A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology

Research output: Contribution to journalJournal article – Annual report year: 2018Researchpeer-review



  • Author: Iglesias, Juan Eugenio

    University College London, United Kingdom

  • Author: Insausti, Ricardo

    University of Castilla-La Mancha, Spain

  • Author: Lerma-Usabiaga, Garikoitz

    Basque Center on Cognition, Brain and Language, Spain

  • Author: Bocchetta, Martina

    University College London, United Kingdom

  • Author: Van Leemput, Koen

    Image Analysis & Computer Graphics, Department of Applied Mathematics and Computer Science , Technical University of Denmark, Denmark

  • Author: Greve, Douglas N.

    Harvard Medical School, United States

  • Author: Van der Kouwe, Andre

    Harvard Medical School, United States

  • Author: Fischl, Bruce

    Massachusetts Institute of Technology, United States

  • Author: Caballero-Gaudes, César

    Basque Center on Cognition, Brain and Language, Spain

  • Author: Paz-Alonso, Pedro M.

    Basque Center on Cognition, Brain and Language, Spain

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The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei are
known to have different functions and to be connected to different areas of the cerebral cortex, it is of great
interest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In this
study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological
data, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manual
delineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combined
with manual segmentations of the whole thalamus and surrounding structures (caudate, putamen, hippocampus,
etc.) made on in vivo brain MR data from 39 subjects. The 3D structure of the histological data and corresponding
manual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographs
acquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptive
tetrahedral mesh, shows a good agreement with previous histological studies of the thalamus in terms of volumes
of representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas shows
excellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differential
thalamic effects in subjects with Alzheimer's disease. The probabilistic atlas and companion segmentation tool are
publicly available as part of the neuroimaging package FreeSurfer.
Original languageEnglish
Pages (from-to)314–326
Publication statusPublished - 2018
CitationsWeb of Science® Times Cited: No match on DOI

    Research areas

  • Thalamus, Atlasing, Histology, Ex-vivo MRI, Segmentation, Bayesian inference

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