eaglevac:MainPage

Eagle Atlas Compilation for Vestibular Research

This collection of atlases is provided by the Post-Concussion Vestibular Dysfunction (PCVD) research group at the Emory University School of Medicine, Atlanta, Georgia, United States. It consists of seven source atlases at 1mm isotropic resolution which are customized to facilitate functional and structural connectivity analyses of the vestibular system. Each source atlas has been processed to ensure that there are no overlaps among the ROIs.

This atlas collection is intended for use with the CONN Toolbox (https://web.conn-toolbox.org). Simply import the GZipped NIfTI files and alert CONN that they are atlases by clicking the "Atlas" checkbox.

We would be thrilled to accept any corrections or modifications to this compilation, including subdivisions of the included ROIs (provided the subdivisioning is supported by peer-reviewed literature). Please submit any such edits on the GitHub website.

Our initial publication on this compilation can be found here.

Source Atlases

• Eickhoff and Indovina ROIs
• Brainnetome Atlas
• Diedrichsen SUIT Cerebellar Atlas
• Najdenovska Anatomical Thalamic Atlas
• Brainstem ROIs from Brainstem Navigator
• Diencephalon ROIs from Brainstem Navigator
• Neudorfer Anatomical Hypothalamus Atlas

Files

• ".nii.gz" files contain the atlas ROIs
• "atlas...txt" files contain the ROI labels for use with the CONN Toolbox
• "roi_numbers.txt" files contain human-readable ROI labels, ROI values, and their descriptions
• "CONN suggested ROI order.txt" can be copied and pasted into CONN for connectome rendering, in order to sort ROIs by hemisphere, region, and function; also includes group labels such as SM (somatomotor), SS (somatosensory), VB (vestibular), BS-DE (brainstem-diencephalon), and CRB (cerebellum)
• "CONN suggested labels.txt" can be copied and pasted into CONN for connectome rendering: this removes the initial atlas source (e.g., "EI.[EI]") which CONN automatically prefixes and shortens ROI labels for rendering

Data Use Agreement/References

If you leverage this atlas collection, in whole or in part, you MUST cite the following references in any publications. There is NO requirement to include the primary reference authors (Smith et al. 2022) as co-authors on your publication.

Primary reference:

• Smith JL, Ahluwalia V, Gore RK, Allen JW. Eagle-449: A volumetric, whole-brain compilation of brain atlases for vestibular functional MRI research. Sci Data. 2023 Jan 14;10(1):29.doi: 10.1038/s41597-023-01938-1. PMID: 36641517; PMCID: PMC9840609.
  

Eickhoff-Julich-Fan:

• Amunts K, Mohlberg H, Bludau S, Zilles K. Julich-Brain: A 3D probabilistic atlas of the human brain’s cytoarchitecture. Science. 2020 Aug 21;369(6506):988-92. https://doi.org/10.1126/science.abb4588
• Fan L, Li H, Zhuo J, Zhang Y, Wang J, Chen L, Yang Z, Chu C, Xie S, Laird AR, Fox PT. The human brainnetome atlas: a new brain atlas based on connectional architecture. Cerebral cortex. 2016 Aug 1;26(8):3508-26. https://doi.org/10.1093/cercor/bhw157

Indovina (posterior insular complex, PIC):

• Indovina I, Bosco G, Riccelli R, Maffei V, Lacquaniti F, Passamonti L, Toschi N. Structural connectome and connectivity lateralization of the multimodal vestibular cortical network. NeuroImage. 2020 Nov 15;222:117247. https://doi.org/10.1016/j.neuroimage.2020.117247

Diedrichsen SUIT (cerebellum):

• Diedrichsen J, Balsters JH, Flavell J, Cussans E, Ramnani N. A probabilistic MR atlas of the human cerebellum. Neuroimage. 2009 May 15;46(1):39-46. https://doi.org/10.1016/j.neuroimage.2009.01.045
• Diedrichsen J, Maderwald S, Küper M, Thürling M, Rabe K, Gizewski ER, Ladd ME, Timmann D. Imaging the deep cerebellar nuclei: a probabilistic atlas and normalization procedure. Neuroimage. 2011 Feb 1;54(3):1786-94. https://doi.org/10.1016/j.neuroimage.2010.10.035

Najdenovska (thalamus):

• Najdenovska, E., Alemán-Gómez, Y., Battistella, G. et al. In-vivo probabilistic atlas of human thalamic nuclei based on diffusion- weighted magnetic resonance imaging. Sci Data 5, 180270 (2018). https://doi.org/10.1038/sdata.2018.270

Brainstem Navigator (brainstem and diencephalon):

• Singh K, Cauzzo S, García-Gomar MG, Stauder M, Vanello N, Passino C, Bianciardi M. Functional connectome of arousal and motor brainstem nuclei in living humans by 7 Tesla resting-state fMRI. Neuroimage. 2022 Apr 1;249:118865. Epub 2022 Jan 12. PMID: 35031472; PMCID: PMC8856580. https://doi.org/10.1016/j.neuroimage.2021.118865
• Singh K, Indovina I, Augustinack JC, Nestor K, García-Gomar MG, Staab JP, Bianciardi M. Probabilistic Template of the Lateral Parabrachial Nucleus, Medial Parabrachial Nucleus, Vestibular Nuclei Complex, and Medullary Viscero-Sensory-Motor Nuclei Complex in Living Humans From 7 Tesla MRI. Front Neurosci. 2020 Jan 23;13:1425. PMID: 32038134; PMCID: PMC6989551. https://doi.org/10.3389/fnins.2019.01425

Neudorfer (hypothalamus):

• Neudorfer, C., Germann, J., Elias, G.J.B. et al. A high-resolution in vivo magnetic resonance imaging atlas of the human hypothalamic region. Sci Data 7, 305 (2020). https://doi.org/10.1038/s41597-020-00644-6

PCVD Lab Contributors

The following PCVD Research Group members performed the preprocessing, merging, and quality assurance operations on the source atlases, or contributed to the primary publication. They did NOT originate the source atlases.

Jeremy L. Smith, PhD, MSDS: compiled the original source atlases, conducted the processing and quality assurance workflows for merging of the source atlases, and performed the technical validation using Human Connectome Project data.

Vishwadeep Ahluwalia, PhD: supervised the analysis and edited the primary publication.

Russell K. Gore, MD and Jason W. Allen, MD, PhD: jointly conceived, designed, and supervised implementation of the study, provided clinical interpretation of the results, and supervised the analysis and edited the primary publication.

PCVD Lab Funding

This project was supported by NIH/NINDS grant R01NS119683 and a seed grant from the Emory University Department of Radiology and Imaging Sciences.