A spatio-temporal atlas of the developing fetal brain with spina bifida aperta

Lucas Fidon; Elizabeth Viola; Nada Mufti; Anna L. David; Andrew Melbourne; Philippe Demaerel; Sébastien Ourselin; Tom Vercauteren; Jan Deprest; Michael Aertsen

doi:10.12688/openreseurope.13914.2

A spatio-temporal atlas of the developing fetal brain with spina bifida aperta

Lucas Fidon^*, Elizabeth Viola, Nada Mufti, Anna L. David, Andrew Melbourne, Philippe Demaerel, Sébastien Ourselin, Tom Vercauteren, Jan Deprest, Michael Aertsen

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

11 Citations (Scopus)

Abstract

Background: Spina bifida aperta (SBA) is a birth defect associated with severe anatomical changes in the developing fetal brain. Brain magnetic resonance imaging (MRI) atlases are popular tools for studying neuropathology in the brain anatomy, but previous fetal brain MRI atlases have focused on the normal fetal brain. We aimed to develop a spatio-temporal fetal brain MRI atlas for SBA. Methods: We developed a semi-automatic computational method to compute the first spatio-temporal fetal brain MRI atlas for SBA. We used 90 MRIs of fetuses with SBA with gestational ages ranging from 21 to 35 weeks. Isotropic and motion-free 3D reconstructed MRIs were obtained for all the examinations. We propose a protocol for the annotation of anatomical landmarks in brain 3D MRI of fetuses with SBA with the aim of making spatial alignment of abnormal fetal brain MRIs more robust. In addition, we propose a weighted generalized Procrustes method based on the anatomical landmarks for the initialization of the atlas. The proposed weighted generalized Procrustes can handle temporal regularization and missing annotations. After initialization, the atlas is refined iteratively using non-linear image registration based on the image intensity and the anatomical land-marks. A semi-automatic method is used to obtain a parcellation of our fetal brain atlas into eight tissue types: white matter, ventricular system, cerebellum, extra-axial cerebrospinal fluid, cortical gray matter, deep gray matter, brainstem, and corpus callosum. Results: An intra-rater variability analysis suggests that the seven anatomical land-marks are sufficiently reliable. We find that the proposed atlas outperforms a normal fetal brain atlas for the automatic segmentation of brain 3D MRI of fetuses with SBA. Conclusions: We make publicly available a spatio-temporal fetal brain MRI atlas for SBA, available here: https://doi.org/10.7303/syn25887675. This atlas can support future research on automatic segmentation methods for brain 3D MRI of fetuses with SBA.

Original language	English
Article number	123
Journal	Open Research Europe
Volume	1
DOIs	https://doi.org/10.12688/openreseurope.13914.2
Publication status	Published - 2022

Keywords

Anatomical landmarks
Fetal brain atlas
Fetal brain development
Fetal brain T2-weighted MRI
Segmentation
Spatio-temporal atlas
Spina bifida aperta
Super resolution and reconstruction

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10.12688/openreseurope.13914.2

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@article{3e9cb885909d4fb8b77157c23a3fd09d,

title = "A spatio-temporal atlas of the developing fetal brain with spina bifida aperta",

abstract = "Background: Spina bifida aperta (SBA) is a birth defect associated with severe anatomical changes in the developing fetal brain. Brain magnetic resonance imaging (MRI) atlases are popular tools for studying neuropathology in the brain anatomy, but previous fetal brain MRI atlases have focused on the normal fetal brain. We aimed to develop a spatio-temporal fetal brain MRI atlas for SBA. Methods: We developed a semi-automatic computational method to compute the first spatio-temporal fetal brain MRI atlas for SBA. We used 90 MRIs of fetuses with SBA with gestational ages ranging from 21 to 35 weeks. Isotropic and motion-free 3D reconstructed MRIs were obtained for all the examinations. We propose a protocol for the annotation of anatomical landmarks in brain 3D MRI of fetuses with SBA with the aim of making spatial alignment of abnormal fetal brain MRIs more robust. In addition, we propose a weighted generalized Procrustes method based on the anatomical landmarks for the initialization of the atlas. The proposed weighted generalized Procrustes can handle temporal regularization and missing annotations. After initialization, the atlas is refined iteratively using non-linear image registration based on the image intensity and the anatomical land-marks. A semi-automatic method is used to obtain a parcellation of our fetal brain atlas into eight tissue types: white matter, ventricular system, cerebellum, extra-axial cerebrospinal fluid, cortical gray matter, deep gray matter, brainstem, and corpus callosum. Results: An intra-rater variability analysis suggests that the seven anatomical land-marks are sufficiently reliable. We find that the proposed atlas outperforms a normal fetal brain atlas for the automatic segmentation of brain 3D MRI of fetuses with SBA. Conclusions: We make publicly available a spatio-temporal fetal brain MRI atlas for SBA, available here: https://doi.org/10.7303/syn25887675. This atlas can support future research on automatic segmentation methods for brain 3D MRI of fetuses with SBA.",

keywords = "Anatomical landmarks, Fetal brain atlas, Fetal brain development, Fetal brain T2-weighted MRI, Segmentation, Spatio-temporal atlas, Spina bifida aperta, Super resolution and reconstruction",

author = "Lucas Fidon and Elizabeth Viola and Nada Mufti and David, {Anna L.} and Andrew Melbourne and Philippe Demaerel and S{\'e}bastien Ourselin and Tom Vercauteren and Jan Deprest and Michael Aertsen",

note = "Publisher Copyright: {\textcopyright} 2022 Fidon L et al.",

year = "2022",

doi = "10.12688/openreseurope.13914.2",

language = "English",

volume = "1",

journal = "Open Research Europe",

issn = "2732-5121",

publisher = "Taylor and Francis",

}

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T1 - A spatio-temporal atlas of the developing fetal brain with spina bifida aperta

AU - Fidon, Lucas

AU - Viola, Elizabeth

AU - Mufti, Nada

AU - David, Anna L.

AU - Melbourne, Andrew

AU - Demaerel, Philippe

AU - Ourselin, Sébastien

AU - Vercauteren, Tom

AU - Deprest, Jan

AU - Aertsen, Michael

PY - 2022

Y1 - 2022

N2 - Background: Spina bifida aperta (SBA) is a birth defect associated with severe anatomical changes in the developing fetal brain. Brain magnetic resonance imaging (MRI) atlases are popular tools for studying neuropathology in the brain anatomy, but previous fetal brain MRI atlases have focused on the normal fetal brain. We aimed to develop a spatio-temporal fetal brain MRI atlas for SBA. Methods: We developed a semi-automatic computational method to compute the first spatio-temporal fetal brain MRI atlas for SBA. We used 90 MRIs of fetuses with SBA with gestational ages ranging from 21 to 35 weeks. Isotropic and motion-free 3D reconstructed MRIs were obtained for all the examinations. We propose a protocol for the annotation of anatomical landmarks in brain 3D MRI of fetuses with SBA with the aim of making spatial alignment of abnormal fetal brain MRIs more robust. In addition, we propose a weighted generalized Procrustes method based on the anatomical landmarks for the initialization of the atlas. The proposed weighted generalized Procrustes can handle temporal regularization and missing annotations. After initialization, the atlas is refined iteratively using non-linear image registration based on the image intensity and the anatomical land-marks. A semi-automatic method is used to obtain a parcellation of our fetal brain atlas into eight tissue types: white matter, ventricular system, cerebellum, extra-axial cerebrospinal fluid, cortical gray matter, deep gray matter, brainstem, and corpus callosum. Results: An intra-rater variability analysis suggests that the seven anatomical land-marks are sufficiently reliable. We find that the proposed atlas outperforms a normal fetal brain atlas for the automatic segmentation of brain 3D MRI of fetuses with SBA. Conclusions: We make publicly available a spatio-temporal fetal brain MRI atlas for SBA, available here: https://doi.org/10.7303/syn25887675. This atlas can support future research on automatic segmentation methods for brain 3D MRI of fetuses with SBA.

AB - Background: Spina bifida aperta (SBA) is a birth defect associated with severe anatomical changes in the developing fetal brain. Brain magnetic resonance imaging (MRI) atlases are popular tools for studying neuropathology in the brain anatomy, but previous fetal brain MRI atlases have focused on the normal fetal brain. We aimed to develop a spatio-temporal fetal brain MRI atlas for SBA. Methods: We developed a semi-automatic computational method to compute the first spatio-temporal fetal brain MRI atlas for SBA. We used 90 MRIs of fetuses with SBA with gestational ages ranging from 21 to 35 weeks. Isotropic and motion-free 3D reconstructed MRIs were obtained for all the examinations. We propose a protocol for the annotation of anatomical landmarks in brain 3D MRI of fetuses with SBA with the aim of making spatial alignment of abnormal fetal brain MRIs more robust. In addition, we propose a weighted generalized Procrustes method based on the anatomical landmarks for the initialization of the atlas. The proposed weighted generalized Procrustes can handle temporal regularization and missing annotations. After initialization, the atlas is refined iteratively using non-linear image registration based on the image intensity and the anatomical land-marks. A semi-automatic method is used to obtain a parcellation of our fetal brain atlas into eight tissue types: white matter, ventricular system, cerebellum, extra-axial cerebrospinal fluid, cortical gray matter, deep gray matter, brainstem, and corpus callosum. Results: An intra-rater variability analysis suggests that the seven anatomical land-marks are sufficiently reliable. We find that the proposed atlas outperforms a normal fetal brain atlas for the automatic segmentation of brain 3D MRI of fetuses with SBA. Conclusions: We make publicly available a spatio-temporal fetal brain MRI atlas for SBA, available here: https://doi.org/10.7303/syn25887675. This atlas can support future research on automatic segmentation methods for brain 3D MRI of fetuses with SBA.

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KW - Fetal brain atlas

KW - Fetal brain development

KW - Fetal brain T2-weighted MRI

KW - Segmentation

KW - Spatio-temporal atlas

KW - Spina bifida aperta

KW - Super resolution and reconstruction

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VL - 1

JO - Open Research Europe

JF - Open Research Europe

M1 - 123

ER -

A spatio-temporal atlas of the developing fetal brain with spina bifida aperta

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