Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology

Kadharbatcha S Saleem, Alexandru V Avram, Daniel Glen, Cecil Chern-Chyi Yen, Frank Q Ye, Michal Komlosh, Peter J Basser
doi: https://doi.org/10.1101/2021.11.23.469706
Kadharbatcha S Saleem
1Center for Neuroscience and Regenerative Medicine (CNRM), Henry M. Jackson Foundation (HJF) for the Advancement of Military Medicine, Bethesda, MD 20817
5Section on Quantitative Imaging and Tissue Sciences (SQITS), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: kadharbatcha.saleem.ctr@usuhs.edu saleemks@mail.nih.gov
Alexandru V Avram
1Center for Neuroscience and Regenerative Medicine (CNRM), Henry M. Jackson Foundation (HJF) for the Advancement of Military Medicine, Bethesda, MD 20817
5Section on Quantitative Imaging and Tissue Sciences (SQITS), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel Glen
2Scientific and Statistical Computing Core, National Institute of Mental Health (NIMH)
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Cecil Chern-Chyi Yen
3National Institute of Neurological Disorders and Stroke (NINDS)
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Frank Q Ye
4Neurophysiology Imaging Facility, NIMH and NINDS, NIH
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michal Komlosh
1Center for Neuroscience and Regenerative Medicine (CNRM), Henry M. Jackson Foundation (HJF) for the Advancement of Military Medicine, Bethesda, MD 20817
5Section on Quantitative Imaging and Tissue Sciences (SQITS), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peter J Basser
1Center for Neuroscience and Regenerative Medicine (CNRM), Henry M. Jackson Foundation (HJF) for the Advancement of Military Medicine, Bethesda, MD 20817
5Section on Quantitative Imaging and Tissue Sciences (SQITS), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Subcortical nuclei and other deep brain structures are known to play an important role in the regulation of the central and peripheral nervous systems. It can be difficult to identify and delineate many of these nuclei and their finer subdivisions in conventional MRI due to their small size, buried location, and often subtle contrast compared to neighboring tissue. To address this problem, we applied a multi-modal approach in ex vivo non-human primate (NHP) brain that includes high-resolution mean apparent propagator (MAP)-MRI and five different histological stains imaged with high-resolution microscopy in the brain of the same subject. By registering these high-dimensional MRI data to high-resolution histology data, we can map the location, boundaries, subdivisions, and micro-architectural features of subcortical gray matter regions in the macaque monkey brain. At high spatial resolution, diffusion MRI in general, and MAP-MRI in particular, can distinguish a large number of deep brain structures, including the larger and smaller white matter fiber tracts as well as architectonic features within various nuclei. Correlation with histology from the same brain enables a thorough validation of the structures identified with MAP-MRI. Moreover, anatomical details that are evident in images of MAP-MRI parameters are not visible in conventional T1-weighted images. We also derived subcortical template “SC21” from segmented MRI slices in three-dimensions and registered this volume to a previously published anatomical template with cortical parcellation (Reveley et al., 2017; Saleem and Logothetis, 2012), thereby integrating the 3D segmentation of both cortical and subcortical regions into the same volume. This newly updated three-dimensional D99 digital brain atlas (V2.0) is intended for use as a reference standard for macaque neuroanatomical, functional, and connectional imaging studies, involving both cortical and subcortical targets. The SC21 and D99 digital templates are available as volumes and surfaces in standard NIFTI and GIFTI formats.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted November 23, 2021.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology
Kadharbatcha S Saleem, Alexandru V Avram, Daniel Glen, Cecil Chern-Chyi Yen, Frank Q Ye, Michal Komlosh, Peter J Basser
bioRxiv 2021.11.23.469706; doi: https://doi.org/10.1101/2021.11.23.469706
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology
Kadharbatcha S Saleem, Alexandru V Avram, Daniel Glen, Cecil Chern-Chyi Yen, Frank Q Ye, Michal Komlosh, Peter J Basser
bioRxiv 2021.11.23.469706; doi: https://doi.org/10.1101/2021.11.23.469706

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Neuroscience
Subject Areas
All Articles
  • Animal Behavior and Cognition (4105)
  • Biochemistry (8808)
  • Bioengineering (6509)
  • Bioinformatics (23446)
  • Biophysics (11784)
  • Cancer Biology (9200)
  • Cell Biology (13314)
  • Clinical Trials (138)
  • Developmental Biology (7430)
  • Ecology (11403)
  • Epidemiology (2066)
  • Evolutionary Biology (15143)
  • Genetics (10431)
  • Genomics (14036)
  • Immunology (9167)
  • Microbiology (22142)
  • Molecular Biology (8802)
  • Neuroscience (47540)
  • Paleontology (350)
  • Pathology (1427)
  • Pharmacology and Toxicology (2489)
  • Physiology (3729)
  • Plant Biology (8076)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2220)
  • Systems Biology (6036)
  • Zoology (1252)