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In this figure, homologous left and right hemisphere regions are coded in the same color
The 486 regions comprising the atlas cover gray matter across the entire brain, including brainstem, cerebellum, subcortex (diencephalon, mesencephalon, telencephalon), and cerebral cortex. The regions are defined based on published papers considered to be high-quality parcellations of specific large-scale zones of the brain or anatomically defined nuclei, including parcellations of the cortex (Glasser et al. 2016), basal ganglia (Pauli et al. 2016), thalamus (Morel et al. 1997, Krauth et al. 2010, Jakab et al. 2012), subcortical forebrain (Pauli et al. 2018), amygdala and hippocampus (Amunts et al. 2005) , specific brainstem regions (Zambreanu et al. 2005, Keren et al. 2009, Nash et al. 2009, Bar et al. 2016, Beliveau et al. 2015, Fairhurst et al. 2007, Brooks et al. 2017, Sclocco et al. 2016) , cerebellum (Diedrichsen et al. 2009), and brainstem areas not otherwise covered by named nuclei (Shen et al. 2013).
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486 regions of interest subdivide the brain for anatomical characterization of sources of predictive information. These regions comprehensively cover brain gray matter from the brainstem through the forebrain, and are based on parcels and subcortical nuclei defined in previous published studies. We obtain 360 cortical regions (180 areas x 2 hemispheres) from the Human Connectome Project’s cortical parcellation, which delineates areas according to neuroimaging derived anatomical and multitask functional criteria (Glasser et al. 2016), mapped to volumetric MNI space using a nonlinear transformation (Wu et al. 2018). T1 and T2 based anatomical criteria delineate striatum, ventral tegmental area, substantia nigra, bed nucleus of the stria terminalis, pallidum, mammillary nuclei and the habenula (25 regions) based on (Pauli et al. 2016). T1 based anatomical criteria delineate the cerebellar lobules, vermis and deep nuclei (denate, interposed, fastigial; 34 regions total) (Diedrichsen et al. 2009). T1 derived tissue boundaries and white matter tractography delineate 16 thalamic nuclei and the hypothalamus (Morel et al. 1997; Krauth, Szekely et al. 2010). A variety of nucleus specific functional and anatomical criteria define monoaminergic brainstem nuclei, the rostroventral medulla, parabrachial nuclei, trigeminal nuclei, nucleus ambiguus, nucleus tractus solitarius, tegmental nuclei, and some subdivisions thereof (24 areas) (Zambreanu et al. 2005; Fairhurst et al. 2007; Nash et al. 2009; Sclocco et al. 2016; Pauli, Nili, and Tyszka 2018; Shen et al. 2013; Keuken et al. 2014; Keren et al. 2009; Beliveau et al. 2015; Bär et al. 2016). Functional homogeneity criteria from a graph theoretic analysis of functional connectivity delineates remaining gross divisions of the brainstem (17 areas) (Shen et al. 2013). Finally, anatomical criteria adapted from post-mortem studies and included in the SPM Anatomy Toolbox subdivide hippocampal formation into CA1, CA2, CA3, dentate gyrus and subiculum, as well as gross subdivisions of the amygdala (superficial, latero-basal, centro-medial) (9 regions) (Amunts et al. 2005; Eickhoff et al. 2005).
An additional summary of regions and references for each is listed below:
Cortex, using the atlas of Glasser et al. (Glasser et al. 2016)
Amygdala/hippocampal regions from SPM Anatomy Toolbox (Amunts et al. 2005)
Basal Ganglia: basal ganglia subregions from Pauli (Pauli et al. 2016, 2018)
Thalamus, using the atlas of Morel et al. (1997) (Morel et al. 1997; Krauth, Szekely et al. 2010)
Key brainstem regions, based on previous papers:
For Parabrachial Nucleus (PBN) from Fairhurst et al. (Fairhurst et al. 2007)
Rostral Ventral Medulla (RVM) from Brooks et al. (Brooks et al. 2017)
For the PAG, we (T.D.W.) hand-drew a region on a 7T high-resolution group T1 (Keuken et al. 2014) and segmented out the cerebral aqueduct to exclude it.
Additional Shen atlas parcels to cover areas (esp. brainstem) not otherwise named (Shen et al. 2013)
Nociceptive thalamic zones were included as defined below:
The second set of regions was based on the Morel atlas ( Krauth, Szekely et al. 2010). We grouped ~80 thalamic/epithalamic regions into 17 functional zones likely to be detectable using fMRI (see Figure 3 for a complete list). Nociceptive thalamic zones included the ventral-posterior-lateral (VPL) and –medial (VPM) zone, the intralaminar group, and the mediodorsal ‘association nucleus’ (MD).
References for Atlases
References for Atlases
Amunts,K. et al., (2005). Anat. Embryol. (Berl) 210, 343-352.
Beliveau, V., Svarer, C., Frokjaer, V. G., Knudsen, G. M., Greve, D. N. & Fisher, P. M. (2015). Functional Connectivity of the Dorsal and Median Raphe Nuclei at Rest. NeuroImage. 116:187–95.
Bär, K.-J., de la Cruz, F., Schumann, A., Koehler, S., Sauer, H., Critchley, H. & Wagner, G. (2016). Functional Connectivity and Network Analysis of Midbrain and Brainstem Nuclei. NeuroImage. 134:53-63.
Diedrichsen, J., Balsters, J. H., Flavell, J., Cussans, E., & Ramnani, N. (2009). A Probabilistic MR Atlas of the Human Cerebellum. NeuroImage. 46(1):39-46.
Fairhurst, M., Wiech, K., Dunckley, P. & Tracey, I. (2007). Anticipatory Brainstem Activity Predicts Neural Processing of Pain in Humans. Pain. 128:101-10.
Glasser, M. F., Coalson, T. S., Robbinson, E. C., Hacher, C. D, Harwell, J., Yacoub, E., Ugurnil, K., Andersson, J., Beckmann, C. F., Jenkinson, M., Smith, S. M. & Van Essen, D. C. (2016). A Multi-Modal Parcellation of Human Cerebral Cortex. Nature. 536:171-78.
Keren, N., Lozar, C. T., Harris, K. C., Morgan, P. S. & Eckert, M. A. (2009). In Vivo Mapping of the Human Locus Coeruleus. NeuroImage. 47 (4):1261–67.
Keuken, M. C., Bazin, P.-L., Crown, L., Hootsmans, J., Laufer, A., Müller-Axt, C., Sier, R., van der Putten, E. J., Schafer, A., Turner, R. & Forstmann, B. U. (2014). Quantifying Inter-Individual Anatomical Variability in the Subcortex Using 7 T Structural MRI. NeuroImage. 94:40–46.
Krauth, A., Blanc, R., Poveda, A., Jeanmonod, D., Morel, A. & Székely, G. (2010). A mean three-dimensional atlas of the human thalamus: generation from multiple histological data. Neuroimage. 49(3):2053-62.
Jakab, A., Blanc, R., Berényi E.L. &, Székely, G. (2012) Generation of Individualized Thalamus Target Maps by Using Statistical Shape Models and Thalamocortical Tractography. AJNR Am J Neuroradiol. 33:2110-2116.
Morel, A., Magnin, M. & Jeanmonod, D., (1997) Multiarchitectonic and stereotactic atlas of the human thalamus . J Comp Neurol. 387:588-630 .
Nash, P. G., Macefield, V. G., Klineberg, I. J., Murray, G. M & Henderson L. A. (2009). Differential Activation of the Human Trigeminal Nuclear Complex by Noxious and Non-Noxious Orofacial Stimulation. Human Brain Mapping. 30 (11):3772-82.
Pauli, W. M., Nili, A. N., & Tyszka, J. M (2018). A High-Resolution Probabilistic in Vivo Atlas of Human Subcortical Brain Nuclei. Scientific Data. 5:180063.
Pauli, W. M., O’Reilly, R. C., Yarkoni, T. & Wager, T. D. (2016). Regional Specialization within the Human Striatum for Diverse Psychological Functions. PNAS. 113(7):1907-12.
Sclocco, R., Beissner, F., Desbordes, G., Polimeni, J. R., Wald, L. L., Kettner, N. W., Kim, J., Garcia, R. G., Renvall, V., Bianchi, A. M., Cerutti, S., Napadow, V. & Barbieri, R. (2016). Neuroimaging Brainstem Circuitry Supporting Cardiovagal Response to Pain: A Combined Heart Rate Variability/ultrahigh-Field (7 T) Functional Magnetic Resonance Imaging Study. Philos Trans R Soc A. 374.
Shen, X., Tokoglu, F., Papademetris, X. & Constable, R. T. (2013). Groupwise Whole-Brain Parcellation from Resting-State fMRI Data for Network Node Identification. NeuroImage. 82:403–15.
Wu, Jianxiao, Gia H. Ngo, Douglas Greve, Jingwei Li, Tong He, Bruce Fischl, Simon B. Eickhoff, and B. T. Thomas Yeo. 2018. “Accurate Nonlinear Mapping between MNI Volumetric and FreeSurfer Surface Coordinate Systems.” Human Brain Mapping 39 (9): 3793–3808.
Zambreanu, L., R. G. Wise, J. C. W. Brooks, G. D. Iannetti, and I. Tracey. (2005). Evidence from Functional Magnetic Resonance Imaging. Pain. 114 (3):397-407.
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