to these tasks is the construction of averages, templates and models to describe how the brain and its component parts are organized. Design of appropriate reference systems and visualization strategies for human brain data presents considerable challenges, since these systems must capture how brain structure and function vary in large populations, across age and gender, in different disease states, across imaging modalities and even across species. This paper will describe the application of brain maps to a variety of questions and problems in health and disease. It includes a brief survey of different types of maps, including those that capture dynamic patterns of brain change over time.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

References

  • Avoli M, Hwa GC, Kostopoulos G et al (1991) Electrophysiological analysis of human neocortex in vitro: experimental techniques and methodological approaches. Can J Neurol Sci 18:636–639

    PubMed  CAS  Google Scholar 

  • Bohm C, Greitz T, Kingsley D et al (1983) Adjustable Computerized Brain Atlas for Transmission and Emission Tomography. Am J Neuroradiol 4:731–733

    PubMed  CAS  Google Scholar 

  • Brodmann K (1960) Vergleichende Lokalisationslehre der Grosshirnrinde in ihren Prinzipien dargestellt auf Grund des Zellenbaues, Barth, Leipzig, 1909. In: Some papers on the cerebral cortex, translated as: On the comparative localization of the cortex, Thomas, Springfield, pp 201–230

  • Cannestra AF, Santori EM, Holmes CJ et al (1997) A 3D multi-modality brain map of the Nemestrina monkey. Brain Res Bull 43(2):141–148

    Article  PubMed  CAS  Google Scholar 

  • Cannon TD, Thompson PM, van Erp T, Toga AW, Poutanen VP, Huttunen M, Lönnqvist J, Standertskjöld-Nordenstam CG, Narr KL, Khaledy M, Zoumalan CI, Dail R, Kaprio J (2002) Cortex mapping reveals regionally specific patterns of genetic and disease-specific gray-matter deficits in twins discordant for Schizophrenia. Proc Natl Acad Sci USA 99(5):3228–3233

    Article  PubMed  CAS  Google Scholar 

  • Christensen GE, Rabbitt RD, Miller MI (1993) A deformable neuroanatomy textbook based on viscous fluid mechanics. In: 27th annual conference on informaion sciences and systems, pp 211–216

  • Christensen GE, Miller MI, Marsh JL et al (1995) Automatic analysis of medical images using a deformable textbook. In: Proceedings of Comparative Assistance in Radiology. Springer, Berlin Heidelberg New York, pp 152–157

  • Christensen GE, Rabbitt RD, Miller MI (1996) Deformable Templates using Large Deformation Kinematics. IEEE Trans Image Process 5(10):1435–1447

    Article  PubMed  CAS  Google Scholar 

  • Collins DL, Holmes CJ, Peters TM et al (1995) Automatic 3D Model-Based Neuroanatomical Segmentation. Hum Brain Mapp 3:190–208

    Article  Google Scholar 

  • Csernansky JG, Joshi S, Wang L et al (1998) Hippocampal morphometry in Schizophrenia by high dimensional brain mapping. Proc Natl Acad Sci USA 95(19):11406–11411

    Article  PubMed  CAS  Google Scholar 

  • Csernansky JG, Wang L, Joshi S et al (2000) Early Dementia of the Alzheimer type is distinguished from aging by high-dimensional mapping of the hippocampus. Neurology 55(11):1636–1643

    PubMed  CAS  Google Scholar 

  • Damasio H (ed) (1995) Human brain anatomy in computerized images. Oxford University Press, Oxford

    Google Scholar 

  • Drury HA, Van Essen DC (1997) Analysis of functional specialization in human cerebral cortex using the visible man surface based atlas. Hum Brain Mapp 5:233–237

    Article  PubMed  CAS  Google Scholar 

  • Duvernoy HM (1991) The human brain. Springer, Berlin Heidelberg New York

    Google Scholar 

  • Fischl B, Liu A, Dale AM (2001) Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. IEEE Trans Med Imaging 20(1):70–80

    Article  PubMed  CAS  Google Scholar 

  • Fox PT, Perlmutter JS, Raichle M (1985) A stereotactic method of localization for positron emission tomography. J Comp Assist Tomogr 9(1):141–153

    Article  CAS  Google Scholar 

  • Fox PT, Mintun MA, Reiman EM et al (1988) Enhanced detection of focal brain responses using inter-subject averaging and change distribution analysis of subtracted PET images. J Cereb Blood Flow Metab 8:642–653

    PubMed  CAS  Google Scholar 

  • Fox NC, Freeborough PA, Rossor MN (1996) Visualization and quantification of rates of cerebral atrophy in Alzheimer’s disease. Lancet 348(9020):94–97

    Article  PubMed  CAS  Google Scholar 

  • Freeborough PA, Woods RP, Fox NC (1996) Accurate registration of serial 3D MR brain images and its application to visualizing change in neurodegenerative disorders. J Comput Assist Tomogr 20(6):1012–1022

    Article  PubMed  CAS  Google Scholar 

  • Friston KJ, Passingham RE, Nutt JG et al (1989) Localization in PET images: direct fitting of the intercommissural (AC-PC) line. J Cereb Blood Flow Metab 9:690–695

    PubMed  CAS  Google Scholar 

  • Friston KJ, Frith CD, Liddle PF et al (1991) Plastic transformation of PET images. J Comp Assist Tomogr 9(1):141–153

    Google Scholar 

  • Gee JC, Reivich M, Bajcsy R (1993) Elastically deforming an atlas to match anatomical brain images. J Comp Assist Tomogr 17(2):225–236

    CAS  Google Scholar 

  • Geschwind N, Levitsky W (1968) Human brain: left–right asymmetries in temporal speech region. Science 1968:161–186

    Google Scholar 

  • Geyer S, Schleicher A, Zilles K (1997) The somatosensory of man: cytoarchitecture and regional distributions of receptor binding sites. Neuroimage 6(1):27–45

    Article  PubMed  CAS  Google Scholar 

  • Haney S, Thompson PM, Cloughesy TF et al (2001) Mapping therapeutic response in a patient with malignant glioma. J Comput Assist Tomogr 25(4):529–536

    Article  PubMed  CAS  Google Scholar 

  • Jacobs RE, Fraser SE (1994) Magnetic resonance microscopy of embryonic cell lineages and movements. Science 263(5147):681–684

    Article  PubMed  CAS  Google Scholar 

  • Kikinis R, Shenton ME, Iosifescu DV et al (1996) A digital brain atlas for surgical planning, model-driven segmentation, and teaching. IEEE Trans Vis Comp Graph 2(3):232–241

    Article  Google Scholar 

  • Le Bihan D (1996) Functional MRI of the brain: principles, applications and limitations. Neuroradiology 23(1):1–5

    CAS  Google Scholar 

  • Mai J, Assheuer J, Paxinos G (1997) Atlas of the human brain. Academic, New York

    Google Scholar 

  • Mazziotta JC, Toga AW, Evans AC et al (1995) A probabilistic atlas of the human brain: theory and rationale for its development. Neuroimage 2:89–101

    Article  PubMed  CAS  Google Scholar 

  • Mazziotta JC, Toga AW, Evans AC et al (2001a) A probabilistic atlas and reference system for the human brain. J R Soc 356:1293–1322

    CAS  Google Scholar 

  • Mazziotta J, Toga AW, Evans A, Fox P, Lancaster J, Zilles K, Woods R, Paus T, Simpson G, Pike B, Holmes C, Collins L, Thompson PM, MacDonald D, Iacoboni M, Schormann T, Amunts K, Palomero-Gallagher N, Geyer S, Parsons L, Narr K, Kabani N, Le Goualher G, Feidler J, Smith K, Boomsma D, Hulshoff H, Cannon T, Kawashima R and Mazoyer B (2001b) A four-dimensional probabilistic atlas of the human brain. J Am Med Inform Assoc 8(5):401–430

    PubMed  CAS  Google Scholar 

  • Mega MS, Chen S, Thompson PM et al (1997) Mapping pathology to metabolism: coregistration of stained whole brain sections to PET in Alzheimer’s disease. NeuroImage 5:147–153

    Article  PubMed  CAS  Google Scholar 

  • Mega MS, Dinov ID, Thompson PM, Manese M, Lindshield C, Moussai J, Tran N, Olsen K, Felix J, Zoumalan C, Woods RP, Toga AW, Mazziotta JC (2004) Automated brain tissue assessment in the elderly and demented population: construction and validation of a sub-volume probabilistic brain atlas. Neuroimage (in press)

  • Meltzer CC, Frost JJ (1994) Partial volume correction in emission-computed tomography: focus on Alzheimer disease. In: Thatcher RW, Hallett M, Zeffiro T, John ER, Huerta M (eds) Functional neuroimaging: technical foundations. Academic, New York, pp 163–170

    Google Scholar 

  • Miller MI, Christensen GE, Amit Y et al (1993) Mathematical textbook of deformable neuroanatomies. Proc Natl Acad Sci USA 90:11944–11948

    Article  PubMed  CAS  Google Scholar 

  • Minoshima S, Koeppe RA, Frey KA et al (1994) Stereotactic PET atlas of the human brain: aid for visual interpretation of functional brain images. J Nucl Med 35:949–954

    PubMed  CAS  Google Scholar 

  • Missir O, Dutheil-Desclercs C, Meder JF et al (1989) Central sulcus patterns at MRI. J Neuroradiol 16:133–144

    PubMed  CAS  Google Scholar 

  • Ono M, Kubik S, Abernathey CD (1990) Atlas of the cerebral sulci. Thieme, Stuttgart

    Google Scholar 

  • Palovcik RA, Reid SA, Principe JC et al (1992) 3D computer animation of electrophysiological responses. J Neurosci Methods 41:1–9

    Article  PubMed  CAS  Google Scholar 

  • Rademacher J, Caviness VS Jr, Steinmetz H et al (1993) Topographical variation of the human primary cortices: implications for neuroimaging, brain mapping and neurobiology. Cereb Cortex 3(4):313–329

    Article  PubMed  CAS  Google Scholar 

  • Rajkowska G, Goldman-Rakic P (1995) Cytoarchitectonic definition of pre-frontal areas in the normal human cortex: ii. variability in locations of areas 9 and 46 and relationship to the Talairach coordinate system. Cereb Cortex 5(4):323–337

    Article  PubMed  CAS  Google Scholar 

  • Rizzo G, Gilardi MC, Prinster A et al (1995) An elastic computerized brain atlas for the analysis of clinical PET/SPET data. Eur J Nucl Med 22(11):1313–1318

    Article  PubMed  CAS  Google Scholar 

  • Roland PE, Zilles K (1994) Brain atlases—a new research tool. Trends Neurosci 17(11):458–467

    Article  PubMed  CAS  Google Scholar 

  • Smith GE (1907) A new topographical survey of the human cerebral cortex, being an account of the distribution of the anatomically distinct cortical areas and their relationship to the cerebral sulci. J Anat 41:237–254

    CAS  Google Scholar 

  • Sowell ER, Thompson PM, Rex D, Kornsand D, Tessner KD, Jernigan TL, Toga AW (2002) Mapping sulcal pattern asymmetry and local cortical surface gray matter distribution in vivo: maturation in perisylvian cortices. Cereb Cortex 12:17–26

    Article  PubMed  Google Scholar 

  • Sowell ER, Thompson PM, Peterson BS, Mattson SN, Welcome SE, Henkenius AL, Riley EP, Jernigan TL, Toga AW (2002b) Mapping cortical gray matter asymmetry patterns in adolescents with heavy prenatal alcohol exposure. Neuroimage 17:1807–1819

    Article  PubMed  Google Scholar 

  • Sowell ER, Peterson BS, Thompson PM, Welcome SE, Henkenius AL, Toga AW (2003) Mapping cortical change across the human life span. Nat Neurosci 6(3):3019–3315

    Article  CAS  Google Scholar 

  • Sowell ER, Thompson PM, Welcome SE, Henkenius AL, Toga AW, Peterson BS (2003b) Cortical abnormalities in children and adolescents with attention deficit hyperactivity disorder. Lancet 362:1699–1707

    Article  PubMed  Google Scholar 

  • Steinmetz H, Furst G, Freund H-J (1989) Cerebral cortical localization: application and validation of the proportional grid system in MR imaging. J Comp Assist Tomogr 13(1):10–19

    CAS  Google Scholar 

  • Steinmetz H, Furst G, Freund H-J (1990) Variation of perisylvian and calcarine anatomic landmarks within stereotaxic proportional coordinates. Am J Neuroradiol 11(6):1123–1130

    PubMed  CAS  Google Scholar 

  • Stensaas SS, Eddington DK, Dobelle WH (1974) The topography and variability of the primary visual cortex in man. J Neurosurg 40:747–755

    Article  PubMed  CAS  Google Scholar 

  • Subsol G, Roberts N, Doran M et al (1997) Automatic analysis of cerebral atrophy. magn reson imaging 15(8):917–927

    Article  PubMed  CAS  Google Scholar 

  • Swanson LW (1992) Brain maps: structure of the rat brain. Elsevier, Amsterdam

    Google Scholar 

  • Talairach J, Szikla G (1967) Atlas d’Anatomie Stereotaxique du Telencephale: Etudes Anatomo-Radiologiques. Masson and Cie, Paris

    Google Scholar 

  • Talairach J, Tournoux P (1988) Co-planar stereotaxic atlas of the human brain. Thieme, New York

    Google Scholar 

  • Thirion J-P, Prima S, Subsol S (1998) Statistical analysis of dissymmetry in volumetric medical images, INRIA Tech Report RR-3178

  • Thompson PM, Toga AW (1997) Detection, visualization and animation of abnormal anatomic structure with a deformable probabilistic brain atlas based on random vector field transformations. Med Image Anal 1(4):271–294

    Article  PubMed  CAS  Google Scholar 

  • Thompson PM, Toga AW (1998) Anatomically-driven strategies for high-dimensional brain image warping and pathology detection. In: Toga AW (ed) Brain warping. Academic, New York

    Google Scholar 

  • Thompson PM, Schwartz C, Lin RT et al (1996) 3D statistical analysis of sulcal variability in the human brain. J Neurosci 16(13):4261–4274

    PubMed  CAS  Google Scholar 

  • Thompson PM, Giedd JN, Woods RP et al (2000a) Growth patterns in the developing brain detected by using continuum-mechanical tensor maps. Nature 404:190–193

    Article  PubMed  CAS  Google Scholar 

  • Thompson PM, Mega MS, Toga AW (2000b) Disease-specific brain atlases. In: Toga AW, Mazziotta JC (eds) Brain mapping: the disorders. Academic, New York

    Google Scholar 

  • Thompson PM, Mega MS, Toga AW (2000c) Disease-specific probabilistic brain atlases. In: IEEE international conference on computer vision and pattern recognition, pp 227–234

  • Thompson PM, Woods RP, Mega MS et al (2000d) Mathematical/computational challenges in creating population-based brain atlases, [invited paper]. Hum Brain Mapp 9(2):81–92

    Article  PubMed  CAS  Google Scholar 

  • Thompson PM, Cannon TD, Narr KL, van Erp T, Poutanen V-P, Hutteunen M, Lönnqvist J, Standertskjöld-Nordenstam C-G, Kaprio J, Khaledy M, Dail R, Zoumalen CI, Toga AW (2001a) Genetic influences on brain structure. Nat Neurosci 4(12):1253–1258

    Article  PubMed  CAS  Google Scholar 

  • Thompson PM, Mega MS, Vidal C et al (2001b) Detecting disease-specific patterns of brain structure using cortical pattern matching and a population-based probabilistic brain atlas. In: IEEE conference on information processing in medical imaging (IPMI), UC Davis

  • Thompson PM, Mega MS, Woods RP et al (2001c) Early cortical change in Alzheimer’s disease detected with a disease-specific population-based brain atlas. Cereb Cortex 11(1):1–16

    Article  PubMed  CAS  Google Scholar 

  • Thompson PM, Vidal C, Giedd JN, Gochman P, Blumenthal J, Nicolson R, Toga AW, Rapoport JL (2001d). Mapping adolescent brain change reveals dynamic wave of accelerated gray matter loss in very early-onset Schizophrenia. In: Proceedings of the National Academy of Sciences of the USA 98(20):11650–11655, 25 September 2001

  • Thompson PM, Rapport JL, Cannon TD, Toga AW (2002) Imaging the brain as schizophrenia develops: dynamic and genetic brain maps. Prim Psychiatry 9(11):40–47

    PubMed  Google Scholar 

  • Thompson PM, Hayashi KM, de Zubicaray G, Janke AL, Rose SE, Semple J, Herman D, Hong MS, Dittmer SS, Doddrell DM, Toga AW (2003) Dynamics of gray matter loss in Alzheimer’s disease. J Neurosci 23(3):994–1005

    PubMed  CAS  Google Scholar 

  • Thompson PM, Hayashi KM, Simon SL, Geaga JA, Hong MS, Sui Y, Lee JY, Toga AW, Ling W, London ED (2004). Structural abnormalities in the brains of human subjects who use methamphetamine. J Neurosci 24(26):6028–6036, 30 June 2004

    Google Scholar 

  • Toga AW (1998) Brain warping. Academic, New York

    Google Scholar 

  • Toga AW, Ambach K, Quinn B et al (1994) Postmortem anatomy from cryosectioned whole human brain. J Neurosci Methods 54(2):239–252

    Article  PubMed  CAS  Google Scholar 

  • Toga AW, Thompson PM, Payne BA (1996) Modeling morphometric changes of the brain during development. In: Thatcher RW, Lyon GR, Rumsey J, Krasnegor N (eds) Developmental neuroimaging: mapping the development of brain and behavior. Academic, New York

    Google Scholar 

  • Van Essen DC, Maunsell JHR (1983) Hierarchical organization an functional streams in the visual cortex. Trends Neurol Sci 6:370–375

    Article  Google Scholar 

  • Watson JDG, Myers R, Frackowiak RSJ et al (1993) Area V5 of the human brain: evidence form a combined study using positron emission tomography and magnetic resonance imaging. Cereb Cortex 3:79–94

    Article  PubMed  CAS  Google Scholar 

  • Woods RP (1996) Modeling for intergroup comparisons of imaging data. Neuroimage 4(3):84–94

    Article  Google Scholar 

  • Zeineh MM, Engel SA, Thompson PM et al (2001) Unfolding the human hippocampus with high-resolution structural and functional mri [invited paper]. New Anat 265(2):111–120

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was generously supported by research grants from the CCB (U54 RR021813), P41 (P41 RR013642), National Library of Medicine (LM/MH005639) and by a Human Brain Project grant known as the International Consortium for Brain Mapping, which is funded jointly by NIMH and NIDA (P01 EB001955).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Arthur W. Toga.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Toga, A.W. Computational biology for visualization of brain structure. Anat Embryol 210, 433–438 (2005). https://doi.org/10.1007/s00429-005-0040-6

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00429-005-0040-6

Keywords

Navigation