A comparison of automated segmentation and manual tracing for quantifying hippocampal and amygdala volumes

Abstract

Large databases of high-resolution structural MR images are being assembled to quantitatively examine the relationships between brain anatomy, disease progression, treatment regimens, and genetic influences upon brain structure. Quantifying brain structures in such large databases cannot be practically accomplished by expert neuroanatomists using hand-tracing. Rather, this research will depend upon automated methods that reliably and accurately segment and quantify dozens of brain regions. At present, there is little guidance available to help clinical research groups in choosing such tools. Thus, our goal was to compare the performance of two popular and fully automated tools, FSL/FIRST and FreeSurfer, to expert hand tracing in the measurement of the hippocampus and amygdala. Volumes derived from each automated measurement were compared to hand tracing for percent volume overlap, percent volume difference, across-sample correlation, and 3-D group-level shape analysis. In addition, sample size estimates for conducting between-group studies were computed for a range of effect sizes. Compared to hand tracing, hippocampal measurements with FreeSurfer exhibited greater volume overlap, smaller volume difference, and higher correlation than FIRST, and sample size estimates with FreeSurfer were closer to hand tracing. Amygdala measurement with FreeSurfer was also more highly correlated to hand tracing than FIRST, but exhibited a greater volume difference than FIRST. Both techniques had comparable volume overlap and similar sample size estimates. Compared to hand tracing, a 3-D shape analysis of the hippocampus showed FreeSurfer was more accurate than FIRST, particularly in the head and tail. However, FIRST more accurately represented the amygdala shape than FreeSurfer, which inflated its anterior and posterior surfaces.

Patch-based segmentation using expert priors: Application to hippocampus and ventricle segmentation

“…For HC segmentation, recently published results (Barnes et al, 2008;Chupin et al, 2007;Morey et al, 2009;Morra et al, 2008;Pohl et al, 2007;van der Lijn et al, 2008) indicated high kappa index values greater than 0.80. The latest published methods based on the nonlinear warping of the best templates and involving a label fusion step (Collins and Pruessner, 2010;Gousias et al, 2008;Lotjonen et al, 2010) obtained kappa index values equal to or greater than 0.88.…”

MAO A VNTR polymorphism and amygdala volume in healthy subjects

“…In fact, given the inherent limitations of any fully automated segmentation software, cortical and subcortical labelling may be influenced by several factors, such as section thickness, MRI noise level, field strength, MRI signal intensities in elderly subjects and anatomic boundary criteria. However, recent methodological studies (Morey et al, 2009;Jovicich et al, 2009) have demonstrated that Freesurfer can be considered an acceptable substitute for manual tracing of automatically quantified amygdala volume, although a large cohort of subjects is warranted. Second, the lack of a significant association between amygdala volume and MAO A VNTR polymorphism could be influenced by further social/psychological variables not taken into consideration in this work, such as impulsivity (Soloff et al, 2008), social disadvantage experiences such as trauma or abuse history (Caspi et al 2002, Kim-Cohen et al 2006 or cigarette smoking behaviour (Caporaso et al, 2009) that could ultimately interact with MAO A functioning.…”

“…This latter term represents a large number of constraints on the space of allowable segmentations and prohibits label configurations that never occur in the training set (e.g., the hippocampus is never anterior to the amygdala). This approach provides advantages similar to manual region-of-interest (ROI) drawing (Morey et al, 2009;Jovicich et al, 2009), without the potential for rater bias, offering an anatomically accurate rendering of regional volumes (Fischl et al, 2002). The entire cortex in each individual subject was visually inspected prior to analysis and, if needed, manually edited.…”

Hippocampal volume and functional connectivity changes during the female menstrual cycle

“…The hippocampal volumes of all participants at each occasion were measured using the fully-automated FreeSurfer hippocampus segmentation, a method to obtain hippocampus volumes automatically, which has been shown to compare well with the gold standard of manual tracing (Morey et al, 2009). The raw images were preprocessed using the FreeSurfer longitudinal stream and a P b 0.05 threshold was applied to the paired t-test of hippocampal volume segmentations between LFP and EFP.…”