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A New MRI-Based Pediatric Subcortical Segmentation Technique (PSST)

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Abstract

Volumetric and morphometric neuroimaging studies of the basal ganglia and thalamus in pediatric populations have utilized existing automated segmentation tools including FIRST (Functional Magnetic Resonance Imaging of the Brain’s Integrated Registration and Segmentation Tool) and FreeSurfer. These segmentation packages, however, are mostly based on adult training data. Given that there are marked differences between the pediatric and adult brain, it is likely an age-specific segmentation technique will produce more accurate segmentation results. In this study, we describe a new automated segmentation technique for analysis of 7-year-old basal ganglia and thalamus, called Pediatric Subcortical Segmentation Technique (PSST). PSST consists of a probabilistic 7-year-old subcortical gray matter atlas (accumbens, caudate, pallidum, putamen and thalamus) combined with a customized segmentation pipeline using existing tools: ANTs (Advanced Normalization Tools) and SPM (Statistical Parametric Mapping). The segmentation accuracy of PSST in 7-year-old data was compared against FIRST and FreeSurfer, relative to manual segmentation as the ground truth, utilizing spatial overlap (Dice’s coefficient), volume correlation (intraclass correlation coefficient, ICC) and limits of agreement (Bland-Altman plots). PSST achieved spatial overlap scores ≥90 % and ICC scores ≥0.77 when compared with manual segmentation, for all structures except the accumbens. Compared with FIRST and FreeSurfer, PSST showed higher spatial overlap (p FDR  < 0.05) and ICC scores, with less volumetric bias according to Bland-Altman plots. PSST is a customized segmentation pipeline with an age-specific atlas that accurately segments typical and atypical basal ganglia and thalami at age 7 years, and has the potential to be applied to other pediatric datasets.

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Abbreviations

ANTs:

Advanced Neuroimaging Tools

BET:

Brain Extraction Tool

CMA:

Center for Morphometric Analysis

CSF:

Cerebrospinal fluid

FDR:

False discovery rate

FIRST:

Functional Magnetic Resonance Imaging of the Brain’s Integrated Registration and Segmentation Tool

FMRIB:

Functional Magnetic Resonance Imaging of the Brain

FSL:

Functional Magnetic Resonance Imaging of the Brain’s Software Library

FWHM:

Full width half maximum

ICC:

Intraclass correlation coefficient

ITK:

Insight Toolkit

LDDM:

Large Deformation Diffeomorphic Metric

MRI:

Magnetic resonance imaging

PSST:

Pediatric Subcortical Segmentation Technique

SPM:

Statistical Parametric Mapping

VIBeS:

Victorian Infant Brain Study

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Information Sharing Statement

The age-specific (7 years) basal ganglia and thalamus atlas which includes the T 1 template and the structure priors is available upon request from W.Y. Loh (corresponding author) and D. K. Thompson.

Acknowledgments

We gratefully recognize the efforts of Terrie Inder who provided insight into the study, Merilyn Bear who recruited the participants, Michael Kean and the radiographers at Melbourne Children’s MRI Centre who scanned the participants, the VIBeS and Developmental Imaging groups at the Murdoch Childrens Research Institute where the research was conducted. We also thank the families and children who participated in this study.

Funding

This study was supported by Australia’s National Health & Medical Research Council (Centre for Clinical Research Excellence 546519 to L.D. and P.A.; Centre for Research Excellence 1060733 to L.D., P.A., J.C., D.T., A.S., and W.Y.L.; Project Grants 237117 to L.D., 491209 to P.A.; Senior Research Fellowship 628371 to P.A., Early Career Fellowships 1053767 to A.S., 1012236 to D.T., 1053787 to J.C., National Institutes of Health (HD058056), the Victorian Government’s Operational Infrastructure Support Program, and The Royal Children’s Hospital Foundation.

Conflict of Interest

The authors declare that they have no conflict of interest.

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Correspondence to Wai Yen Loh.

Appendices

Appendix A

Manual tracing boundaries

A. Basal ganglia

The basal ganglia nuclei were segmented in the following order: caudate, putamen, pallidum and accumbens. Segmentation of the caudate began at the slice it first appeared and tracing stopped when it was difficult to visualize (the tail of the caudate was not included). The medial and lateral borders of the caudate were respectively defined by the lateral border of the lateral ventricle and the medial border of the internal capsule. Delineation of the putamen began anteriorly when it was first visualized at the ventrolateral section of the caudate and ended when it could no longer be seen. The medial border of the putamen was marked by the structure of the pallidum, while its lateral border was defined by the medial border of the external capsule. Striations in between the caudate and putamen were excluded. For the pallidum, tracing began when it was first seen medial to the putamen and ended when poorly visualized. Segmentation of the accumbens was done last as this structure was inferiorly connected to both the caudate and putamen. The first anterior slice of the accumbens was defined to start five slices after the putamen was first seen, while the last slice was defined to be two slices anterior to the anterior commissure. Before the caudate and putamen were connected inferiorly, the accumbens was superiorly bordered by a line which was drawn from the most inferiolateral voxel of the lateral ventricle to the most inferiomedial voxel of the putamen. Once the caudate and putamen were visualized as an integrated structure, the superior border of the accumbens was marked by a line connecting the most inferiolateral voxel of the lateral ventricle to the most inferiolateral point of the internal capsule; while its lateral border was defined by a vertical line drawn from the internal capsule’s most inferiolateral voxel.

B. Thalamus

Tracing of the thalamus began when it was first visualized a few slices after the anterior commissure appeared and ended when it could no longer be seen. Segmentation of the thalamus included both the lateral and medial geniculate nucleus, as well as the interthalamic adhesion.

Appendix B

Table 2 Intrarater reliability scores for manual tracing

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Loh, W.Y., Connelly, A., Cheong, J.L.Y. et al. A New MRI-Based Pediatric Subcortical Segmentation Technique (PSST). Neuroinform 14, 69–81 (2016). https://doi.org/10.1007/s12021-015-9279-0

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