WIC 2014 Tutorial - Atlas of the human brain, head and neck

Atlas of the human brain, head and neck: introducing a new standard

Wiesław L. Nowinski - Biomedical Imaging Lab, Agency for Science Technology and Research, Singapore

The 21st century is considered a century of the brain, and we recently witness unprecedented brain projects. Our contribution is to create adult human brain atlases in health and disease, and to develop atlas-based applications. So far, we have created 34 brain atlases.
The latest generation of our brain atlases has been constructed from in vivo imaging by employing multiple MR 3 and 7 Tesla, and high resolution CT scans of the same brain specimen. The virtual model of the brain, head and neck has been parcellated into about 3,000 3D components, including the cerebrum (with the cortex parcellated into lobes, gyri, gyri and sulci, and Brodmann's areas), cerebellum, brainstem, spinal cord, (cerebral, posterior fossa and deep) white matter, deep gray nuclei, ventricles, intracranial arteries, intracranial veins, dural sinuses, white matter tracts, visual system, cranial nerves with nuclei, extracranial arteries, extracranial veins, head muscles, pharynx, glands, cervical vertebrae, skull, and skin.

Our objectives are: 

    • To overview the existing big brain atlas projects
    • To provide taxonomy of the brain atlases developed in our lab
    • To present the design principles, methods, tools and applications of the new atlas
    • To explore the brain, head and neck by means of the new atlas.


    1. 1.Nowinski WL, Chua BC, Puspitasari F, et al. Three-dimensional reference and stereotactic atlas of human cerebrovasculature from 7 Tesla. NeuroImage 2011;55(3):986-98.

    2. Nowinski WL, Chua BC, Qian GY, et al. The human brain in 1700 pieces: design and development of a three-dimensional, interactive and reference atlas. J. Neurosci. Methods 2012;15;204(1):44-60.

    3. Nowinski WL, Chua BC, Yang GL, et al. Three-dimensional interactive human brain atlas of white matter tracts. Neuroinformatics 2012;10(1):33-55.

    4. Nowinski WL, Johnson A, Chua BC, et al. Three-dimensional interactive and stereotactic atlas of cranial nerves and nuclei correlated with surface neuroanatomy, vasculature and magnetic resonance imaging. J. Neurosci. Methods 2012;206(2):205-216.

    5. Nowinski WL, Chua BC, Johnson A, et al. Three-dimensional interactive and stereotactic atlas of head muscles and glands correlated with cranial nerves and surface and sectional neuroanatomy. J. Neurosci. Methods 2013;215(1):12-18.

    6. Nowinski WL. Proposition of a new classification of the cerebral veins based on their termination. Surgical and Radiologic Anatomy 2012;34(2):107-114.

    7. Nowinski WL. Towards constructing an ideal stereotactic brain atlas. Acta Neurochirurgica 2008;150(1):1-14.

    8. Nowinski WL, A Thirunavuukarasuu A, Ananthasubramaniam A, Chua BC, Qian G, Nowinska NG, et al. Automatic testing and assessment of neuroanatomy using a digital brain atlas: method and development of computer- and mobile-based applications. Anatomical Sciences Education 2009;2(5):244-52.

    9. Nowinski WL, A Thirunavuukarasuu, Volkau I, Marchenko Y, et al. A new presentation and exploration of human cerebral vasculature correlated with surface and sectional neuroanatomy. Anatomical Sciences Education 2009;2(1):24-33.

    10. Nowinski WL. Analysis of medical images by means of brain atlases. Computer Graphics and Vision 1999;8(3):449-468.

    11. Nowinski WL, Thirunavuukarasuu A. Atlas-assisted localization analysis of functional images. Medical Image Analysis 2001 Sep;5(3):207-220.

    12. Nowinski WL. Human brain atlases in education, research and clinical applications. In: Complex Medical Engineering (eds Wu JL, Ito K, Tobimatsu S, Nishida T, Fukuyama H), Springer, Tokyo 2007:335-349.

    13. Nowinski WL: Electronic brain atlases: features and applications. In: 3D Image Processing: Techniques and Clinical Applications (eds. Caramella D, Bartolozzi C). Medical Radiology series, Springer, Berlin 2002:79-93.

    14. Nowinski WL. Anatomical and probabilistic functional atlases in stereotactic and functional neurosurgery. In: Textbook of Stereotactic and Functional Neurosurgery (eds. Lozano A, Gildenberg P, Tasker R), 2ed edition. Springer, Berlin 2009:395-441.

    15. Nowinski WL, Benabid AL. New directions in atlas-assisted stereotactic functional neurosurgery. In: Advanced Techniques in Image-Guided Brain and Spine Surgery (ed. Germano IM), Thieme, New York, 2002:162-174.

    16. Nowinski WL. Computerized brain atlases for surgery of movement disorders. Seminars in Neurosurgery 2001;12(2):183-194.

    17. Nowinski WL, Qian G, Bhanu Prakash KN, Thirunavuukarasuu A, et al. Analysis of ischemic stroke MR images by means of brain atlases of anatomy and blood supply territories. Academic Radiology 2006;13(8):1025-34.

    18. Nowinski WL, Qian G, Bhanu Prakash KN, Hu Q, Aziz A. Fast Talairach Transformation for magnetic resonance neuroimages. Journal of Computer Assisted Tomography 2006;30(4):629-41.

    19. Nowinski WL, Belov D. Towards atlas-assisted automatic interpretation of MRI morphological brain scans in the presence of tumor. Academic Radiology 2005;12:1049–1057.

    20. Nowinski WL, Thirunavuukarasuu A. A locus-driven mechanism for rapid and automated atlas-assisted analysis of functional images by using the Brain Atlas for Functional Imaging. Neurosurgical Focus, 15(1), Article 3, 2003.

    21. Nowinski WL, Chua BC, Qian GY, Nowinska NG. The Human Brain in 1969 Pieces: Structure, Vasculature, Tracts, Cranial Nerves, and Systems. Thieme, New York, 2013.

    22. Nowinski WL, Chua BC. The Human Brain in 1969 Pieces: Structure, Vasculature, Tracts, Cranial Nerves, Systems, Head Muscles, and Glands (version 2.0). Thieme, New York, 2014.

    23. Nowinski WL, Chua BC. The Complete Human Brain (version 1.0 for iPad). Thieme, New York, 2013/AppStore.

    24. Nowinski WL, Chua BC, Volkau I, Puspitasari F, Marchenko Y, Runge VM, Knopp MV. Simulation and assessment of cerebrovascular damage in deep brain stimulation using a stereotactic atlas of vasculature and structure derived from multiple 3T and 7T scans. Journal of Neurosurgery 2010;113(6):1234-41.

    25. Nowinski WL, Chua BC. Bridging neuroanatomy, neuroradiology and neurology: three-dimensional interactive atlas of neurological disorders. The Neuroradiology Journal 2013;26(3):252-62.

    26. Nowinski WL, Chua BC. Three-dimensional interactive atlas of cranial nerve-related disorders. The Neuroradiology Journal 2013;26(3):263-75.

    27. Nowinski WL, Chua BC. Stroke Atlas: a 3D interactive tool correlating cerebrovascular pathology with underlying neuroanatomy and resulting neurological deficits. The Neuroradiology Journal 2013;26(1):56-65.

    28. Nowinski WL, Chua BC, Ngai V. 3D Atlas of Neurologic Disorders (version 1.0 for iPad). Thieme, New York, 2013/AppStore.

    29. Nowinski WL, Fang A, Nguyen BT, Raphel JK, Jagannathan L, Raghavan R, Bryan RN, Miller G. Multiple brain atlas database and atlas-based neuroimaging system. Computer Aided Surgery 1997;2(1):42-66.

    30. Nowinski WL, Belov D, Benabid AL. An algorithm for rapid calculation of a probabilistic functional atlas of subcortical structures from electrophysiological data collected during functional neurosurgery procedures. NeuroImage 2003;18(1):143-155.

    31. Nowinski WL, Belov D, Pollak P, Benabid AL: A probabilistic functional atlas of the human subthalamic nucleus. Neuroinformatics 2004;2(4):381-398.

    32. Nowinski WL, Belov D, Pollack P, Benabid AL. Statistical analysis of 168 bilateral subthalamic nucleus implantations by means of the probabilistic functional atlas. Neurosurgery 2005 Oct;57(4 Suppl):319-330.

    33. Nowinski WL, Belov D, A. Thirunavuukarasuu, Benabid AL. A probabilistic functional atlas of the VIM nucleus constructed from pre-, intra- and post-operative electrophysiological and neuroimaging data acquired during the surgical treatment of Parkinson’s disease patients. Stereotactic and Functional Neurosurgery 2006 Jan;83(5-6):190-196.

    34. Nowinski WL, Thirunavuukarasuu A, Liu J, Benabid AL. Correlation between the anatomical and functional human subthalamic nucleus. Stereotactic and Functional Neurosurgery 2007;85(2-3):88-93.

    35. Nowinski WL. Co-registration of the Schaltenbrand-Wahren microseries with the probabilistic functional atlas. Stereotactic and Functional Neurosurgery 2004;82:142-146.

    36. Nowinski WL, A. Thirunnavuukarasuu, Volkau I, Marchenko Y, Aminah B, Puspitasaari F, Runge VM. A three-dimensional interactive atlas of cerebral arterial variants. Neuroinformatics 2009;7(4):255-264.


    Prof. Wiesław L. Nowinski, DSc, PhD is principal scientist and director of the Biomedical Imaging Lab, Agency for Science, Technology and Research, Singapore. His research includes brain atlases, stroke, deep brain stimulation, brain quantification, neuroinformatics, medical image processing, virtual reality, computer-assisted diagnosis and treatment, and future directions in computer-aided radiology and surgery.
    He has 535 publications, filed 51 patent applications (32 already granted, 15 in US), and developed with his team 34 brain atlas products used worldwide in neurosurgery, neuroradiology, neurology, brain mapping, and neuroeducation. These atlases have been licensed to 62 companies and institutions. Fourteen brain atlases have been distributed by Thieme Medical Publishers, New York - Stuttgart. The atlases are also installed in 1,500 surgical workstations.
    Dr. Nowinski has been conferred with 42 awards and honours; 25 awards are from leading medical societies, including Pioneer in Medicine in 2013 from Society for Brain Mapping & Therapeutics, Magna cum Laude (radiological Oscar) from Radiological Society of North America in 2009 and 2004; Magna cum Laude from European Congress of Radiology in 2000; Summa cum Laude in 2014, 2012, 2008 and 1997, and Magna cum Laude in 2009 and 2005 from American Society of Neuroradiology. He has been named The Outstanding Pole (in the world) in 2012. His work has been featured in The Wall Street Journal and on The Discovery Channel.

    More at www.WieslawNowinski.com



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