A resource for the detailed 3D mapping of white matter pathways in the marmoset brain


While the fundamental importance of the white matter in supporting neuronal communication is well known, existing publications of primate brains do not feature a detailed description of its complex anatomy. The main barrier to achieving this is that existing primate neuroimaging data have insufficient spatial resolution to resolve white matter pathways fully. Here we present a resource that allows detailed descriptions of white matter structures and trajectories of fiber pathways in the marmoset brain. The resource includes: (1) the highest-resolution diffusion-weighted MRI data available to date, which reveal white matter features not previously described; (2) a comprehensive three-dimensional white matter atlas depicting fiber pathways that were either omitted or misidentified in previous atlases; and (3) comprehensive fiber pathway maps of cortical connections combining diffusion-weighted MRI tractography and neuronal tracing data. The resource, which can be downloaded from marmosetbrainmapping.org, will facilitate studies of brain connectivity and the development of tractography algorithms in the primate brain.

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Fig. 1: Comparison of isotropic data resolution, brain volume and fiber volumes between marmosets, macaques and humans.
Fig. 2: The corona radiata imaged at different spatial resolutions.
Fig. 3: The FOF and the Muratoff bundle.
Fig. 4: White matter fiber pathways in the marmoset occipital lobe.
Fig. 5: The VHC of primates.
Fig. 6: Atlas V2 and its applications in preclinical research.
Fig. 7: Atlas-guided dMRI tractography.
Fig. 8: Fiber pathway profiles of cortical connections and regions.

Data availability

The resource presented here includes (1) dMRI data with the highest resolution available to date revealing white matter features not previously described, (2) a comprehensive 3D white matter atlas depicting fiber pathways that were either omitted or misidentified in previous atlases and (3) comprehensive fiber pathway maps of cortical connections combining dMRI tractography and neuronal tracing data. The raw data and all other features of the resource can be downloaded in NIFTI format from our website (marmosetbrainmapping.org).

Code availability

The resource presented here includes code and analysis routines for each dataset that are available for downloading under the corresponding “Detailed info” section in our website at https://marmosetbrainmapping.org/data.html. More information is available in the Supplementary Software.


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We thank the Scientific and Statistical Computing Core of the NIMH Intramural Research Program for their support of the software AFNI and thank the NIH Fellows Editorial Board and the NIH library for language-editing services. We also thank J. Guy for providing the optimized T2* sequence. This work utilized the computational resources of the NIH High Performing Computation Biowulf cluster (hpc.nih.gov). This research was supported by the Intramural Research Program of the NIH, NINDS (ZIA NS003041), including the Neurophysiology Imaging Facility Core (NIMH, NINDS, NEI, ZIC MH002899). The neuronal tracing data are from the Australian Research Council (DP110101200, DP140101968 and CE140100007) and an International Neuroinformatics Coordinating Facility Seed Funding Grant.

Author information

C.L., A.C.S., F.Q.Y. and J.D.N. designed the research. C.L., F.Q.Y. and C.C.-C.Y. collected the MRI data. C.L., J.D.N. and D.S. annotated the white matter structures. C.L. analyzed all the data, drew the white matter ROIs and constructed the atlas. C.L. and X.T. constructed the https://marmosetbrainmapping.org resource website. D.G. and C.L. implemented the atlas into AFNI. M.G.P.R. and P.M. provided the neuronal tracing data. C.L., D.A.L. and A.C.S. wrote the original draft. C.L., A.C.S., D.A.L., F.Q.Y., J.D.N., M.G.P.R., C.C.-C.Y. and D.S. revised the draft. A.C.S., D.A.L., M.G.P.R. and P.M. secured funding for the study.

Correspondence to Cirong Liu or Afonso C. Silva.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–5.

Reporting Summary

Supplementary Tables 1 and 2

Supplementary Tables 1 and 2.

Supplementary Software

Supplementary Software.

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Liu, C., Ye, F.Q., Newman, J.D. et al. A resource for the detailed 3D mapping of white matter pathways in the marmoset brain. Nat Neurosci 23, 271–280 (2020). https://doi.org/10.1038/s41593-019-0575-0

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