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Society for the Study of Addiction.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