Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2024 Apr 20;34(4):bhae120. doi: 10.1093/cercor/bhae120

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/pages/standard-publication-reuse-rights)

PMC Copyright notice

Fig. 4 — Subcortical areas for the 3D atlas (SAM). (A–D) More examples show the subcortical areas at the brainstem level (pons and medulla) that are identified and segmented on MAP-MRI (DEC-FOD) with reference to matched histological sections stained with SMI-32, and other stained sections (not shown here). Abbreviations: 6th, abducent nuclei; 7th, facial nuclei; 7n, facial nerve; 8n, vestibulocochlear nerve; 8vn, vestibular nerve; 12th, hypoglossal nucleus; AN, ambiguous nucleus; CBT, corticobulbar tract; cn, cuneate nucleus; CST, corticospinal tract; denv (10), dorsal motor nucleus of vagus; fc, facial colliculus; ICP, inferior cerebellar peduncle; ion, inferior olivary nucleus; irn, intermediate reticular nucleus; lcn, lateral cuneate nucleus; lrn, lateral reticular nucleus; MCP, middle cerebellar peduncle; ml, medial lemniscus; mlf, medial longitudinal fasciculus; mVN, medial vestibular nucleus; np, nucleus prepositus; nrm, nucleus raphe magnus; nro, nucleus raphe obscurus; nrp, nucleus raphe pallidus; prn, parvicelluar reticular nucleus; RF (ngc), reticular formation, nucleus gigantocellularis; RF (npo), reticular formation, nucleus pontis centralis oralis; SCP, superior cerebellar peduncle; sn, solitary nucleus; spVN, spinal vestibular nucleus; st, solitary tract; stn, spinal trigeminal nucleus; stt, spinal trigeminal tract; sVN, superior vestibular nucleus; vcn, ventral cochlear nucleus; vsct, ventral spinocerebellar tract. Subcortical segmentation and 3D ex vivo digital template atlas. (E) Two hundred and fifty-one deep brain regions, including the HF and cerebellum, were manually segmented through a series of 150 μm thick MAP-MRI sections using ITK-SNAP. (F) A 3D isosurface rendering of the individual regions within a volume rendering of the T2W dataset. This new MRI-histology-based segmented volume (called ex vivo “SAM”) is registered to an in vivo multi-subject population-based T1W MRI volume oriented to the EBZ stereotaxic coordinate system (Liu et al. 2021) or a range of in vivo T2W MRI volumes of marmoset monkeys with different age groups and genders. For more details, see Figs 6 and 7.