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  Size and shape matter: The impact of voxel geometry on the identification of small nuclei

Mulder, M. J., Keuken, M. C., Bazin, P.-L., Alkemade, A., & Forstmann, B. U. (2019). Size and shape matter: The impact of voxel geometry on the identification of small nuclei. PLoS One, 14(4): e0215382. doi:10.1371/journal.pone.0215382.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0003-7E92-B Version Permalink: http://hdl.handle.net/21.11116/0000-0003-8BEB-8
Genre: Journal Article

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 Creators:
Mulder, Martijn J. 1, Author
Keuken, Max C. 1, Author
Bazin, Pierre-Louis1, 2, Author              
Alkemade, Anneke 1, Author
Forstmann, Birte U. 1, Author
Affiliations:
1Integrative Model-Based Cognitive Neuroscience Research Unit (IMCN), University of Amsterdam, the Netherlands, ou_persistent22              
2Department Neurology, MPI for Human Cognitive and Brain Sciences, Max Planck Society, ou_634549              

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 Abstract: How, and to what extent do size and shape of a voxel measured with magnetic resonance imaging (MRI) affect the ability to visualize small brain nuclei? Despite general consensus that voxel geometry affects volumetric properties of regions of interest, particularly those of small brain nuclei, no quantitative data on the influence of voxel size and shape on labeling accuracy is available. Using simulations, we investigated the selective influence of voxel geometry by reconstructing simulated ellipsoid structures with voxels varying in shape and size. For each reconstructed ellipsoid, we calculated differences in volume and similarity between the labeled volume and the predefined dimensions of the ellipsoid. Probability functions were derived from one or two individual raters and a simulated ground truth for reference. As expected, larger voxels (i.e., coarser resolution) and increasing anisotropy results in increased deviations of both volume and shape measures, which is of particular relevance for small brain structures. Our findings clearly illustrate the anatomical inaccuracies introduced by the application of large and/or anisotropic voxels. To ensure deviations occur within the acceptable range (Dice coefficient scores; DCS > 0.75, corresponding to < 57% volume deviation), the volume of isotropic voxels should not exceed 5% of the total volume of the region of interest. When high accuracy is required (DCS > 0.90, corresponding to a < 19% volume deviation), the volumes of isotropic voxels should not exceed 0.08%, of the total volume. Finally, when large anisotropic factors (>3) are used, and the ellipsoid is orthogonal to the slice axes, having its long axis in the imaging plane, the voxel volume should not exceed 0.005% of the total volume. This allows sufficient compensation of anisotropy effects, in order to reach accuracy in the acceptable range (DCS > 0.75, corresponding to >57% volume deviation).

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Language(s): eng - English
 Dates: 2018-10-032019-04-012019-04-12
 Publication Status: Published online
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 Rev. Method: Peer
 Identifiers: DOI: 10.1371/journal.pone.0215382
PMID: 30978242
Other: eCollection 2019
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Project name : -
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Funding program : Vidi Grant
Funding organization : Dutch Organization for Scientific Research
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Funding program : ERC Grant
Funding organization : European Union (EU)
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Funding program : STW Grant
Funding organization : Dutch Organization for Scientific Research
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Funding program : ABC Talent Grant
Funding organization : University of Amsterdam

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Title: PLoS One
Source Genre: Journal
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Publ. Info: San Francisco, CA : Public Library of Science
Pages: - Volume / Issue: 14 (4) Sequence Number: e0215382 Start / End Page: - Identifier: ISSN: 1932-6203
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000277850