Desikan-Killiany-Tourville Atlas compatible version of m-CRIB neonatal parcellated whole brain atlas

The m-Crib 2.0

Bonnie Alexander, Wai Yen Loh, Lillian G. Matthews, Andrea L. Murray, Chris Adamson, Richard Beare, Jian Chen, Claire E. Kelly, Peter J. Anderson, Lex W. Doyle, Alicia J. Spittle, Jeanie L.Y. Cheong, Marc L. Seal, Deanne K. Thompson

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Our recently published M-CRIB atlas comprises 100 neonatal brain regions including 68 compatible with the widely-used Desikan-Killiany adult cortical atlas. A successor to the Desikan-Killiany atlas is the Desikan-Killiany-Tourville atlas, in which some regions with unclear boundaries were removed, and many existing boundaries were revised to conform to clearer landmarks in sulcal fundi. Our first aim here was to modify cortical M-CRIB regions to comply with the Desikan-Killiany-Tourville protocol, in order to offer: (a) compatibility with this adult cortical atlas, (b) greater labeling accuracy due to clearer landmarks, and (c) optimisation of cortical regions for integration with surface-based infant parcellation pipelines. Secondly, we aimed to update subcortical regions in order to offer greater compatibility with subcortical segmentations produced in FreeSurfer. Data utilized were the T2-weighted MRI scans in our M-CRIB atlas, for 10 healthy neonates (post-menstrual age at MRI 40-43 weeks, four female), and corresponding parcellated images. Edits were performed on the parcellated images in volume space using ITK-SNAP. Cortical updates included deletion of frontal and temporal poles and 'Banks STS,' and modification of boundaries of many other regions. Changes to subcortical regions included the addition of 'ventral diencephalon,' and deletion of 'subcortical matter' labels. A detailed updated parcellation protocol was produced. The resulting whole-brain M-CRIB 2.0 atlas comprises 94 regions altogether. This atlas provides comparability with adult Desikan-Killiany-Tourville-labeled cortical data and FreeSurfer-labeed subcortical data, and is more readily adaptable for incorporation into surface-based neonatal parcellation pipelines. As such, it offers the ability to help facilitate a broad range of investigations into brain structure and function both at the neonatal time point and developmentally across the lifespan.

Original languageEnglish
Article number34
Number of pages9
JournalFrontiers in Neuroscience
Volume13
DOIs
Publication statusPublished - 5 Feb 2019

Keywords

  • Ground truth
  • Infant
  • Manual tracing
  • Newborn
  • Parcellation
  • Segmentation

Cite this

Alexander, Bonnie ; Loh, Wai Yen ; Matthews, Lillian G. ; Murray, Andrea L. ; Adamson, Chris ; Beare, Richard ; Chen, Jian ; Kelly, Claire E. ; Anderson, Peter J. ; Doyle, Lex W. ; Spittle, Alicia J. ; Cheong, Jeanie L.Y. ; Seal, Marc L. ; Thompson, Deanne K. / Desikan-Killiany-Tourville Atlas compatible version of m-CRIB neonatal parcellated whole brain atlas : The m-Crib 2.0. In: Frontiers in Neuroscience. 2019 ; Vol. 13.
@article{d0394fdc42fb4228a4d9bad6bdee2c36,
title = "Desikan-Killiany-Tourville Atlas compatible version of m-CRIB neonatal parcellated whole brain atlas: The m-Crib 2.0",
abstract = "Our recently published M-CRIB atlas comprises 100 neonatal brain regions including 68 compatible with the widely-used Desikan-Killiany adult cortical atlas. A successor to the Desikan-Killiany atlas is the Desikan-Killiany-Tourville atlas, in which some regions with unclear boundaries were removed, and many existing boundaries were revised to conform to clearer landmarks in sulcal fundi. Our first aim here was to modify cortical M-CRIB regions to comply with the Desikan-Killiany-Tourville protocol, in order to offer: (a) compatibility with this adult cortical atlas, (b) greater labeling accuracy due to clearer landmarks, and (c) optimisation of cortical regions for integration with surface-based infant parcellation pipelines. Secondly, we aimed to update subcortical regions in order to offer greater compatibility with subcortical segmentations produced in FreeSurfer. Data utilized were the T2-weighted MRI scans in our M-CRIB atlas, for 10 healthy neonates (post-menstrual age at MRI 40-43 weeks, four female), and corresponding parcellated images. Edits were performed on the parcellated images in volume space using ITK-SNAP. Cortical updates included deletion of frontal and temporal poles and 'Banks STS,' and modification of boundaries of many other regions. Changes to subcortical regions included the addition of 'ventral diencephalon,' and deletion of 'subcortical matter' labels. A detailed updated parcellation protocol was produced. The resulting whole-brain M-CRIB 2.0 atlas comprises 94 regions altogether. This atlas provides comparability with adult Desikan-Killiany-Tourville-labeled cortical data and FreeSurfer-labeed subcortical data, and is more readily adaptable for incorporation into surface-based neonatal parcellation pipelines. As such, it offers the ability to help facilitate a broad range of investigations into brain structure and function both at the neonatal time point and developmentally across the lifespan.",
keywords = "Ground truth, Infant, Manual tracing, Newborn, Parcellation, Segmentation",
author = "Bonnie Alexander and Loh, {Wai Yen} and Matthews, {Lillian G.} and Murray, {Andrea L.} and Chris Adamson and Richard Beare and Jian Chen and Kelly, {Claire E.} and Anderson, {Peter J.} and Doyle, {Lex W.} and Spittle, {Alicia J.} and Cheong, {Jeanie L.Y.} and Seal, {Marc L.} and Thompson, {Deanne K.}",
year = "2019",
month = "2",
day = "5",
doi = "10.3389/fnins.2019.00034",
language = "English",
volume = "13",
journal = "Frontiers in Neuroscience",
issn = "1662-453X",
publisher = "Frontiers Research Foundation",

}

Alexander, B, Loh, WY, Matthews, LG, Murray, AL, Adamson, C, Beare, R, Chen, J, Kelly, CE, Anderson, PJ, Doyle, LW, Spittle, AJ, Cheong, JLY, Seal, ML & Thompson, DK 2019, 'Desikan-Killiany-Tourville Atlas compatible version of m-CRIB neonatal parcellated whole brain atlas: The m-Crib 2.0', Frontiers in Neuroscience, vol. 13, 34. https://doi.org/10.3389/fnins.2019.00034

Desikan-Killiany-Tourville Atlas compatible version of m-CRIB neonatal parcellated whole brain atlas : The m-Crib 2.0. / Alexander, Bonnie; Loh, Wai Yen; Matthews, Lillian G.; Murray, Andrea L.; Adamson, Chris; Beare, Richard; Chen, Jian; Kelly, Claire E.; Anderson, Peter J.; Doyle, Lex W.; Spittle, Alicia J.; Cheong, Jeanie L.Y.; Seal, Marc L.; Thompson, Deanne K.

In: Frontiers in Neuroscience, Vol. 13, 34, 05.02.2019.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Desikan-Killiany-Tourville Atlas compatible version of m-CRIB neonatal parcellated whole brain atlas

T2 - The m-Crib 2.0

AU - Alexander, Bonnie

AU - Loh, Wai Yen

AU - Matthews, Lillian G.

AU - Murray, Andrea L.

AU - Adamson, Chris

AU - Beare, Richard

AU - Chen, Jian

AU - Kelly, Claire E.

AU - Anderson, Peter J.

AU - Doyle, Lex W.

AU - Spittle, Alicia J.

AU - Cheong, Jeanie L.Y.

AU - Seal, Marc L.

AU - Thompson, Deanne K.

PY - 2019/2/5

Y1 - 2019/2/5

N2 - Our recently published M-CRIB atlas comprises 100 neonatal brain regions including 68 compatible with the widely-used Desikan-Killiany adult cortical atlas. A successor to the Desikan-Killiany atlas is the Desikan-Killiany-Tourville atlas, in which some regions with unclear boundaries were removed, and many existing boundaries were revised to conform to clearer landmarks in sulcal fundi. Our first aim here was to modify cortical M-CRIB regions to comply with the Desikan-Killiany-Tourville protocol, in order to offer: (a) compatibility with this adult cortical atlas, (b) greater labeling accuracy due to clearer landmarks, and (c) optimisation of cortical regions for integration with surface-based infant parcellation pipelines. Secondly, we aimed to update subcortical regions in order to offer greater compatibility with subcortical segmentations produced in FreeSurfer. Data utilized were the T2-weighted MRI scans in our M-CRIB atlas, for 10 healthy neonates (post-menstrual age at MRI 40-43 weeks, four female), and corresponding parcellated images. Edits were performed on the parcellated images in volume space using ITK-SNAP. Cortical updates included deletion of frontal and temporal poles and 'Banks STS,' and modification of boundaries of many other regions. Changes to subcortical regions included the addition of 'ventral diencephalon,' and deletion of 'subcortical matter' labels. A detailed updated parcellation protocol was produced. The resulting whole-brain M-CRIB 2.0 atlas comprises 94 regions altogether. This atlas provides comparability with adult Desikan-Killiany-Tourville-labeled cortical data and FreeSurfer-labeed subcortical data, and is more readily adaptable for incorporation into surface-based neonatal parcellation pipelines. As such, it offers the ability to help facilitate a broad range of investigations into brain structure and function both at the neonatal time point and developmentally across the lifespan.

AB - Our recently published M-CRIB atlas comprises 100 neonatal brain regions including 68 compatible with the widely-used Desikan-Killiany adult cortical atlas. A successor to the Desikan-Killiany atlas is the Desikan-Killiany-Tourville atlas, in which some regions with unclear boundaries were removed, and many existing boundaries were revised to conform to clearer landmarks in sulcal fundi. Our first aim here was to modify cortical M-CRIB regions to comply with the Desikan-Killiany-Tourville protocol, in order to offer: (a) compatibility with this adult cortical atlas, (b) greater labeling accuracy due to clearer landmarks, and (c) optimisation of cortical regions for integration with surface-based infant parcellation pipelines. Secondly, we aimed to update subcortical regions in order to offer greater compatibility with subcortical segmentations produced in FreeSurfer. Data utilized were the T2-weighted MRI scans in our M-CRIB atlas, for 10 healthy neonates (post-menstrual age at MRI 40-43 weeks, four female), and corresponding parcellated images. Edits were performed on the parcellated images in volume space using ITK-SNAP. Cortical updates included deletion of frontal and temporal poles and 'Banks STS,' and modification of boundaries of many other regions. Changes to subcortical regions included the addition of 'ventral diencephalon,' and deletion of 'subcortical matter' labels. A detailed updated parcellation protocol was produced. The resulting whole-brain M-CRIB 2.0 atlas comprises 94 regions altogether. This atlas provides comparability with adult Desikan-Killiany-Tourville-labeled cortical data and FreeSurfer-labeed subcortical data, and is more readily adaptable for incorporation into surface-based neonatal parcellation pipelines. As such, it offers the ability to help facilitate a broad range of investigations into brain structure and function both at the neonatal time point and developmentally across the lifespan.

KW - Ground truth

KW - Infant

KW - Manual tracing

KW - Newborn

KW - Parcellation

KW - Segmentation

UR - http://www.scopus.com/inward/record.url?scp=85065822929&partnerID=8YFLogxK

U2 - 10.3389/fnins.2019.00034

DO - 10.3389/fnins.2019.00034

M3 - Article

VL - 13

JO - Frontiers in Neuroscience

JF - Frontiers in Neuroscience

SN - 1662-453X

M1 - 34

ER -