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Neuroradiology

, Volume 61, Issue 2, pp 129–136 | Cite as

T1-MPRAGE and T2-FLAIR segmentation of cortical and subcortical brain regions—an MRI evaluation study

  • Ebba BellerEmail author
  • Daniel Keeser
  • Antonia Wehn
  • Berend Malchow
  • Temmuz Karali
  • Andrea Schmitt
  • Irina Papazova
  • Boris Papazov
  • Franziska Schoeppe
  • Giovanna Negrao de Figueiredo
  • Birgit Ertl-Wagner
  • Sophia Stoecklein
Diagnostic Neuroradiology

Abstract

Purpose

Development of a warp-based automated brain segmentation approach of 3D fluid-attenuated inversion recovery (FLAIR) images and comparison to 3D T1-based segmentation.

Methods

3D FLAIR and 3D T1-weighted sequences of 30 healthy subjects (mean age 29.9 ± 8.3 years, 8 female) were acquired on the same 3T MR scanner. Warp-based segmentation was applied for volumetry of total gray matter (GM), white matter (WM), and 116 atlas regions. Segmentation results of both sequences were compared using Pearson correlation (r).

Results

Correlation of GM segmentation results based on FLAIR and T1 was overall good for cortical structures (mean r across all cortical structures = 0.76). Comparatively weaker results were found in the occipital lobe (r = 0.77), central region (mean r = 0.58), basal ganglia (mean r = 0.59), thalamus (r = 0.30), and cerebellum (r = 0.73). FLAIR segmentation underestimated volume of the central region compared to T1, but showed a better anatomic concordance with the occipital lobe on visual review and subcortical structures, when also compared to manual segmentation. Visual analysis of FLAIR-based WM segmentation revealed frequent misclassification of regions of high signal intensity as GM.

Conclusion

Warp-based FLAIR segmentation yields comparable results to T1 segmentation for most cortical GM structures and may provide anatomically more congruent segmentation of subcortical GM structures. Selected cortical regions, especially the central region and total WM, seem to be underestimated on FLAIR segmentation.

Keywords

Magnetic resonance imaging Brain Neuroanatomy Cohort studies 

Abbreviations

GM

Gray matter

WM

White matter

CSF

Cerebrospinal fluid

FLAIR

Fluid-attenuated inversion recovery

AAL

Automatic Anatomical Labeling

3D

Three-dimensional

TI

Inversion time

TR

Repetition time

TE

Echo time

FSL

Functional magnetic resonance imaging of the brain (FMRIB) software library

FAST

FMRIB’s Automated Segmentation Tool

BET

Brain extraction

AFNI

Analyses of functional images

MNI

Montreal Neurological Institute

FLIRT

FMRIB’s linear image registration tool

FNIRT

FMRIB’s nonlinear image registration tool

ICV

Intracranial volume

r

Pearson correlation

R

Right

L

Left

Notes

Compliance with ethical standards

Funding

No funding was received for this study.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in the studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

234_2018_2121_MOESM1_ESM.docx (104 kb)
Supplementary Table 1a (DOCX 104 kb)
234_2018_2121_MOESM2_ESM.docx (132 kb)
Supplementary Table 1b (DOCX 131 kb)
234_2018_2121_MOESM3_ESM.docx (40 kb)
Supplementary Table 2 (DOCX 40 kb)
234_2018_2121_MOESM4_ESM.docx (97 kb)
Supplementary Table 3 (DOCX 96 kb)
234_2018_2121_MOESM5_ESM.pdf (157 kb)
ESM 1 (PDF 156 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Ebba Beller
    • 1
    • 2
    Email author
  • Daniel Keeser
    • 1
    • 3
  • Antonia Wehn
    • 1
  • Berend Malchow
    • 3
  • Temmuz Karali
    • 1
    • 3
  • Andrea Schmitt
    • 3
    • 4
  • Irina Papazova
    • 3
  • Boris Papazov
    • 1
    • 3
  • Franziska Schoeppe
    • 1
  • Giovanna Negrao de Figueiredo
    • 1
  • Birgit Ertl-Wagner
    • 1
    • 5
  • Sophia Stoecklein
    • 1
  1. 1.Department of RadiologyLudwig-Maximilians University MunichMunichGermany
  2. 2.Institut für Diagnostische und Interventionelle Radiologie, Kinder- und NeuroradiologieUniversitätsmedizin RostockRostockGermany
  3. 3.Department of Psychiatry and PsychotherapyUniversity Hospital, LMU MunichMunichGermany
  4. 4.Laboratory of Neuroscience (LIM27), Institute of PsychiatryUniversity of Sao PauloSão PauloBrazil
  5. 5.Department of Medical Imaging, The Hospital for Sick ChildrenUniversity of TorontoTorontoCanada

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