AN 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. Our initial publication on this compilation can be found here.
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.
- 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
| File | Usage |
|---|---|
| *.nii.gz | Contain the atlas ROIs |
| atlas*.txt | Contain the ROI labels for use with the CONN Toolbox |
| roi_numbers.txt | 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 |
Currently, the files in this compilation are optimized for use with the CONN Toolbox. (We are working on adapting it for use with FSL.) Simply add the GZipped NIfTI files as atlases in the SETUP tab of the toolbox. CONN will automatically associate the ROIs in each NIfTI file with a label as long as the atlas*.txt files are in the same folder. Naturally, you can also conduct analyses on only a subset of these ROIs; the included Excel spreadsheet not only includes ROI values and labels for each atlas, but two tabs highlighting the "vestibular" and "extended vestibular" ROIs as well, for ease of reference. (See Smith et al 2023 for definitions of these groups.)
You also may wish to use abbreviated labels and an alternate ROI order for visualization. The "CONN suggested ROI order" and "CONN suggested labels" text files can be copied and pasted into CONN for manual ROI grouping and ordering. NOTE: (1) These files assume you're using all 449 ROIs, and (2) manual ROI ordering may affect the way CONN sees "clusters" of ROIs (e.g., "Network-Based Statistics" and "Functional Network Connectivity" methods), since these methods perform hierarchical ROI clustering by default.
We welcome edits and additions to this compilation — we only ask that any additions are based on peer-reviewed results. Examples include subdivisions of ROIs based on ICA or anatomical findings, cross-modality mapping such as genome expression, and new labels. Future versions will be provided to the scientific community as new project branches (subdirectories under the main project folder). These versions will likely be called something other than "449," since this designates that the current version includes 449 ROIs!
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. 2023) as co-authors on your publication.
The GPL license associated with this repository applies only to the BASH code (merge_code.bash) used in the development of this project. The authors have no claim over the source atlases, several of which are provided by their authors on other sites under specific licenses, such as Creative Commons (CC-NA).
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
Members of the PCVD lab who contributed to this atlas compilation:
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.
This project was supported by NIH/NINDS grant R01NS119683 and a seed grant from the Emory University Department of Radiology and Imaging Sciences.