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

Juan Eugenio Iglesias*, Ricardo Insausti, Garikoitz Lerma-Usabiaga, Martina Bocchetta, Koen Van Leemput, Douglas N. Greve, Andre van der Kouwe, Bruce Fischl, César Caballero-Gaudes, Pedro M. Paz-Alonso

*Corresponding author for this work

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Abstract

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
JournalNeuroImage
Volume183
Pages (from-to)314–326
ISSN1053-8119
DOIs
Publication statusPublished - 2018

Keywords

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

Cite this

Iglesias, J. E., Insausti, R., Lerma-Usabiaga, G., Bocchetta, M., Van Leemput, K., Greve, D. N., ... Paz-Alonso, P. M. (2018). A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. NeuroImage, 183, 314–326. https://doi.org/10.1016/j.neuroimage.2018.08.012
Iglesias, Juan Eugenio ; Insausti, Ricardo ; Lerma-Usabiaga, Garikoitz ; Bocchetta, Martina ; Van Leemput, Koen ; Greve, Douglas N. ; van der Kouwe, Andre ; Fischl, Bruce ; Caballero-Gaudes, César ; Paz-Alonso, Pedro M. / A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. In: NeuroImage. 2018 ; Vol. 183. pp. 314–326.
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title = "A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology",
abstract = "The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei areknown to have different functions and to be connected to different areas of the cerebral cortex, it is of greatinterest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In thisstudy, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histologicaldata, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manualdelineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combinedwith 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 correspondingmanual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographsacquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptivetetrahedral mesh, shows a good agreement with previous histological studies of the thalamus in terms of volumesof representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas showsexcellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differentialthalamic effects in subjects with Alzheimer's disease. The probabilistic atlas and companion segmentation tool arepublicly available as part of the neuroimaging package FreeSurfer.",
keywords = "Thalamus, Atlasing, Histology, Ex-vivo MRI, Segmentation, Bayesian inference",
author = "Iglesias, {Juan Eugenio} and Ricardo Insausti and Garikoitz Lerma-Usabiaga and Martina Bocchetta and {Van Leemput}, Koen and Greve, {Douglas N.} and {van der Kouwe}, Andre and Bruce Fischl and C{\'e}sar Caballero-Gaudes and Paz-Alonso, {Pedro M.}",
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language = "English",
volume = "183",
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Iglesias, JE, Insausti, R, Lerma-Usabiaga, G, Bocchetta, M, Van Leemput, K, Greve, DN, van der Kouwe, A, Fischl, B, Caballero-Gaudes, C & Paz-Alonso, PM 2018, 'A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology', NeuroImage, vol. 183, pp. 314–326. https://doi.org/10.1016/j.neuroimage.2018.08.012

A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. / Iglesias, Juan Eugenio; Insausti, Ricardo; Lerma-Usabiaga, Garikoitz; Bocchetta, Martina; Van Leemput, Koen; Greve, Douglas N.; van der Kouwe, Andre; Fischl, Bruce; Caballero-Gaudes, César; Paz-Alonso, Pedro M.

In: NeuroImage, Vol. 183, 2018, p. 314–326.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology

AU - Iglesias, Juan Eugenio

AU - Insausti, Ricardo

AU - Lerma-Usabiaga, Garikoitz

AU - Bocchetta, Martina

AU - Van Leemput, Koen

AU - Greve, Douglas N.

AU - van der Kouwe, Andre

AU - Fischl, Bruce

AU - Caballero-Gaudes, César

AU - Paz-Alonso, Pedro M.

PY - 2018

Y1 - 2018

N2 - The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei areknown to have different functions and to be connected to different areas of the cerebral cortex, it is of greatinterest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In thisstudy, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histologicaldata, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manualdelineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combinedwith 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 correspondingmanual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographsacquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptivetetrahedral mesh, shows a good agreement with previous histological studies of the thalamus in terms of volumesof representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas showsexcellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differentialthalamic effects in subjects with Alzheimer's disease. The probabilistic atlas and companion segmentation tool arepublicly available as part of the neuroimaging package FreeSurfer.

AB - The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei areknown to have different functions and to be connected to different areas of the cerebral cortex, it is of greatinterest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In thisstudy, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histologicaldata, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manualdelineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combinedwith 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 correspondingmanual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographsacquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptivetetrahedral mesh, shows a good agreement with previous histological studies of the thalamus in terms of volumesof representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas showsexcellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differentialthalamic effects in subjects with Alzheimer's disease. The probabilistic atlas and companion segmentation tool arepublicly available as part of the neuroimaging package FreeSurfer.

KW - Thalamus

KW - Atlasing

KW - Histology

KW - Ex-vivo MRI

KW - Segmentation

KW - Bayesian inference

U2 - 10.1016/j.neuroimage.2018.08.012

DO - 10.1016/j.neuroimage.2018.08.012

M3 - Journal article

VL - 183

SP - 314

EP - 326

JO - NeuroImage

JF - NeuroImage

SN - 1053-8119

ER -