Macaque templates & atlases

Overview

Details

Cortical Hierarchy Atlas of the Rhesus Macaque (CHARM)

Authors : Benjamin Jung, Paul A. Taylor, Jakob Seidlitz, Caleb Sponheim, Pierce Perkins, Leslie G. Ungerleider, Daniel Glen, Adam Messinger
Description : A novel anatomical parcellation of the macaque cerebral cortex, where the cortical sheet is subdivided into six-levels of increasingly fine-grained parcellation. The broadest level consists of the four cortical lobes and the finest level is based on the D99 atlas, with modifications that make the regions more robust when applied to low resolution (e.g. fMRI) data.
Documentation : AFNI
Link : AFNI
Language : Volumetric files are in NIFTI (.nii) format, while surface files are in GIFTI (.gii) format.
Publication : Jung et al. (2021) Neuroimage Communication : Email to Dr. Adam Messinger
Restrictions : Please cite the above publication

D99 Template and Atlas v1 (NB! surpassed by v2 below)

Authors : Reveley C, Gruslys A, Ye FQ, Glen D, Samaha J, Russ BE, Saad Z, Seth AK, Leopold DA, & Saleem KS.
Description : Digital version of the Saleem and Logothetis atlas with a newer, higher quality D99 surrogate MRI template. Integrated into AFNI/SUMA software.
Documentation : AFNI site
Link : D99 v1
Language : NIFTI format
Publication : Reveley et al. (2017)
Communication : email K. Saleem, email D. Glen, AFNI message board
Restrictions : Please cite the publication above. The original cortical and subcortical parcellations on the atlas should not be modified without prior consent from the authors.

D99 Template and Atlas v2

Authors : Saleem KS, Avram AV, Glen D, Yen CC, Ye FQ, Komlosh M, Basser PJ.
Description : D99 Atlas v2.0: a macaque template and cortical and subcortical atlas. A comprehensive, MRI-histology based atlas of the Rhesus macaque monkey brain with segmentation of both cortical and subcortical areas in one 3D volume.
Documentation : AFNI site
Link : D99 v2
Language : NIFTI format
Publication : Saleem et al. (2021)
Communication : email K. Saleem, email D. Glen, AFNI message board
Restrictions : Please cite the publication above. The original cortical and subcortical parcellations on the atlas should not be modified without prior consent from the authors.

NMT v1.3 (NIMH Macaque Template - version 1.3)

Authors : Adam Messinger, Benjamin Jung, Jakob Seidlitz, Paul Taylor, Daniel Glen
Description : A volumetric template of the rhesus macaque created by nonlinear averaging of T1-weighted anatomical MRIs from multiple adult monkeys. Surface files are included. Version 1.3 updates include: an improved mapping of the D99 atlas, improved brain masking and normalization, and files that are defined in a common template space (NMT space), using the short data type for improved storage efficiency.
Documentation : Github
Link : Github
Language : Volumetric files are in NIFTI (.nii) format, while surface files are in GIFTI (.gii) format. Scripts for processing single subjects rely on bash shell and AFNI. Some scripts also require ANTs.
Publication : Seidlitz, J., Sponheim, C., Glen, D., Ye, F.Q., Saleem, K.S., Leopold, D.A., Ungerleider, L., Messinger, A. A population MRI brain template and analysis tools for the macaque. NeuroImage 170:121-131 (2018). https://doi.org/10.1016/j.neuroimage.2017.04.063
Communication : Through the GitHub repo or via email to Dr. Adam Messinger
Restrictions : To use the NMT_v1.3 cite the above article: Seidlitz et al., (2018). To use the D99 atlas cite Reveley et al. (2016).

NMT 2.0 Templates (NIMH Macaque Template - version 2.0)

Authors : Benjamin Jung, Paul A. Taylor, Jakob Seidlitz, Caleb Sponheim, Pierce Perkins, Leslie G. Ungerleider, Daniel Glen, Adam Messinger
Description : A collection of volumetric templates of the rhesus macaque created by nonlinear averaging of T1-weighted anatomical MRIs from multiple adult monkeys. Surface files are included. The NMT 2.0 provides increased flexibility in macaque group analysis by providing symmetric and asymmetric templates. Both templates are available with an expanded, full head field of view in Horsley-Clarke stereotaxic orientation. Updates to the templates include: an improved mapping of the D99 atlas, the addition of the CHARM and SARM atlases, improved brain masking and normalization, and files that are defined in a common template space (NMT space), using the short data type for improved storage efficiency.
Documentation : AFNI
Link : AFNI
Language : Volumetric files are in NIFTI (.nii) format, while surface files are in GIFTI (.gii) format. Scripts for processing single subjects rely on bash shell and AFNI.
Publication : Jung et al. (2021) Neuroimage
Communication : Email to Dr. Adam Messinger
Restrictions : Please cite the above publication

Subcortical Atlas of the Rhesus Macaque (SARM)

Authors : Renée Hartig, Daniel Glen, Benjamin Jung, Nikos K. Logothetis, George Paxinos, Eduardo A. Garza-Villarreal, Adam Messinger, Henry C. Evrard
Description : An anatomical parcellation of the entire macaque subcortex tailored for magnetic resonance imaging (MRI). The regions-of-interest (ROIs) are hierarchically organized, with grouping levels suited for both fine structural and spatially broader functional analyses. SARM aims to facilitate the identification, localization, and study of neural interactions involving subcortical regions of the brain.
Documentation : AFNI
Link : AFNI
Language : Volumetric files are in NIFTI (.nii) format, while surface files are in GIFTI (.gii) format.
Publication : Hartig et al. (2021) Neuroimage
Communication : Email to Dr. Henry Evrard or Dr. Adam Messinger
Restrictions : Please cite the above publication

UNC-LPBR 4D Cynomolgus Macaque Atlases from Birth to 48 Months

Authors : Tao Zhong, Jingkuan Wei, Kunhua Wu, Liangjun Chen, Fenqiang Zhao, Yuchen Pei, Ya Wang, Hongjiang Zhang, Zhengwang Wu, Ying Huang, Tengfei Li, Li Wang, Yongchang Chen, Weizhi Ji, Yu Zhang, Gang Li, Yuyu Niu
Description : We construct a comprehensive set of longitudinal brain atlases and associated tissue probability maps (gray matter, white matter, and cerebrospinal fluid) with a totally of 12 time-points from birth to 4 years of age (i.e., 1, 2, 3, 4, 5, 6, 9, 12, 18, 24, 36, and 48 months of age) based on 175 longitudinal structural MRI scans from 39 typically-developing cynomolgus macaques. To facilitate region-based analysis using the atlases, we also provide two popular hierarchy parcellations from NMT v2, i.e., cortical hierarchy maps (6 levels) and subcortical hierarchy maps (6 levels), on these longitudinal macaque brain atlases.
Documentation : NITRC
Link : NITRC
Language : NIFTI (.nii.gz) format
Publication : Zhong et al. (2022) Neuroimage
Communication : Email
Restrictions : None