Neuroinform (2012) 10:341–350 DOI 10.1007/s12021-012-9147-0 ORIGINAL ARTICLE Volume Estimation of the Thalamus Using Freesurfer and Stereology: Consistency between Methods Simon S. Keller & Jan S. Gerdes & Siawoosh Mohammadi & Christoph Kellinghaus & Harald Kugel & Katja Deppe & E. Bernd Ringelstein & Stefan Evers & Wolfram Schwindt & Michael Deppe Published online: 6 April 2012 # The Author(s) 2012. This article is published with open access at Springerlink.com Abstract Freely available automated MR image analysis techniques are being increasingly used to investigate neuro- anatomical abnormalities in patients with neurological disor- ders. 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 S. S. Keller : J. S. Gerdes : E. B. Ringelstein : S. Evers : M. Deppe Department of Neurology, University of Münster, Münster, Germany S. S. Keller Department of Clinical Neuroscience, Institute of Psychiatry, King’s College London, London, UK S. Mohammadi Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, University College London, London, UK C. Kellinghaus Department of Neurology, Klinikum Osnabrück, Osnabrück, Germany H. Kugel : W. Schwindt Department of Clinical Radiology, University of Münster, Münster, Germany K. Deppe Department of Radiology, Klinikum Osnabrück, Osnabrück, Germany M. Deppe (*) Universität Münster, Klinik und Poliklinik für Neurologie, Funktionelle Bildgebung, Albert-Schweitzer-Campus 1, Gebäude A1, 48129 Münster, Germany e-mail: mail@michael-deppe.de 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 meas- urements 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 demon- strating impressive consistency between stereological and FreeSurfer volume estimates of the thalamus in healthy sub- jects 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 meth- ods 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. Keywords FreeSurfer . Diffusion tensor imaging . Fractional anisotropy . MR image analysis . Stereology . Volume Introduction The thalamus is of central interest in many disorders of the nervous system (Andreasen 1997; Dom, et al. 1976; Lee and Marsden 1994; Meador-Woodruff, et al. 2003; Speedie and Heilman 1983; Williams 1965; Xuereb, et al. 1991). The functioning of the thalamus is crucial to many sensory, motor and cognitive systems, and therefore has also been subject to a great deal of investigation in the cognitive neurosciences (Basso, et al. 2005; Engelborghs, et al. 1998; Herrero, et al. 2002). It is in these capacities that