This is a 3D atlas of the human brain on the MNI ICBM152 2009c template, the standard space of most brain imaging papers. It joins four open atlases in one view. They are the CerebrA cortical and deep labels, the CIT168 subcortical nuclei, the Harvard Ascending Arousal Network of the brainstem, and the Yeo 2011 resting-state networks. Type a coordinate from a paper and the atlas reports the region at that point in each of the four, on the 3D model and on MRI slices.
The arousal network is the reason this atlas is on a site about consciousness. Clinical neurology separates consciousness into arousal, being awake, and awareness, having experience. The Harvard atlas maps the brainstem nuclei that the Edlow group links to wakefulness, the structures whose damage is studied in coma. A consciousness layer marks where each theory of consciousness places its key structures, and where clinical studies of coma and the minimally conscious state found them, with the source for every statement.
Tap a structure, or search for one. Details
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Slices of the MNI 2009c template load when you scroll here (4.1 MB).
The opening download is 2.3 MB. The slices, the label grids and the other layers load when you use them, 9.3 MB in all.
| Layer | Atlas | Structures here | Licence |
|---|---|---|---|
| Cortex, deep structures | CerebrA, Manera et al. 2020 | 102, 51 per hemisphere | CC0 1.0 |
| Subcortical nuclei | CIT168, Pauli, Nili and Tyszka 2018 | 32, 16 per hemisphere | CC BY 4.0 |
| Arousal network | Harvard Ascending Arousal Network v2.0, Edlow and Kinney 2023 | 16 brainstem nuclei | CC0 1.0 |
| Resting-state networks | Yeo 2011 seven networks, Yeo et al. 2011 | 14, 7 per hemisphere | MIT |
| Template and slices | MNI ICBM152 2009c nonlinear symmetric, Fonov et al. 2011 | MNI notice below |
CerebrA is the Mindboggle-101 labelling registered to the 2009c symmetric template and corrected by hand. CIT168 is a probabilistic atlas built from 168 Human Connectome Project subjects. This atlas uses its deterministic labels, split at the midline into left and right. The Harvard atlas is built from ex vivo MRI and histology of brainstem specimens. The Yeo networks come from resting-state fMRI of 1,000 people.
The layer has three groups. Theories place consciousness in different parts of the brain. Integrated information theory points to a posterior hot zone of the cortex, the global neuronal workspace to prefrontal and parietal association cortex, higher-order theories to prefrontal cortex, and recurrent processing to visual cortex itself. Merker argues for the upper brainstem, and dendritic integration for the loop between thalamus and cortex. The arousal network of the Harvard atlas is shown as its own group, because it sustains being awake, not the content of experience. Clinical evidence shows where lesions cause coma, which cortical network loses its connections in patients who cannot communicate, and where stimulation helped a patient in the minimally conscious state.
Each overlay states what the source says and, separately, how we matched its regions to the labels of this atlas. A paper names a region in words, such as a posterior hot zone or the dorsolateral pontine tegmentum. The atlas marks whole labels. The match is ours and is written down for each overlay, so it can be checked and argued with. Where the 2025 Cogitate adversarial test bears on a theory, its result is shown beside the claim.
Every number on this page is computed by our build script from the released files, not copied by hand. A structure’s volume is its count of 1 mm voxels on the template grid. Its centre is the mean position of those voxels in MNI millimetres. The surfaces are traced from the label voxels with marching cubes, smoothed lightly and reduced to a triangle budget, so their edges are approximate at the scale of a millimetre. The coordinate lookup reads the label voxels themselves, not the surfaces.
The four atlases do not share one template. CerebrA uses the symmetric 2009c template and CIT168 the asymmetric 2009c template on the same grid. The Harvard and Yeo atlases were made on the FSL MNI152 template and are resampled here by their world coordinates. The templates differ by a few millimetres, so treat a label near a boundary with care. An atlas is also an average. It gives the most likely region at a point for a group of brains, not the region in any one person’s brain.
The thalamus appears as one structure per hemisphere. A version with its separate nuclei waits on a licence question. The cerebellum has three vermis labels and its grey and white matter, not its separate lobules, because the main cerebellar atlas is licensed for non-commercial use only.
The Connectome Atlas shows complete nervous systems neuron by neuron, from the fruit fly to a fragment of human cortex. States of Consciousness shows how brain networks change under anaesthesia and in the unresponsive wakefulness syndrome. The Theory Arena sorts the experiments that support or challenge each theory of consciousness. Zap and Zip shows the brain’s echo to a magnetic pulse, a measure used to assess consciousness at the bedside.
The template and the slices derived from it are distributed under this notice, reproduced as the licence requires.
Copyright (C) 1993-2004 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies. The authors and McGill University make no representations about the suitability of this software for any purpose. It is provided “as is” without express or implied warranty. The authors are not responsible for any data loss, equipment damage, property loss, or injury to subjects or patients resulting from the use or misuse of this software package.