An Engineering Diagram of the Brain

This is a system level “engineering diagram” of the mammalian brain. (Why an engineering diagram?) The details in the thalamus and cortex are based on data for the macaque monkey brain, while the rest is common to the rat, cat, and monkey. As far as is known, everything shown at this level applies to the human brain as well (see accuracy)

                                                                    Click here to see higher size image.

The overall organization of the diagram roughly parallels the physical organization of the actual structures, which itself roughly parallels phylogenetic (and to an extent, ontogenetic) development. Some exceptions are made in order to better reflect systems organization or to facilitate an uncluttered spatial arrangement. By and large, the physical arrangement of the brain is such that the lengths of the interconnections between its parts is minimal (to reduce metabolic requirements), and therefore we should expect that arranging a diagram in the same way will result in the fewest number of long lines obscuring the view. Over the course of evolution, however, some connections have grown in importance beyond the ability of the ontogenetic development process to rearrange things, and therefore long fiber bundles and the like are seen in the brain. I have tried to minimize these here, not always possible with only two dimensions to work with rather than three.

At the top in violet is the cerebral neocortex, divided into functional zones each consisting of some 2-8 individual areas. At the individual area level, there are a few connections that are not bidirectional, however at the macro level displayed here all connections can be considered bidirectional. In the spatial arrangement, the left-right axis mirrors the anterior-posterior axis in the brain, placing the sensory structures towards the left, the decision-making structures towards the right, and the somatosensory / motor structures in the middle. (The temporal “limbic” areas and the cingulate cortex are placed anteriorally due to functional allegiance.) Note that this portion of the diagram, as well as all others, illustrate essentially one hemispheric side of the brain, not both.

The linear structure beneath the neocortex represents the thalamus. The outline around the boxes representing nuclei represents the reticular nucleus, although in the case of some of the neuromodulatory connections, connections to this in the diagram also represent actual connections to all or most of the nuclei as well. Thalamic nuclei fall into three categories based on the localization of their terminations in the cortex as well as their primary sources of input (Herkenham (1986); “New Perspectives on the Organization and Evolution of Nonspecific Thalamocortical Projections” in Jones, E.G., Peters, A. (ed.s), Cerebral Cortex Vol. 5.). The arrangement of nuclei elongates a three-dimensional structure and again represents the posterior-anterior dimension from left to right.

Type 1 nuclei (colored in brightest red) receive their primary input from sub-cortical sources and make very narrowly focused connections to a few cortical areas. Type 2 nuclei (colored in somewhat faded red) receive their primary input from the neocortex, and make moderately narrowly focused connections to a generally different set of cortical areas, together sometimes with more diffuse input to others. (At the level of coarseness of the neocortical representation here, the unidirectionality is concealed.) Type 3 nuclei (colored in washed-out red) receive input from both cortical and subcortical sources and make diffuse connections to broad sets of areas. The intralaminar nuclei are the most extreme example, connecting to most of the cortex in low density. The Type 1 nuclei are thought to serve as the primary relays of sensory information to the neocortex, the Type 2 nuclei seem to serve an integrative function, while the Type 3 nuclei relate to arousal and perhaps more specific modulation of overall functioning.

To the right of the neocortex are two major structures of the limbic system, the hippocampus and the amygdala, together with the brainstem reticular formation. These three form half of a bent axis with the three structures along the bottom: the habenula, hypothalamus, and basal forebrain nuclei. All six of these are highly interconnected and their primary external interactions are with the frontal/limbic neocortical areas.

The decision to place three of these along the bottom near the neuromodulators was governed both by constraints of space as well as connectivity. The three on the right side have the most extensive interactions with the anterior neocortex and thalamus. However, it may have been better to place the basal forebrain structures next to the amygdala and move the reticular formation down to the bottom. In addition, it would probably be best to swap the three neuromodulating nuclei with the three lower-placed limbic structures.

Immediately beneath the thalamus are the basal ganglia, together with a hodge-podge of midbrain and hindbrain structures that interact heavily with the thalamus. Note that the output neurons of the substantia nigra pars compacta (SNpc) employ dopamine as their neurotransmitter.

Finally, beneath these structures are the primary neuromodulating nuclei in the brainstem: the locus coeruleus (norepinephrine), Raphe nuclei (serotonin), and ventral tegmental area (dopamine). These send diffuse projections to most of the cortex, and it is through interference with these effects that many known psychoactive substances operate. These include hallucinogens (NE, 5-HT), SSRI anti-depressants (5-HT), tricyclic antidepressants (all three), antipsychotics (NE, DA), and others. (The major effects of some dopamine-affecting drugs such as cocaine, amphetamines, and L-DOPA are thought to originate primarily from effects on the substantia nigra’s connections in the basal ganglia. Heroin and related narcotics operate on endorphin (a type of neuropeptide) transmitters. The effects of more common drugs such as alcohol, caffeine, and cannabis are less localized and less well understood.)

Diagram Conventions

  • Arrow connection endings indicate excitatory synapses, balls indicate inhibitory synapses.
  • All connection lines without arrows are bidirectional and excitatory.
  • All dashed connection lines represent neuromodulatory effects (mediated by transmitters like dopamine, norepinephrine, serotonin, etc.); acetylcholine connections terminating at muscarinic receptors are considered neuromodulatory.

Abbreviations Used

Abbrev Description Abbrev Description Abbrev Description Abbrev Description
5HT serotonin A anterior nucleus ACh acetylcholine (neurotransmitter) Amyg amygdala
ant anterior Aud auditory bsrf brainstem reticular formation CA1 CA1 hippocampal field
CA3 CA3 hippocampal field Cb cerebellum Cing cingulate cortex D deep (amygdalar nuclei)
D-L dorso-lateral DA dopamine DG dentate gyrus Diag Band diagonal band nucleus
FTC GPe globus pallidus, external segment GPi globus pallidus, internal segment H higher areas (cortical hierarchy)
Hypo hypothalamus IC inferior colliculus Intralam intralaminar nuclei L lower areas (cortical hierarchy)
Lat lateral LC locus coeruleus LD lateral dorsal nucleus LGNd lateral geniculate nucleus, dorsal
Lim-SG limitans-suprageniculate nucleus Limb limbic LOT lateral olfactory tract LP lateral posterior nucleus
M1 primary motor cortex Mamm mammillary body matrix striatum, matrix component MD medial dorsal nucleus
med medial Med Sept medial septum MGNd,mc medial geniculate nucleus, dorsal, magnocellular MGNv medial geniculate nucleus, ventral
Mot motor MV medioventral nucleus N Acc nucleus accumbens NE norepinephrine
Nuc Bas nucleus basilis (of Meynert) O-F orbito-frontal occ occipital (visual cortex) olf olfactory cortex
par parietal (visual cortex) patch striatum, patch component PB parabrachial nucleus peri perirhinal cortex
PFC prefrontal cortex Pl-a,m pulvinar, anterior, medial Pl-i,l pulvinar, inferior, lateral PM premotor cortex
Po posterior nucleus (thalamus) Poly polysensory post posterior preopt preoptic area
Pt parataenial nucleus Raphe Raphe nuclei Ret form reticular formation S superficial (amygdalar nuclei)
SC superior colliculus SM submedial nucleus (part of VM) SMA supplementary motor area SNpc substantia nigra pars compacta
SNpr substantia nigra pars reticulata Spin cord spinal cord SS somatosensory STN subthalamic nucleus
STP superior temporal polysensory area Sub subiculum (hippocampus) temp temporal (visual cortex) TF temporal area TF
TF temporal area TH VA ventral anterior nucleus Vis visual VL ventrolateral nucleus
VM ventromedial nucleus VPI ventral posterior inferior nucleus VPM/L ventral posteromedial /-lateral nucleus VTA ventral tegmental area


The purpose of this diagram was to obtain a global perspective on the functional organization of the brain while discarding as little detail as possible. When detail is discarded, someone has made a decision as to what to discard, and that decision may not accord with the ultimate importance it may own in a hypothetical true theory of brain functioning. More immediately relevant, it may not accord with its importance in whatever collection of ideas and speculations is percolating in the individual viewer’s mind, that they are attempting to solidify somewhat through the use of a visual aid.

An engineering diagram seemed the most natural format, since the physical appearance of brain structures is not relevant to their functional role. However, this is more than just a wiring diagram because it tries to convey certain features of the structures themselves through illustration, not just their connections. Thus, each structure is not illustrated as a uniformly-sized box, but as a colored shape that represents its relative size and functional allegiance.

A second purpose was to emphasize the prominent roles of subcortical structures and their relations with the neocortex. Since the latter has undergone the most significant expansion in human evolution, and it is the largest, most prominent part of the brain, there is a tendency to credit it as the primary substrate of human intelligence. However there can be no question that the other structures are absolutely crucial in contributing to this functioning, and it is only through understanding the nature of their coordination that significant insight will be gained. This point is especially relevant to those who actually carry out neurobiological research, for it is necessary then to narrow focus and specialize on one structure, making it easy to forget about its role as part of a larger system.


The structure and connectivity data used to construct the diagram was drawn largely from secondary sources, with a few primary and tertiary instances. Data from the macaque monkey was used in most cases, however data from the rat was used when monkey data was not available and the connections in question were believed by the authors to be phylogenetically conserved. A partial list of references used is given at the end.

Many of the structures represented on the diagram represent agglomerations of smaller structures. For example, the Raphe nuclei are comprised of about ten distinct cell groups. Each cortical region subsumes several individual areas distinguished on cytoarchitectonic, connectivity, or functional grounds. Similarly, some structures, such as the olfactory bulb and the medial habenula, are excluded entirely. There were two reasons for excluding such detail from the diagram. First, including it would have made the diagram too cluttered to serve any clarifying function. Second, the finer the level of detail, the more limited the accuracy of the data available for it. While techniques improve, anatomical tracing is an inexact science.

Finally, a disclaimer: I am not a neuroanatomist. There may be portions of this diagram that are incorrect outright, or where important information is left out. It should be used as a guide to thinking about brain function from a global systems perspective, not as an authoritative source of connection data. Verify connectivity that you see here before drawing any definitive conclusions based on it.

Comments and questions to arobert at interstitiality dot net.



Aggleton, J.P. (1992); The Amygdala.
Aggleton, J.P., Mishkin, M. (1984); "Projections of the Amygdala to
	the Thalamus in the Cynomolgus Monkey" in J. Comp. Neurol.
Alexander, G.E., DeLong, M.R., Strick, P.L. (1986); "Parallel Organization of
	Functional Segregated Circuits Linking Basal Ganglia and Cortex" in
	Ann. Rev. Neurosci. 9:357-81.
Amaral, D.G., Cowan, W.M. (1980); "Subcortical Afferents to the
	Hippocampal Formation in the Monkey" in J. Comp. Neurol.
Barbas, H., Pandya, D.N. (1987); "Architecture and Frontal Cortical Conn-
	ections of the Premotor Cortex (Area 6) in the Rhesus Monkey" in
	J. Comp. Neurol. 256:211-28.
Barbas, H., Pandya, D.N. (1989); "Architecture and Intrinsic Connections of
	the Prefrontal Cortex in the Rhesus Monkey" in J. Comp. Neurol.
Felleman, D.J., Van Essen, D.C. (1991); "Distributed Hierarchical Processing in
	the Primate Cerebral Cortex" in Cerebral Cortex 1:1-47.
Foote, S.L., Bloom, F.E., Aston-Jones, G. (1983); "Nucleus Locus Coeruleus:
	New Evidence of Anatomical and Physiological Specificity" in Physiol.
	Rev. 63:844-913.
Foote, S.L., Morrison, J.H. (1987); "Extrathalamic Modulation of Cortical
	Function" in Ann. Rev. Neurosci. 19:67-95.
Herkenham, M. (1986); "New Perspectives on the Organization and Evolution
	of Nonspecific Thalamocortical Projections" in Jones, E.G., Peters, A.
	(ed.s), Cerebral Cortex Vol. 5.
Insausti, R., Amaral, D.G., Cowan, W.M. (1987); "The Entorhinal Cortex of the
	Monkey III. Subcortical Afferents" in J. Comp. Neurol. 264:396-408.
Jones, E.G. (1985); The Thalamus.
Kovits, M., Zaborszky, L. (1979); "Neural Connections of the Hypothalamus" in
	Morgane, P.J., Panksepp, J. (ed.s), Anatomy of the Hypothalamus.
Lewis, D.A., Campbell, M.J., Foote, S.L. (1986); "The Monoaminergic
	Innervation of Primate Neocortex" in Human Neurbio. 5:181-8.
Mesulam, M.M., Mufson, E.J., Levey, A.I., Wainer, B.H. (1983); "Cholinergic
	Innvervation of Cortex by the Basal Forebrain: Cytochemistry and
	Cortical Connections of the Septal Area, Diagonal Band Nuclei, Nucleus
	Basilis (Substantia Innominata), and Hypothalamus in the Rhesus Monkey"
	in J. Comp. Neurol.214:170-97.
Steriade, M., Glenn, L.L. (1982); "Neocortical and Caudate Project-
	ions of Intralaminar Thalamic Neurons and their Synaptic
	Excitation from Midbrain Reticular Core" in J. Neurophysiol.
Steriade, M., Parei, D., Parent, A., Smith, Y. (1988); "Projections of Cholin-
	ergic and Non-cholinergic Neurons of the Brainstem Core to Relay and
	Associational Thalamic Nuclei in the Cat and Monkey" in Neurosci. 25:
Swanson, L.W., Cowan, W.M. (1975); "A Note on the Connections and
	Development of the Nucleus Accumbens" in Brn. Res. 92:324-30.
Wilson, C.J. (1990); "Basal Ganglia" in The Synaptic Organization of the
	Brain, ed. Shepherd, G..
Young, M.P. (1993); "The Organization of Neural Systems in the Primate Cerebral
	Cortex" in Proc. R. Soc. Long. B 252:13-8.
Zaborszky, L. (1982); "Afferent Connections of the Medial Basal Hypothalamus"
	in Adv. Anat., Embryol., and Cell Biol. 69:1-107.

Revision History

Version Date Comment
1 2005/11 First public version
2 2008/09 Added neocortex -> Cb conn


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