IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1005350.html
   My bibliography  Save this article

Mindboggling morphometry of human brains

Author

Listed:
  • Arno Klein
  • Satrajit S Ghosh
  • Forrest S Bao
  • Joachim Giard
  • Yrjö Häme
  • Eliezer Stavsky
  • Noah Lee
  • Brian Rossa
  • Martin Reuter
  • Elias Chaibub Neto
  • Anisha Keshavan

Abstract

Mindboggle (http://mindboggle.info) is an open source brain morphometry platform that takes in preprocessed T1-weighted MRI data and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis. In this article, we document the software and demonstrate its use in studies of shape variation in healthy and diseased humans. The number of different shape measures and the size of the populations make this the largest and most detailed shape analysis of human brains ever conducted. Brain image morphometry shows great potential for providing much-needed biological markers for diagnosing, tracking, and predicting progression of mental health disorders. Very few software algorithms provide more than measures of volume and cortical thickness, while more subtle shape measures may provide more sensitive and specific biomarkers. Mindboggle computes a variety of (primarily surface-based) shapes: area, volume, thickness, curvature, depth, Laplace-Beltrami spectra, Zernike moments, etc. We evaluate Mindboggle’s algorithms using the largest set of manually labeled, publicly available brain images in the world and compare them against state-of-the-art algorithms where they exist. All data, code, and results of these evaluations are publicly available.

Suggested Citation

  • Arno Klein & Satrajit S Ghosh & Forrest S Bao & Joachim Giard & Yrjö Häme & Eliezer Stavsky & Noah Lee & Brian Rossa & Martin Reuter & Elias Chaibub Neto & Anisha Keshavan, 2017. "Mindboggling morphometry of human brains," PLOS Computational Biology, Public Library of Science, vol. 13(2), pages 1-40, February.
    • Handle: RePEc:plo:pcbi00:1005350
    DOI: 10.1371/journal.pcbi.1005350
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350
    Download Restriction: no
    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005350&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pcbi.1005350?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Matthew F. Glasser & Timothy S. Coalson & Emma C. Robinson & Carl D. Hacker & John Harwell & Essa Yacoub & Kamil Ugurbil & Jesper Andersson & Christian F. Beckmann & Mark Jenkinson & Stephen M. Smith , 2016. "A multi-modal parcellation of human cerebral cortex," Nature, Nature, vol. 536(7615), pages 171-178, August.
    2. Hyuk Jin Yun & Kiho Im & Jin-Ju Yang & Uicheul Yoon & Jong-Min Lee, 2013. "Automated Sulcal Depth Measurement on Cortical Surface Reflecting Geometrical Properties of Sulci," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-10, February.
    3. Ravi Bansal & Lawrence H Staib & Andrew F Laine & Xuejun Hao & Dongrong Xu & Jun Liu & Myrna Weissman & Bradley S Peterson, 2012. "Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-21, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Angelika Maurer & Julian Klein & Jannik Claus & Neeraj Upadhyay & Leonie Henschel & Jason Anthony Martin & Lukas Scheef & Marcel Daamen & Theresa Schörkmaier & Rüdiger Stirnberg & Tony Stöcker & Alexa, 2022. "Effects of a 6-Month Aerobic Exercise Intervention on Mood and Amygdala Functional Plasticity in Young Untrained Subjects," IJERPH, MDPI, vol. 19(10), pages 1-19, May.
    2. Zachariah M. Reagh & Charan Ranganath, 2023. "Flexible reuse of cortico-hippocampal representations during encoding and recall of naturalistic events," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Benjamin Lahner & Kshitij Dwivedi & Polina Iamshchinina & Monika Graumann & Alex Lascelles & Gemma Roig & Alessandro Thomas Gifford & Bowen Pan & SouYoung Jin & N. Apurva Ratan Murty & Kendrick Kay & , 2024. "Modeling short visual events through the BOLD moments video fMRI dataset and metadata," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
    4. Kristjan Kalm & Dennis Norris, 2021. "Sequence learning recodes cortical representations instead of strengthening initial ones," PLOS Computational Biology, Public Library of Science, vol. 17(5), pages 1-34, May.
    5. Alexander Nitsch & Mona M. Garvert & Jacob L. S. Bellmund & Nicolas W. Schuck & Christian F. Doeller, 2024. "Grid-like entorhinal representation of an abstract value space during prospective decision making," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    6. Qi Huang & Zhibing Xiao & Qianqian Yu & Yuejia Luo & Jiahua Xu & Yukun Qu & Raymond Dolan & Timothy Behrens & Yunzhe Liu, 2024. "Replay-triggered brain-wide activation in humans," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    7. Hannah Tarder-Stoll & Christopher Baldassano & Mariam Aly, 2024. "The brain hierarchically represents the past and future during multistep anticipation," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    8. Nir Moneta & Mona M. Garvert & Hauke R. Heekeren & Nicolas W. Schuck, 2023. "Task state representations in vmPFC mediate relevant and irrelevant value signals and their behavioral influence," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    9. Farnaz Zamani Esfahlani & Joshua Faskowitz & Jonah Slack & Bratislav Mišić & Richard F. Betzel, 2022. "Local structure-function relationships in human brain networks across the lifespan," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    10. Maria Salfer & Javier F Collado & Wolfgang Baumeister & Rubén Fernández-Busnadiego & Antonio Martínez-Sánchez, 2020. "Reliable estimation of membrane curvature for cryo-electron tomography," PLOS Computational Biology, Public Library of Science, vol. 16(8), pages 1-29, August.
    11. Rotem Botvinik-Nezer & Bogdan Petre & Marta Ceko & Martin A. Lindquist & Naomi P. Friedman & Tor D. Wager, 2024. "Placebo treatment affects brain systems related to affective and cognitive processes, but not nociceptive pain," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    12. M. Lumaca & P. E. Keller & G. Baggio & V. Pando-Naude & C. J. Bajada & M. A. Martinez & J. H. Hansen & A. Ravignani & N. Joe & P. Vuust & K. Vulić & K. Sandberg, 2024. "Frontoparietal network topology as a neural marker of musical perceptual abilities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Leon D. Lotter & Amin Saberi & Justine Y. Hansen & Bratislav Misic & Casey Paquola & Gareth J. Barker & Arun L. W. Bokde & Sylvane Desrivières & Herta Flor & Antoine Grigis & Hugh Garavan & Penny Gowl, 2024. "Regional patterns of human cortex development correlate with underlying neurobiology," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Haewon Nam & Chongwon Pae & Jinseok Eo & Maeng-Keun Oh & Hae-Jeong Park, 2021. "Inter-species cortical registration between macaques and humans using a functional network property under a spherical demons framework," PLOS ONE, Public Library of Science, vol. 16(10), pages 1-22, October.
    3. Ann Hillier & Ryan P Kelly & Terrie Klinger, 2016. "Narrative Style Influences Citation Frequency in Climate Change Science," PLOS ONE, Public Library of Science, vol. 11(12), pages 1-12, December.
    4. Manish Saggar & James M. Shine & Raphaël Liégeois & Nico U. F. Dosenbach & Damien Fair, 2022. "Precision dynamical mapping using topological data analysis reveals a hub-like transition state at rest," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    5. Casey Paquola & Reinder Vos De Wael & Konrad Wagstyl & Richard A I Bethlehem & Seok-Jun Hong & Jakob Seidlitz & Edward T Bullmore & Alan C Evans & Bratislav Misic & Daniel S Margulies & Jonathan Small, 2019. "Microstructural and functional gradients are increasingly dissociated in transmodal cortices," PLOS Biology, Public Library of Science, vol. 17(5), pages 1-28, May.
    6. Peter Zhukovsky & Earvin S. Tio & Gillian Coughlan & David A. Bennett & Yanling Wang & Timothy J. Hohman & Diego A. Pizzagalli & Benoit H. Mulsant & Aristotle N. Voineskos & Daniel Felsky, 2024. "Genetic influences on brain and cognitive health and their interactions with cardiovascular conditions and depression," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    7. Tingting Bo & Jie Li & Ganlu Hu & Ge Zhang & Wei Wang & Qian Lv & Shaoling Zhao & Junjie Ma & Meng Qin & Xiaohui Yao & Meiyun Wang & Guang-Zhong Wang & Zheng Wang, 2023. "Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    8. Gustavo Deco & Diego Vidaurre & Morten L. Kringelbach, 2021. "Revisiting the global workspace orchestrating the hierarchical organization of the human brain," Nature Human Behaviour, Nature, vol. 5(4), pages 497-511, April.
    9. Martin Gell & Simon B. Eickhoff & Amir Omidvarnia & Vincent Küppers & Kaustubh R. Patil & Theodore D. Satterthwaite & Veronika I. Müller & Robert Langner, 2024. "How measurement noise limits the accuracy of brain-behaviour predictions," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    10. Sofie L. Valk & Ting Xu & Casey Paquola & Bo-yong Park & Richard A. I. Bethlehem & Reinder Vos de Wael & Jessica Royer & Shahrzad Kharabian Masouleh & Şeyma Bayrak & Peter Kochunov & B. T. Thomas Yeo , 2022. "Genetic and phylogenetic uncoupling of structure and function in human transmodal cortex," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    11. Natalie Weed & Trygve Bakken & Nile Graddis & Nathan Gouwens & Daniel Millman & Michael Hawrylycz & Jack Waters, 2019. "Identification of genetic markers for cortical areas using a Random Forest classification routine and the Allen Mouse Brain Atlas," PLOS ONE, Public Library of Science, vol. 14(9), pages 1-13, September.
    12. Zachariah M. Reagh & Charan Ranganath, 2023. "Flexible reuse of cortico-hippocampal representations during encoding and recall of naturalistic events," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    13. Daniel S. Kluger & Carina Forster & Omid Abbasi & Nikos Chalas & Arno Villringer & Joachim Gross, 2023. "Modulatory dynamics of periodic and aperiodic activity in respiration-brain coupling," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    14. Andrea I. Luppi & Helena M. Gellersen & Zhen-Qi Liu & Alexander R. D. Peattie & Anne E. Manktelow & Ram Adapa & Adrian M. Owen & Lorina Naci & David K. Menon & Stavros I. Dimitriadis & Emmanuel A. Sta, 2024. "Systematic evaluation of fMRI data-processing pipelines for consistent functional connectomics," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    15. Svenja Küchenhoff & Şeyma Bayrak & Rachel G. Zsido & Amin Saberi & Boris C. Bernhardt & Susanne Weis & H. Lina Schaare & Julia Sacher & Simon Eickhoff & Sofie L. Valk, 2024. "Relating sex-bias in human cortical and hippocampal microstructure to sex hormones," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    16. Gregory Kroliczak & Lukasz Przybylski, 2024. "Handedness and the control of human technology and language," Palgrave Communications, Palgrave Macmillan, vol. 11(1), pages 1-11, December.
    17. Ernst Schwartz & Karl-Heinz Nenning & Katja Heuer & Nathan Jeffery & Ornella C. Bertrand & Roberto Toro & Gregor Kasprian & Daniela Prayer & Georg Langs, 2023. "Evolution of cortical geometry and its link to function, behaviour and ecology," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    18. Mohamed Abdelhack & Peter Zhukovsky & Milos Milic & Shreyas Harita & Michael Wainberg & Shreejoy J. Tripathy & John D. Griffiths & Sean L. Hill & Daniel Felsky, 2023. "Opposing brain signatures of sleep in task-based and resting-state conditions," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    19. Santarnecchi, Emiliano & Emmendorfer, Alexandra & Pascual-Leone, Alvaro, 2017. "Dissecting the parieto-frontal correlates of fluid intelligence: A comprehensive ALE meta-analysis study," Intelligence, Elsevier, vol. 63(C), pages 9-28.
    20. Panagiotis Fotiadis & Matthew Cieslak & Xiaosong He & Lorenzo Caciagli & Mathieu Ouellet & Theodore D. Satterthwaite & Russell T. Shinohara & Dani S. Bassett, 2023. "Myelination and excitation-inhibition balance synergistically shape structure-function coupling across the human cortex," Nature Communications, Nature, vol. 14(1), pages 1-21, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1005350. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.