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

Department of Neurology, University of Münster, Münster, Germany.
Neuroinformatics (Impact Factor: 2.83). 04/2012; 10(4):341-50. DOI: 10.1007/s12021-012-9147-0
Source: PubMed


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.

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    • "First, CA2 and CA3 were sampled together using the automated morphometric analysis, and therefore a direct comparison with CA2 alone is not permitted. We were aware of the lack of differentiation between CA2–3 at the onset of this study, and we chose to employ routines incorporated into FreeSurfer software to estimate hippocampal subfield volume given the software's free availability , fully automated image processing pipelines, and independently determined consistency between FreeSurfer automatically determined volumes and " gold standard " manually determined volumes of hippocampal (Dewey et al., 2010; Morey et al., 2009; Pardoe et al., 2009) and extrahippocampal (Dewey et al., 2010; Keller et al., 2012a) structures . More recent techniques have offered the possibility of automatically differentiating CA2 and CA3 (Bonnici et al., 2012). "
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    ABSTRACT: A particularly popular automated magnetic resonance imaging (MRI) hippocampal subfield mapping technique is the one described by Van Leemput et al. (2009: Hippocampus 19:549–557) that is currently distributed with FreeSurfer software. This method assesses the probabilistic locations of subfields based on a priori knowledge of subfield topology determined from high-field MRI. Many studies have applied this technique to conventionally acquired T1-weighted MRI data. In the present study, we investigated the relationship between this technique applied to conventional T1-weighted MRI data acquired at 3 T and postsurgical hippocampal histology in patients with medically intractable mesial temporal lobe epilepsy (mTLE) and hippocampal sclerosis (HS). Patients with mTLE (n = 82) exhibited significant volume loss of ipsilateral CA1, CA2-3, CA4-dentate gyrus (DG), subiculum, and fimbria relative to controls (n = 81). Histopathological analysis indicated that the most significant neuronal loss was observed in CA1, then CA4 and CA3, and more subtle neuronal loss in CA2, consistent with classical HS. Neuronal density of CA1 significantly correlated with MRI-determined volume of CA1, and increasingly so with CA2-3 and CA4–DG. Patients with increased HS based on histopathology had greater volume loss of the ipsilateral hippocampal regions on MRI. We conclude by suggesting that whilst time efficient and fully reproducible when applied to conventional single acquisition sequences, the use of the automated subfield technique described here may necessitate the application to multiacquisition high-resolution MR sequences for accurate delineation of hippocampal subfields. Hum Brain Mapp, 2014. © 2014 Wiley Periodicals, Inc.
    Human Brain Mapping 09/2014; 35(9). DOI:10.1002/hbm.22506 · 5.97 Impact Factor
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    • "Volumes of bilateral thalami were generated according to the standard FreeSurfer segmentation and parcellation procedures, relying upon variations in voxel signal intensities, probabilistic atlas location, and local spatial relationships between the structures (Fischl et al., 2002). Previous research provided strong evidence for the reliability of thalamus volume estimation using FreeSurfer (Keller et al., 2012). See Supplemental Materials Fig. S1 for Freesurfer subcortical segmentation of the thalamus for two extreme examples from this study. "
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    ABSTRACT: The GABRB1 gene encodes the beta 1 subunit of gamma-aminobutyric acid A receptor (GABA A receptor), which is responsible for mediating inhibitory neurotransmission in the thalamus. Potential relationships between the GABRB1 gene, thalamus volume, and intelligence have been suggested by previous clinical studies, but have not been directly examined among nonclinical samples. The current study collected structural MRI, genetic, and behavioral data in 316 healthy Chinese adults (including 187 females and 129 males), and examined associations between GABRB1 variants, thalamus volume, and intelligence (measured by the Wechsler Adult Intelligence Scale Revised). After controlling for intracranial volume, sex, and age, GABRB1 genetic polymorphism at the SNP rs7435958 had the strongest association with thalamus volume (p=0.002 and 0.00008 for left and right thalamus volumes, respectively), with GG homozygotes having smaller bilateral thalamus volumes than the other genotypes. Furthermore, there were positive correlations between bilateral thalamus volumes and intelligence, especially for GABRB1 rs7435958 GG female homozygotes (r's=0.31 and 0.29, p<0.01, for the correlations of intelligence with left and right thalamus volumes, respectively). This study provides the first evidence for the involvement of the GABRB1 gene in thalamus structure and their interactive effects on intelligence. Future studies of the thalamus-intelligence associations should consider genetic factors as potential moderators.
    NeuroImage 09/2014; 102. DOI:10.1016/j.neuroimage.2014.08.048 · 6.36 Impact Factor
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    • "The procedures for the measurement of volumes have been validated against manual tracing methods (e.g. Keller et al., 2012). Raw volumetric data composed 139 brain regions for each participant. "
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    ABSTRACT: Objectives: Body dysmorphic disorder (BDD) is characterized by a preoccupation with a misperceived flaw in appearance, causing significant distress and disability. Neuropsychological research has revealed deficits in executive function and inhibitory control of emotional responses. The few previous structural neuroimaging studies have had inconclusive findings and we aimed to take this field of research forward by contributing high quality structural data. Methods: To investigate regional brain volumes we compared 20 BDD participants and 20 matched controls using high-resolution structural T1-weighted magnetic resonance imaging (MRI). The MRI data was subjected to cortical reconstruction and volumetric segmentation using Freesurfer software. Results: Results showed the right orbitofrontal cortex, bilateral thalamus, left anterior cingulate cortex, hippocampus and amygdala were significantly smaller in the BDD sample compared to controls. The most pronounced differences were in the right orbitofrontal cortex and left anterior cingulate cortex, as these areas were smaller in BDD participants independent of reduced global brain volumes. Duration of illness significantly negatively correlated with right orbitofrontal cortex volumes. Conclusions: This is the largest volumetric neuroimaging study in BDD to date and provides important data on volumetric differences that implicate fronto-limbic circuits.
    Australian and New Zealand Journal of Psychiatry 02/2014; 48(7). DOI:10.1177/0004867413520253 · 3.41 Impact Factor
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