Multi-contrast anatomical subcortical structures parcellation

Abstract
Data availability
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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

1. Alkemade A
2. Mulder MJ
3. Groot JM
4. Isaacs BR
5. van Berendonk N
6. Lute N
7. Isherwood SJ
8. Bazin P-L
9. Forstmann BU
(2020) The Amsterdam Ultra-high field adult lifespan database (AHEAD): A freely available multimodal 7 Tesla submillimeter magnetic resonance imaging database
FigShare University of Amsterdam / Amsterdam University of Applied Sciences.

https://doi.org/10.21942/uva.10007840.v1
1. Van Essen DC
2. Smith SM
3. Barch DM
4. Behrens TEJ
5. Yacoub E
6. Ugurbil K
(2013) The WU-Minn Human Connectome Project
WU-Minn HCP Retest Data.

https://www.humanconnectome.org/study/hcp-young-adult

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0002-0141-5510
Anneke Alkemade

IMCN, University of Amsterdam, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3234-353X
Martijn J Mulder

Psychology, Universiteit Utrecht, Utrecht, Netherlands

Competing interests
The authors declare that no competing interests exist.
Amanda G Henry

Archaeological Sciences, Leiden University, Leiden, Netherlands

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2923-4199
Birte U Forstmann

Department of Psychology, University of Amsterdam, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.

"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.

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.

Copyright

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.