Volume Estimation of the Thalamus Using Freesurfer and Stereology: Consistency between Methods

Abstract

Freely available automated MR image analysis techniques are being increasingly used to investigate neuroanatomical abnormalities in patients with neurological disorders. It is important to assess the specificity and validity of automated measurements of structure volumes with respect to reliable manual methods that rely on human anatomical expertise. The thalamus is widely investigated in many neurological and neuropsychiatric disorders using MRI, but thalamic volumes are notoriously difficult to quantify given the poor between-tissue contrast at the thalamic gray-white matter interface. In the present study we investigated the reliability of automatically determined thalamic volume measurements obtained using FreeSurfer software with respect to a manual stereological technique on 3D T1-weighted MR images obtained from a 3 T MR system. Further to demonstrating impressive consistency between stereological and FreeSurfer volume estimates of the thalamus in healthy subjects and neurological patients, we demonstrate that the extent of agreeability between stereology and FreeSurfer is equal to the agreeability between two human anatomists estimating thalamic volume using stereological methods. Using patients with juvenile myoclonic epilepsy as a model for thalamic atrophy, we also show that both automated and manual methods provide very similar ratios of thalamic volume loss in patients. This work promotes the use of FreeSurfer for reliable estimation of global volume in healthy and diseased thalami.

Amygdala volume is reduced in early course schizophrenia

“…Still, differences in other parameters of segmentation may account for differences among studies. FreeSurfer segmentation of additional subcortical regions, including thalamus and hippocampus, has also been shown to be similar to manual segmentation (Keller et al, 2012; Morey et al, 2009). …”

Normative data for subcortical regional volumes over the lifetime of the adult human brain

“…Ventricles and corpus callosum volumes were generated using the sum of all subregions. FreeSurfer subcortical segmentation showed a high overlap and high volumetric correlations with manual segmentation (Dewey et al, 2010;Fischl et al, 2002;Keller et al, 2012) and high test-retest reliability Morey et al, 2010).…”

Age-related differences in the structural complexity of subcortical and ventricular structures

“…Validation studies have shown that this automated segmentation procedure corresponds well with manual tracing (e.g., Fischl et al, 2002; Jovicich et al, 2009; Keller et al, 2012; Lehmann et al, 2010; Mulder et al, 2014; Pardoe et al, 2009; Tae et al, 2008; Wenger et al, 2014). FreeSurfer has been used in a large number of studies investigating age-differences in subcortical structures (e.g., Inano et al, 2013; Jovicich et al, 2009; Long et al, 2012; Potvin et al, 2016; Tamnes et al, 2013; Walhovd et al, 2005, 2011; Wenger et al, 2014; Yang et al, 2016).…”