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Cited by 84Medical Image Segmentation TechniquesAdvanced MRI Techniques and ApplicationsAdvanced Neuroimaging Techniques and Applications

Volume estimation of the thalamus using freesurfer and stereology: consistency between methods

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Keller, Simon S., Gerdes, Jan S., Mohammadi, Siawoosh, Kellinghaus, Christoph, Kugel, Harald, Deppe, Katja, Ringelstein, E. Bernd, Evers, Stefan +2 more·2012·Neuroinformatics
DOI 10.1007/s12021-012-9147-0PMC PMC3464372
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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.

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  • Various evaluations have revealed limitations of Freesurfer that might be critical in aging and multi-site studies.

    “However, various evaluations have also revealed limitations of that approach (Mccarthy 2015; Keller et al., 2012; Mulder et al., 2014), which might be critical in aging and multi-site studies.”

    From A comparison of Freesurfer and multi-atlas MUSE for brain anatomy segmentation: Findings about size and age bias, and inter-scanner stability in multi-site aging studies (2020) · cites this paper as Keller et al., 2012

    The Discussion identifies limitations relevant to FreeSurfer: the study could not measure thalamic subregions, and differences in MRI systems or head coils could potentially affect automated analysis. It does not establish a limitation specific to aging studies; it also notes that scanner manufacturer has been shown to have little effect on thalamic volume estimates. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

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Authors
Keller, S. S., Gerdes, J. S., Mohammadi, S., Kellinghaus, C., Kugel, H., Deppe, K., Ringelstein, E. B., Evers, S., Schwindt, W., & Deppe, M.
Affiliations
  • University of Münster (DE)
  • Wellcome Centre for Human Neuroimaging (GB)
  • Klinikum Osnabrück (DE)
Corresponding author
Deppe, Michael
ORCID
Venue
Neuroinformatics
Publisher
Springer Science and Business Media LLC
Published
2012-04-06
Volume
10
Issue
4
Pages
341-350
ISSN
  • 1539-2791 (ISSN-L)
  • 1559-0089
DOI
10.1007/s12021-012-9147-0
PMC
PMC3464372
OpenAlex
W2075799467
Cited by
84
References
85
Citations by year
2026: 3 · 2025: 3 · 2024: 2 · 2023: 9 · 2022: 9 · 2021: 8 · 2020: 6 · 2019: 4 · 2018: 7 · 2017: 9 · 2016: 8 · 2015: 5 · 2014: 7 · 2013: 1 · 2012: 2
FWCI
4.94
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Neuroinformatics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • UCL Discovery (University College London) (submittedVersion)
  • Research Portal (King's College London) (submittedVersion)
Funders
  • Wellcome Trust (091593, 091593/Z/10/, 091593/Z/10/Z, grant number 091593/Z/10/Z)
  • Deutsche Forschungsgemeinschaft (091593/Z/10/Z.)
Topics
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
Keywords
thalamus, FreeSurfer, stereology, automated MRI segmentation, inter-rater reliability, juvenile myoclonic epilepsy, thalamic atrophy, T1-weighted imaging
MeSH terms
Adult, Analysis of Variance, Atrophy, Brain Mapping, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Nerve Fibers, Myelinated, Software, Stereotaxic Techniques, Thalamus, Linear Models, Myoclonic Epilepsy, Juvenile, Imaging, Three-Dimensional, Young Adult

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