Neuroanatomy

Published

March 31, 2026

Modified

January 22, 2026

Resources

Atlases

Harvard Brain Atlas http://www.med.harvard.edu/aanlib/cases/caseNA/pb9.htm
Neurotorium https://neurotorium.org/tool/brain-atlas/
Allen Brain Atlas
- Human female adult (modified Brodmann)
- Human female adult (gyral)

Datasets

OpenNeuro: https://openneuro.org
Neurosynth (fMRI meta-analysis): http://neurosynth.org
Table 1 from Rahimzadeh et al. (2023)

Directional terms

Anterior/Posterior
Medial/Lateral
Superior/Inferior
Dorsal/Ventral
Rostral/Caudal

Bipeds vs. quadripeds

Image axes

Horizontal/Axial
Coronal/Transverse/Frontal
Sagittal (from the side)

Planes of section from http://www.scienceteacherprogram.org/

Supporting structures

Skull

- Occipital - Parietal (2x) - Temporal (2x) - Frontal

Meninges (outside -> in)

Dura mater (‘tough mother’)
Arachnoid membrane
Subarachnoid space
Pia mater (‘gentle mother’)
Cerebrospinal fluid (CSF) between Arachnoid membrane and Pia Mater

Ventricular system

Also known as cerebral ventricles
Lateral (1st & 2nd)
- Forebrain/telencephalon
3rd
- Diencephalon
Cerebral aqueduct
- Midbrain
4th
- Hindbrain

Ventricles filled with cerebrospinal fluid (CSF)
- CSF clears metabolites during sleep (Xie et al., 2013)?
- Blockage of CSF flow -> hydrocephalus
Ventricles are useful landmarks for brain regions

Blood Supply

Left and right carotid arteries & basilar arterry converge in Circle of Willis
Anterior, Middle, and Posterior Cerebral arteries main output

Basal view of the brain from https://previews.123rf.com/images/hfsimaging/hfsimaging1208/hfsimaging120800005/14672522-drawing-of-the-blood-vessels-at-the-base-of-the-brain-called-the-circle-of-willis.jpg

Blood supply to the cerebrum from https://teachmeanatomy.info/wp-content/uploads/Regional-Blood-Supply-to-the-Cerebrum-1024x380.jpg

Lateral view of cerebrovascular system from Wikipedia

Blood/brain barrier

Cells forming blood vessel walls tightly packed
Active transport of molecules typically required

Transport across the blood/brain barrier. Figure 3 from Abbott et al. (2006)

Area Postrema

In brainstem, blood-brain barrier thin
Chemoreceptors (chemical receptors) detect toxins, trigger emesis (vomiting) if necessary

Organization of the Nervous System

Central Nervous System (CNS)
- Brain
- Spinal Cord
Peripheral Nervous System (PNS)
- Somatic division
- Autonomic division
  - Sympathetic
  - Parasympathetic
  - Enteric

Nervous system of Harriet Cole from https://www.pastmedicalhistory.co.uk/the-nervous-system-of-harriet-cole/

Brain

Major division	Ventricular Landmark	Embryonic Division	Structure
Forebrain	Lateral	Telencephalon	Cerebral cortex
			Basal ganglia
			Hippocampus, amygdala
	Third	Diencephalon	Thalamus
			Hypothalamus
Midbrain	Cerebral Aqueduct	Mesencephalon	Tectum, tegmentum
Hindbrain	4th	Metencephalon	Cerebellum, pons
	–	Mylencephalon	Medulla oblongata

Embryonic precursors

Forebrain, midbrain, hindbrain terminology derives from embryonic stages in CNS development.

Cross section of embryonic brain from Wikipedia

Hindbrain

Structures adjacent (or caudal to) 4th ventricle
Components
- Medulla oblongata
- Cerebellum
- Pons

– Source: floris (2012d)

Mid-sagittal view of human brain via MRI from http://webspace.ship.edu/cgboer/medial-labelled.gif

Medulla oblongata

Cardiovascular regulation
Muscle tone
Fibers of passage
- Ascending fibers (from body), a.k.a. afferents
- Descending fibers (exiting brain), a.k.a., efferents

Illustration of brainstem from Wikipedia

By Anatomography - Anatomography (setting page of this image.), CC BY-SA 2.1 jp, https://commons.wikimedia.org/w/index.php?curid=21741021

Cerebellum

“Little brain”
Dorsal to pons
Movement coordination, simple learning (classical conditioning)
Largest number of neurons in the brain

By Images are generated by Life Science Databases(LSDB). - from Anatomography[1] website maintained by Life Science Databases(LSDB).You can get this image through URL below. 次のアドレスからこのファイルで使用している画像を取得できますURL., CC BY-SA 2.1 jp, https://commons.wikimedia.org/w/index.php?curid=7769113

– Source: floris (2012e)

Pons

Bulge on ventral brain stem
Neuromodulatory nuclei
- Nucleus (anatomically discrete cluster of neurons
- Neuromodulators: neurotransmitters that modulate/alter function of other neurons
- e.g., Serotonin (5-HT), norepinephrine (NE), acetylcholine (ACh), dopamine (DA)
Relay to cerebellum

Midbrain

Tectum (roof), dorsal
Tegmentum (floor), ventral

Tectum

“Roof” of the midbrain
Superior and inferior colliculus (colliculi is plural for ‘little hill’)
Superior colliculus: Reflexive orienting of eyes, head, ears (superior colliculi)
- Input from FEF, parietal lobe
- Output to cranial nerve nuclei (III, IV, VI) in tegmentum, pons
Inferior colliculus: Auditory processing (from brainstem to auditory thalamus)

Tegmentum

“Floor” of the midbrain
Species-typical movement sequences
Neuromodulatory nuclei release NTs
- Norepinephrine (NE)
- Serotonin (5-HT)
- Dopamine (DA) – from ventral tegmental area (VTA) and substantia nigra

Forebrain

Diencephalon
Telencephalon

Diencephalon

“Between brain”
Thalamus
Hypothalamus

Diencephalon from Wikipedia Labelled MRI including thalamus and hypothalamus

Thalamus

Input to cortex
Functionally distinct nuclei
- Lateral geniculate nucleus (LGN), vision
- Medial geniculate nucleus (MGN), audition
- Pulvinar, attention?

Hypothalamus

Five Fs: fighting, fleeing/freezing, feeding, and reproduction
Controls pituitary gland (“master” gland)
- Anterior pituitary (indirect release of hormones)
  - e.g., Corticotropin Releasing Hormone (CRH) -> release of cortisol from Adrenal Cortex (adjacent to kidney)
- Posterior pituitary (direct release of hormones)
  - Oxytocin
  - Vasopressin (aka, Arginine Vasopressin – AVP; Anti-diuretic Hormone – ADH)

Nuclei of the hypothalamus

Pituitary gland and connections to the hypothalamus

Telencephalon

Basal ganglia
Hippocampus, amygdala
Cerebral cortex

Basal Ganglia

Skill and habit learning
Linked to Tourette Syndrome, Obsessive-Compulsive Disorder (OCD), addiction, movement disorders (e.g., Parkinson’s Disease)
Striatum
- Caudate nucleus
- Putamen
Globus pallidus
Subthalamic nucleus
Substantia nigra (tegmentum)

– Source: floris (2012a)

Hippocampus

Hippocampus means “sea horse”

Medial to lateral ventricles
Store memories of specific facts (semantic memory) or events (episodic memory)
Place memory in non-human animals (& humans?)
Fornix (axon fiber bundle) projects to (mammillary bodies of) hypothalamus

– Source: floris (2012c)

Amygdala (“almond”)

Physiological state, behavioral readiness, affect
NOT the fear center! (LeDoux, 2015).
Projection to hypothalamus

– Source: floris (2012b)

Cerebral Cortex

Cerebral hemispheres
Groove (sulcus or sulci)
Bumps (gyrus or gyri)
Grey vs. white matter
Lobes

Lateral view

Medial view

Nissl stain

Stains cell bodies
LGd is the lateral geniculate nucleus of the thalamus
Circled area is the hippocampus
Ins is the insula

Lobes of the cerebral cortex

Frontal
Temporal
Parietal
Occipital
Names derive from underlying bones of the skull

Alternative view of the relationship between bones of the skull and lobes of the cerebral cortex

– Challenged (2025)

Longitudinal fissure

Also known as superior longitudinal fissure
Sometimes the medial longitudinal or interhemispheric fissure
Divides the cerebral hemispheres

Lateral sulcus/fissure

Also known as Sylvian Fissure
Divides frontal from temporal lobe

Sylvian Fissure or Lateral Fissure/Sulcus from Wikipedia

Central sulcus

Also known as Rolandic Fissure or Fissure of Rolando
Divides frontal from parietal lobe

Frontal lobe

Anterior to central sulcus
Superior to lateral fissure
Dorsal to temporal lobe

Primary motor cortex (M-I or M1)
- Precentral gyrus

Secondary motor areas
- Supplementary motor cortex (SMC)
- Frontal eye fields (FEF)
Prefrontal cortex
- Planning, problem solving, working memory…?
Components of olfactory system

Olfactory cortex from (Saive, Royet, & Plailly, 2014). Figure 1. Schematic view of the human olfactory system. The primary and secondary olfactory cortices are represented in blue and green, respectively. Amyg, amygdala; Ento, entorhinal cortex; Hipp, hippocampus; OFC, orbitofrontal cortex; PC, piriform cortex; Thal, thalamus (adapted from Royet et al., 2014) — Olfactory cortex from (Saive et al., 2014). Figure 1. Schematic view of the human olfactory system. The primary and secondary olfactory cortices are represented in blue and green, respectively. Amyg, amygdala; Ento, entorhinal cortex; Hipp, hippocampus; OFC, orbitofrontal cortex; PC, piriform cortex; Thal, thalamus (adapted from Royet et al., 2014)

Basal forebrain
- Nucleus accumbens (NAcc), part of ventral striatum

Cingulate Gyrus

Anterior cingulate cortex (ACC)

Inferior Frontal Gyrus (IFG)

Home to Broca’s Area

Middle Frontal Gyrus (MFG)

Home to Dorsolateral Prefrontal Cortex (DLPFC)

Superior Frontal Gyrus (SFG)

Brodmann Area 8
Frontal Eye Fields (FEF)
Laughter and self-awareness?

Temporal lobe

Ventral to frontal, parietal lobes
Inferior to lateral fissure

Primary auditory cortex (A-I or A1)

Primary Auditory Cortex from https://en.wikipedia.org/wiki/Auditory_cortex

Superior Temporal Gyrus

Neurons sensitive to objects, faces; biological motion processing
Language processing

Inferior Temporal Gyrus (ITG)

Continuation of ventral visual processing stream

Coronal MRI views of inferior temporal gyrus

Entorhinal (ER) & Parahippocampal Cortex

Storage of memories about events, objects
Amygdala, hippocampus

Parietal lobe

Caudal to frontal lobe
Dorsal to temporal lobe
Posterior to central sulcus

Primary somatosensory cortex (S-I or S1)
- information from sensors in skin, muscles, tendons, joints and viscera
Post-central gyrus

Perception of spatial relations, action planning

Inferior Parietal Lobule

Inferior parietal lobule - e.g., language, mathematical operations, body image, etc.

Superior Parietal Lobule

damage to can cause spatial hemi-neglect

MRI sequence of superior parietal lobule from https://en.wikipedia.org/wiki/Superior_parietal_lobule

Occipital lobe

Caudal to parietal & temporal lobes

Primary visual cortex (V1)
Secondary visual areas (V2…V7)

Visual cortex from https://www.aao.org/education/bcscsnippetdetail.aspx?id=da6920e2-a380-4857-be07-82770a46de03

Insular cortex (insula)

medial to temporal lobe
deep inside lateral fissure

Primary gustatory cortex
Self-awareness, interpersonal experiences, motor control, interoception

Namkung, Kim, & Sawa (2017) Figure 1 — Namkung et al. (2017) Figure 1

Brodmann Areas

Cytoarchitectonic (cellular architecture) differences in cerebral cortex
Numbered areas, e.g. V1 == Area 17 or BA 17

White matter pathways

Diffusion Tensor Imaging (DTI) of axon fiber tracts in the human CNS from https://teslamri.com/services/dti/. Color coding is used to indicate the orientation of fibers.

Brainstem
Projection fibers
Association fibers
Commissural fibers

Schematic of brain stem white matter pathways from (Oishi, Faria, Zijl, & Mori, 2010, Chapter 3, Figure 1.) — Schematic of brain stem white matter pathways from (Oishi et al., 2010, Chapter 3, Figure 1.)

Brainstem projections

Corticospinal tract (descending/efferent)
Dorsal column/medial lemniscus (ascending/afferent)
Superior/inferior cerebellar peduncles (from/to cerebellum)

White matter projections from (Oishi et al., 2010, Chapter 3, Figure 8.)

Projection fiber tracts

Internal capsule
- Thalamic radiation
- Cortico-{pontine, bulbar, reticular} tracts

Schematic of brain stem white matter pathways from (Oishi et al., 2010, Chapter 3, Figure 12.)

Cortical white matter tracts

Superior/inferior longitudinal fasciculus
- Arcuate fasciculus part of sup. long. f.
Superior/inferior fronto-occipital fasciculus
Cingulum, fornix (hyp-hip), stria terminalis (hyp-amyg)

Commissural fibers

Corpus callosum
Anterior commissure (AC)
Posterior commissure (PC)

Corpus callosum Dissection of human corpus callosum

Anterior, Posterior Commissures

Anterior and posterior commissures from Wikipedia

Spinal cord

Spinal column w/ vertebrae
Moving rostral -> caudal…
Cervical (8), thoracic (12), lumbar (5), sacral (5), coccygeal (1)
Spinal segments & 31 nerve pairs
Cauda equina
- Nerves not shielded by pia, arachnoid or dura mater

Spinal segments (rostral to caudal) ennervate specific body segments
When focusing on the skin, these are called dermatomes

Dorsal/Ventral
- Dorsal root (sensory)
- Ventral root (mostly motor)
Grey (interior) vs. white matter (exterior)
- Cerebral cortex opposite (grey exterior, white interior)

Anterior and posterior roots of spinal cord

Organization of the PNS

Somatic division
Autonomic division (Autonomic Nervous System)

Somatic division

Innervates skeletal muscles
Receives sensory information from skin, tendons, joints, muscles, and the viscera

Cranial nerves

Afferents (input), efferents (output), or mixed
Innervate head and neck
Olfactory (I), optic (II), (VIII) auditory, vagus (X), etc.
Spinal nerves

Spinal nerves

Autonomic division (ANS)

CNS & PNS components
Controls “vegetative functions”
- Limited voluntary control
Three divisions
- Sympathetic
- Parasympathetic
- Enteric (gut, intestinal tract)

Bipolar (continuum) vs. bivariate autonomic space (Berntson, Cacioppo, & Quigley, 1991)

Sympathetic division

Prepares body for action
“Fight or flight”
Spinal cord
- ganglion chain along spinal column to End organs
Neurotransmitters (NTs)
- Preganglionic: acetylcholine (ACh)
- Post: norepinephrine (NE)

Parasympathetic division

“Around” sympathetic
Restorative function
“Rest & digest”
Spinal cord (or Vagus n. from Xth cranial n.) -> ganglia near end organs -> end organ
- NT: ACh

Enteric division

Illustrative measures of ANS function

Heart rate variability

Galvanic skin response (GSR)

Pupillary response

See https://en.wikipedia.org/wiki/Pupillary_response

Electrogastrogram (EGG) (Al Taee & Al-Jumaily, 2020)

Electrogastogram from Al Taee & Al-Jumaily (2020). Fig. 1. Gastric pacesetter potentials or slow waves originate from the pacemaker area on the greater curve. Pacesetter potentials travel in a circumferential and aboral direction at a rate of approximately 3 cycles per minute (cpm). The cutaneously recorded electrogastrogram shows 3-cpm wave pattern. The fundus has no rhythmic electrical activity.

References

Abbott, N. J., Rönnbäck, L., & Hansson, E. (2006). Astrocyte-endothelial interactions at the blood-brain barrier. Nature Reviews. Neuroscience, 7(1), 41–53. https://doi.org/10.1038/nrn1824

Al Taee, A., & Al-Jumaily, A. (2020). Electrogastrogram based medical applications an overview and processing frame work. In Hybrid intelligent systems (pp. 511–520). Springer International Publishing. https://doi.org/10.1007/978-3-030-14347-3\_50

Begg, D. P., & Woods, S. C. (2013). The endocrinology of food intake. Nature Reviews. Endocrinology, 9(10), 584–597. https://doi.org/10.1038/nrendo.2013.136

Berntson, G. G., Cacioppo, J. T., & Quigley, K. S. (1991). Autonomic determinism: The modes of autonomic control, the doctrine of autonomic space, and the laws of autonomic constraint. Psychological Review, 98(4), 459–487. https://doi.org/10.1037/0033-295X.98.4.459

Challenged, N. (2025). Sulci & gyri - major landmarks of the cerebral cortex. YouTube. Retrieved from https://www.youtube.com/watch?v=f9ZMChDGjRQ

floris. (2012a, August). 3D brain from MRI 4 basal ganglia. Youtube. Retrieved from https://www.youtube.com/watch?v=q7z-373pwuI

floris. (2012b, August). 3D brain from MRI 6 amygdala. Youtube. Retrieved from https://www.youtube.com/watch?v=YB9rs4tEAaE

floris. (2012c, August). 3D brain from MRI 7 hippocampus. Youtube. Retrieved from https://www.youtube.com/watch?v=wjvDDH-uJ0s

floris. (2012d, August). 3D brain from MRI 8 brain stem. YouTube. Retrieved from https://www.youtube.com/watch?v=Wq8EVQUc9a4

floris. (2012e, August). 3D brain from MRI 9 cerebellum. Youtube. Retrieved from https://www.youtube.com/watch?v=6szEeD0n-oU

Furness, J. B. (2012). The enteric nervous system and neurogastroenterology. Nature Reviews. Gastroenterology & Hepatology, 9(5), 286–294. https://doi.org/10.1038/nrgastro.2012.32

LeDoux, J. (2015, August 10). The Amygdala Is NOT the Brain’s Fear Center. Psychology Today. Retrieved from https://www.psychologytoday.com/blog/i-got-mind-tell-you/201508/the-amygdala-is-not-the-brains-fear-center

Namkung, H., Kim, S.-H., & Sawa, A. (2017). The insula: An underestimated brain area in clinical neuroscience, psychiatry, and neurology. Trends in Neurosciences, 40(4), 200–207. https://doi.org/10.1016/j.tins.2017.02.002

Oishi, K., Faria, A. V., Zijl, P. C. van, & Mori, S. (2010). MRI atlas of human white matter. Academic Press.

Rahimzadeh, V., Jones, K. M., Majumder, M. A., Kahana, M. J., Rutishauser, U., Williams, Z. M., … NIH Research Opportunities in Humans (ROH) Consortium. (2023). Benefits of sharing neurophysiology data from the BRAIN initiative research opportunities in humans consortium. Neuron, 111(23), 3710–3715. https://doi.org/10.1016/j.neuron.2023.09.029

Saive, A.-L., Royet, J.-P., & Plailly, J. (2014). A review on the neural bases of episodic odor memory: From laboratory-based to autobiographical approaches. Frontiers in Behavioral Neuroscience, 8, 240. https://doi.org/10.3389/fnbeh.2014.00240

Xie, L., Kang, H., Xu, Q., Chen, M. J., Liao, Y., Thiyagarajan, M., et al.others. (2013). Sleep drives metabolite clearance from the adult brain. Science, 342(6156), 373–377. https://doi.org/10.1126/science.1241224