Accuracy of automated amygdala MRI segmentation approaches in Huntington's disease in the IMAGE-HD cohort

Bonnie Alexander, Nellie Georgiou-Karistianis, Richard Beare, Lotta M. Ahveninen, Valentina Lorenzetti, Julie C. Stout, Yifat Glikmann-Johnston

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Smaller manually-segmented amygdala volumes have been associated with poorer motor and cognitive function in Huntington's disease (HD). Manual segmentation is the gold standard in terms of accuracy; however, automated methods may be necessary in large samples. Automated segmentation accuracy has not been determined for the amygdala in HD. We aimed to determine which of three automated approaches would most accurately segment amygdalae in HD: FreeSurfer, FIRST, and ANTS nonlinear registration followed by FIRST segmentation. T1-weighted images for the IMAGE-HD cohort including 35 presymptomatic HD (pre-HD), 36 symptomatic HD (symp-HD), and 34 healthy controls were segmented using FreeSurfer and FIRST. For the third approach, images were nonlinearly registered to an MNI template using ANTS, then segmented using FIRST. All automated methods overestimated amygdala volumes compared with manual segmentation. Dice overlap scores, indicating segmentation accuracy, were not significantly different between automated approaches. Manually segmented volumes were most statistically differentiable between groups, followed by those segmented by FreeSurfer, then ANTS/FIRST. FIRST-segmented volumes did not differ between groups. All automated methods produced a bias where volume overestimation was more severe for smaller amygdalae. This bias was subtle for FreeSurfer, but marked for FIRST, and moderate for ANTS/FIRST. Further, FreeSurfer introduced a hemispheric bias not evident with manual segmentation, producing larger right amygdalae by 8%. To assist choice of segmentation approach, we provide sample size estimation graphs based on sample size and other factors. If automated segmentation is employed in samples of the current size, FreeSurfer may effectively distinguish amygdala volume between controls and HD.

Original languageEnglish
Pages (from-to)1875-1888
Number of pages14
JournalHuman Brain Mapping
Issue number7
Publication statusPublished - May 2020


  • amygdala
  • atrophy
  • Huntington's disease
  • segmentation
  • subcortical
  • tracing

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