1. Neuroscience

Multi-contrast anatomical subcortical structures parcellation

  1. Pierre-Louis Bazin  Is a corresponding author
  2. Anneke Alkemade
  3. Martijn J Mulder
  4. Amanda G Henry
  5. Birte U Forstmann
  1. University of Amsterdam, Netherlands
  2. Universiteit Utrecht, Netherlands
  3. Leiden University, Netherlands
https://doi.org/10.7554/eLife.59430
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  1. Pierre-Louis Bazin
  2. Anneke Alkemade
  3. Martijn J Mulder
  4. Amanda G Henry
  5. Birte U Forstmann
(2020)
Multi-contrast anatomical subcortical structures parcellation
eLife 9:e59430.
https://doi.org/10.7554/eLife.59430
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Abstract

The human subcortex is comprised of more than 450 individual nuclei which lie deep in the brain. Due to their small size and close proximity, up until now only 7% have been depicted in standard MRI atlases. Thus, the human subcortex can largely be considered as terra incognita. Here we present a new open source parcellation algorithm to automatically map the subcortex. The new algorithm has been tested on 17 prominent subcortical structures based on a large quantitative MRI dataset at 7 Tesla. It has been carefully validated against expert human raters and previous methods, and can easily be extended to other subcortical structures and applied to any quantitative MRI dataset. In sum, we hope this novel parcellation algorithm will facilitate functional and structural neuroimaging research into small subcortical nuclei and help to chart terra incognita.

Data availability

The tool presented in this article is available in open source on Github (https://github.com/nighres/nighres). The atlases necessary to run the algorithm have been deposited on the University of Amsterdam FigShare (https://doi.org/10.21942/uva.12074175.v1 and https://doi.org/10.21942/uva.12301106.v2). A single sample subject data set has been deposited on the University of Amsterdam FigShare (https://doi.org/10.21942/uva.12280316.v2). All the measurements used to generate the figures included in the article have been deposited on the University of Amsterdam FigShare (https://doi.org/10.21942/uva.12452444.v1).

The following previously published data sets were used

Article and author information

Author details

  1. Pierre-Louis Bazin

    Psychology, University of Amsterdam, Amsterdam, Netherlands
    For correspondence
    pilou.bazin@uva.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0141-5510

  2. Anneke Alkemade

    IMCN, University of Amsterdam, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3234-353X

  3. Martijn J Mulder

    Psychology, Universiteit Utrecht, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.

  4. Amanda G Henry

    Archaeological Sciences, Leiden University, Leiden, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2923-4199

  5. Birte U Forstmann

    Department of Psychology, University of Amsterdam, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1005-1675

Funding

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (VICI)

  • Birte U Forstmann

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (STW)

  • Anneke Alkemade
  • Birte U Forstmann

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Timothy Verstynen, Carnegie Mellon University, United States

Ethics

Human subjects: Informed consent and consent to publish, including consent to publish anonymized imaging data, was obtained for all subjects. Ethical approval was obtained with the University of Amsterdam Faculty of Social and Behavioral Sciences LAB Ethics Review Board, with ERB number 2016-DP-6897.

Version history

  1. Received: May 28, 2020
  2. Accepted: December 15, 2020
  3. Accepted Manuscript published: December 16, 2020 (version 1)
  4. Version of Record published: December 29, 2020 (version 2)

Copyright

© 2020, Bazin et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Pierre-Louis Bazin
  2. Anneke Alkemade
  3. Martijn J Mulder
  4. Amanda G Henry
  5. Birte U Forstmann
(2020)
Multi-contrast anatomical subcortical structures parcellation
eLife 9:e59430.
https://doi.org/10.7554/eLife.59430

Share this article

https://doi.org/10.7554/eLife.59430

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