eprintid: 10055215 rev_number: 25 eprint_status: archive userid: 608 dir: disk0/10/05/52/15 datestamp: 2018-09-03 14:59:54 lastmod: 2021-09-19 22:14:30 status_changed: 2019-02-04 15:32:52 type: article metadata_visibility: show creators_name: Iglesias, JE creators_name: Insausti, R creators_name: Lerma-Usabiaga, G creators_name: Bocchetta, M creators_name: Van Leemput, K creators_name: Greve, DN creators_name: van der Kouwe, A creators_name: Alzheimer's Disease Neuroimaging Initiative, creators_name: Fischl, B creators_name: Caballero-Gaudes, C creators_name: Paz-Alonso, PM title: A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology ispublished: pub divisions: UCL divisions: B02 divisions: C07 divisions: D07 divisions: F86 divisions: B04 divisions: C05 divisions: F42 keywords: Atlasing, Bayesian inference, Ex-vivo MRI, Histology, Segmentation, Thalamus note: © 2018 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) 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. date: 2018-12 date_type: published official_url: http://dx.doi.org/10.1016/j.neuroimage.2018.08.012 oa_status: green full_text_type: pub language: eng primo: open primo_central: open_green article_type_text: Journal Article verified: verified_manual elements_id: 1577722 doi: 10.1016/j.neuroimage.2018.08.012 pii: S1053-8119(18)30710-9 lyricists_name: Bocchetta, Martina lyricists_name: Iglesias Gonzalez, Juan lyricists_id: MBOCC01 lyricists_id: JEIGL66 actors_name: Bracey, Alan actors_id: ABBRA90 actors_role: owner full_text_status: public publication: NeuroImage volume: 183 pagerange: 314-326 event_location: United States issn: 1095-9572 citation: Iglesias, JE; Insausti, R; Lerma-Usabiaga, G; Bocchetta, M; Van Leemput, K; Greve, DN; van der Kouwe, A; ... Paz-Alonso, PM; + view all <#> Iglesias, JE; Insausti, R; Lerma-Usabiaga, G; Bocchetta, M; Van Leemput, K; Greve, DN; van der Kouwe, A; Alzheimer's Disease Neuroimaging Initiative; Fischl, B; Caballero-Gaudes, C; Paz-Alonso, PM; - view fewer <#> (2018) A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. NeuroImage , 183 pp. 314-326. 10.1016/j.neuroimage.2018.08.012 <https://doi.org/10.1016/j.neuroimage.2018.08.012>. Green open access document_url: https://discovery.ucl.ac.uk/id/eprint/10055215/1/1-s2.0-S1053811918307109-main.pdf