Atlases Hub

Published in 2018


Atlases of cortical parcellations (including subcortical regions) based on 150um multi-modal ex-vivo MRI data
(Liu C, et al, Neuroimage, 2018)

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Published in 2020

Nature Neuroscience

Most detailed white matter pathway atlas based on ultra-high resoultion multi-modal ex-vivo MRI data (80um, 64um and 50um)
(Liu C, et al, Nature Neuroscience, 2020)

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Coming Soon


Population-based templates and analysis tools based on in-vivo data from 27 marmosets for neuroimaging and connectome studies.    
(We presented our progress in SfN2019)

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Version1 - Published in 2018

The Version-1 Focused on Cortical Parcellations

Liu C, et al. A digital 3D atlas of the marmoset brain based on multi-modal MRI. Neuroimage. 2018

Abstract The common marmoset (Callithrix jacchus) is a New-World monkey of growing interest in neuroscience. Magnetic resonance imaging (MRI) is an essential tool to unveil the anatomical and functional organization of the marmoset brain. To facilitate identification of regions of interest, it is desirable to register MR images to an atlas of the brain. However, currently available atlases of the marmoset brain are mainly based on 2D histological data, which are difficult to apply to 3D imaging techniques. Here, we constructed a 3D digital atlas based on high-resolution ex-vivo MRI images, including magnetization transfer ratio (a T1-like contrast), T2w images, and multi-shell diffusion MRI. Based on the multi-modal MRI images, we manually delineated 54 cortical areas and 16 subcortical regions on one hemisphere of the brain (the core version). The 54 cortical areas were merged into 13 larger cortical regions according to their locations to yield a coarse version of the atlas, and also parcellated into 106 sub-regions using a connectivity-based parcellation method to produce a refined atlas. Finally, we compared the new atlas set with existing histology atlases and demonstrated its applications in connectome studies, and in resting state and stimulus-based fMRI. The atlas set has been integrated into the widely-distributed neuroimaging data analysis software AFNI and SUMA, providing a readily usable multi-modal template space with multi-level anatomical labels (including labels from the Paxinos atlas) that can facilitate various neuroimaging studies of marmosets.

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Download the associated MRI Data (150um)
Version2 - Published in 2020

The Version-2 Focused on White Matter Pathways

Liu C, et al. A resource for detailed 3D mapping of white matter pathways in the marmoset brain. Nature Neuroscience. 2020

Abstract While the fundamental importance of the white matter in supporting neuronal communication is well known, a detailed description of its complex anatomy is not prominently featured in existing publications of primate brains. One main barrier is that existing neuroimaging data of the primate brain have either insufficient spatial resolution or image contrast to fully resolve white matter pathways. Here, we present an open resource that allows detailed descriptions of white matter structures and the trajectory of fiber-pathways in the marmoset brain. The resource includes 1) diffusion MRI (dMRI) data with the highest resolution available to date revealing white matter features never previously described; 2) a comprehensive 3D white matter atlas depicting fiber pathways that were either omitted or misidentified in previous atlases; 3) comprehensive fiber-pathway maps of cortical connections combining dMRI tractography and neuronal tracing data. Our data will facilitate studying brain connectivity and developing tractography algorithms in the primate brain.

Download the V2 Atlases

Download the associated MRI Data (80um, 64um and 50um)

Download All Tracing-guided Tracking Probilities Maps

Online-viewing Tracing-guided Tracking Probilities Maps Online-viewing the Merged Atlas (v2.0.1) with cortex_vH Online-viewing the Merged Atlas (v2.0.1) with cortex_vPaxinos
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Coming Soon

We presented the progress of the Version-3 at SfN2019

Session Number: 753, 10/23/2019 1:00:00 PM - 10/23/2019 5:00:00 PM

with Dynamic Poster and on-site demo

Population-based templates and analysis tools

By acquiring super-resolution MRI of ex-vivo brains, we constructed a full 3D anatomical atlas of the marmoset brain. Version 1 contained the cortical parcellation, and version 2 the white matter pathways. However, these two previous versions were based on only a few brains of male marmosets, which imposes a limitation to their application in neuroimaging studies of large cohorts of animals. To address this problem, we collected in-vivo multi-modal MRI from 27 marmosets of both genders. The new in-vivo MRI dataset includes anatomical T1-weighted, T2-weighted, and multi-shell diffusion MRI, as well as functional resting-state fMRI. From the anatomical MRI, head profiles were created and compared to profiles based on CT images of the same subjects' heads. Analysis of the new MRI- and CT-based dataset revealed significant variations in head and brain shape and size, regional volumes of several brain structures, and brain connectivity, highlighting substantial individual variabilities in the marmoset population. We used the new dataset to create multimodal brain templates and co-registered them into a new and standard population-based template space. We then used the previous atlas versions to perform complete labeling of anatomical structures. We constructed population-based tissue types to facilitate volumetric analyses and built a population-based brain surface to facilitate 3D visualization and surface-based analyses. Combining information obtained from the MRI with that of the CT dataset allows a more accurate estimation of stereotaxic coordinates of different brain regions, which can be used, for example, for a more precise surgical planning. These templates and associated tools will comprise version 3 of our marmoset brain atlas project, which will significantly aid in a wide range of MRI and connectome studies.