Beissner, F. Functional MRI of the brainstem: common problems and their solutions. Clin. Neuroradiol. 25, 251–257 (2015).

Article  PubMed  Google Scholar 

Kanwisher, N. Functional specificity in the human brain: a window into the functional architecture of the mind. Proc. Natl Acad. Sci. USA 107, 11163–11170 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yeo, B. T. et al. The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J. Neurophysiol. 106, 1125–1165 (2011).

Article  PubMed  Google Scholar 

Smith, S. M. et al. Correspondence of the brain’s functional architecture during activation and rest. Proc. Natl Acad. Sci. USA 106, 13040–13045 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Assem, M., Glasser, M. F., van Essen, D. C. & Duncan, J. A domain-general cognitive core defined in multimodally parcellated human cortex. Cereb. Cortex 30, 4361–4380 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Foote, S. L. & Morrison, J. H. Extrathalamic modulation of cortical function. Annu. Rev. Neurosci. 10, 67–95 (1987).

Article  CAS  PubMed  Google Scholar 

Shine, J. M. et al. Human cognition involves the dynamic integration of neural activity and neuromodulatory systems. Nat. Neurosci. 22, 289–296 (2019).

Article  CAS  PubMed  Google Scholar 

van den Brink, R. L., Pfeffer, T. & Donner, T. H. Brainstem modulation of large-scale intrinsic cortical activity correlations. Front. Hum. Neurosci. 13, 340 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Niblock, M. M. et al. Comparative anatomical assessment of the piglet as a model for the developing human medullary serotonergic system. Brain Res. Rev. 50, 169–183 (2005).

Article  CAS  PubMed  Google Scholar 

Paxinos, G. & Huang, X.-F. Atlas of the Human Brainstem (Elsevier, 2013).

Edlow, B. L. et al. Disconnection of the ascending arousal system in traumatic coma. J. Neuropathol. Exp. Neurol. 72, 505–523 (2013).

Article  PubMed  Google Scholar 

Guardia, T., Geerligs, L., Tsvetanov, K. A., Ye, R. & Campbell, K. L. The role of the arousal system in age-related differences in cortical functional network architecture. Hum. Brain Mapp. 43, 985–997 (2022).

Article  PubMed  Google Scholar 

Cauzzo, S. et al. Functional connectome of brainstem nuclei involved in autonomic, limbic, pain and sensory processing in living humans from 7 Tesla resting state fMRI. Neuroimage 250, 118925 (2022).

Article  PubMed  Google Scholar 

Singh, K. et al. Functional connectome of arousal and motor brainstem nuclei in living humans by 7 Tesla resting-state fMRI. Neuroimage 249, 118865 (2022).

Article  PubMed  Google Scholar 

Bianciardi, M. et al. Toward an in vivo neuroimaging template of human brainstem nuclei of the ascending arousal, autonomic and motor systems. Brain Connect. 5, 597–607 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Schaefer, A. et al. Local–global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI. Cereb. Cortex 28, 3095–3114 (2018).

Article  PubMed  Google Scholar 

van Essen, D. C. et al. The WU-Minn Human Connectome Project: an overview. Neuroimage 80, 62–79 (2013).

Article  PubMed  Google Scholar 

Salvador, R. et al. Neurophysiological architecture of functional magnetic resonance images of human brain. Cereb. Cortex 15, 1332–1342 (2005).

Article  PubMed  Google Scholar 

Haines, D. E. et al. Neuroanatomy in Clinical Context: An Atlas of Structures, Sections, Systems and Syndromes (Wolters Kluwer Health, 2015).

Bullmore, E. & Sporns, O. The economy of brain network organization. Nat. Rev. Neurosci. 13, 336–349 (2012).

Article  CAS  PubMed  Google Scholar 

Markello, R. D. et al. neuromaps: structural and functional interpretation of brain maps. Nat. Methods 19, 1472–1479 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yarkoni, T., Poldrack, R. A., Nichols, T. E., van Essen, D. C. & Wager, T. D. Large-scale automated synthesis of human functional neuroimaging data. Nat. Methods 8, 665 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hansen, J. Y. et al. Mapping neurotransmitter systems to the structural and functional organization of the human neocortex. Nat. Neurosci. 25, 1569–1581 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Azen, R. & Budescu, D. V. The dominance analysis approach for comparing predictors in multiple regression. Psychol. Methods 8, 129 (2003).

Article  PubMed  Google Scholar 

Margulies, D. S. et al. Situating the default-mode network along a principal gradient of macroscale cortical organization. Proc. Natl Acad. Sci. USA 113, 12574–12579 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mesulam, M. M. From sensation to cognition. Brain 121, 1013–1052 (1998).

Article  PubMed  Google Scholar 

Bär, K.-J. et al. Functional connectivity and network analysis of midbrain and brainstem nuclei. Neuroimage 134, 53–63 (2016).

Article  PubMed  Google Scholar 

Fischl, B. et al. Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron 33, 341–355 (2002).

Article  CAS  PubMed  Google Scholar 

García-Gomar, M. G. et al. In vivo probabilistic structural atlas of the inferior and superior colliculi, medial and lateral geniculate nuclei and superior olivary complex in humans based on 7 Tesla MRI. Front. Neurosci. 13, 764 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Pauli, W. M., Nili, A. N. & Tyszka, J. M. A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei. Sci. Data 5, 180063 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Katsumi, Y. et al. Correspondence of functional connectivity gradients across human isocortex, cerebellum and hippocampus. Commun. Biol. 6, 401 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Mueller, S. et al. Individual variability in functional connectivity architecture of the human brain. Neuron 77, 586–595 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sclocco, R., Beissner, F., Bianciardi, M., Polimeni, J. R. & Napadow, V. Challenges and opportunities for brainstem neuroimaging with ultrahigh field MRI. Neuroimage 168, 412–426 (2018).

Article  PubMed  Google Scholar 

Bianciardi, M. et al. Sources of functional magnetic resonance imaging signal fluctuations in the human brain at rest: a 7 T study. Magn. Reson. Imaging 27, 1019–1029 (2009).

Article  PubMed  PubMed Central  Google Scholar 

Brooks, J. C. W., Faull, O. K., Pattinson, K. T. S. & Jenkinson, M. Physiological noise in brainstem fMRI. Front. Hum. Neurosci. 7, 623 (2013).