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Diencephalon and brainstem

Last updated: September 24, 2020


The diencephalon is the caudal part of the forebrain (prosencephalon) located between the midbrain (mesencephalon) and the cerebrum (telencephalon). It consists of the thalamus, hypothalamus, epithalamus, and subthalamus. The thalamus is the relay center for sensory information. The hypothalamus regulates autonomic function and the endocrine system. The epithalamus, which consists of the pineal gland, habenula, habenular commissure, and stria medullaris, regulates the sleep-wake cycle. The subthalamus, which contains the subthalamic nuclei, is part of the indirect basal ganglia circuit and is involved in the inhibition of unnecessary movements. The brain stem is the caudal part of the brain and consists of the midbrain, pons, and medulla oblongata. The brain stem regulates autonomic function (respiration, circulation, lacrimation, salivation), controls visual and auditory reflexes, and maintains vigilance. It is also a hub through which run all ascending sensory pathways, descending motor pathways, and other local pathways of the central nervous system. The limbic system is a group of brain pathways that consists of the amygdala, hypothalamus, thalamus, hippocampus, and limbic cortex. These are involved in memory formation, regulation of appetite and satiety, attention, emotional responses, and sexual arousal. The ventricular system consists of four interconnected ventricles (a pair of lateral ventricles, third ventricle, and fourth ventricle). It is involved in the production, transport, and drainage of cerebrospinal fluid, which plays a role in waste removal and cushioning the brain.


The diencephalon makes up the caudal part of the forebrain between the telencephalon and midbrain. It consists of the hypothalamus, thalamus, epithalamus, and the subthalamus.


The hypothalamus functions as the central control center for the autonomic nervous system and endocrine function. Its nuclei produce releasing hormones for the anterior pituitary and the hormones that are released by the posterior pituitary.

Structure Function Associated pathology
Lateral nucleus
Ventromedial nucleus
  • Satiety: stimulated by leptin
Anterior nucleus (hypothalamus)
Posterior nucleus
Suprachiasmatic nucleus

Supraoptic nucleus

Paraventricular nucleus

Preoptic nucleus
Arcuate nucleus (hypothalamus)
  • Neuroendocrine dysregulation


The thalamus consists of several nuclei that are tightly connected to the cerebral cortex and functions as the main conductor of sensory information.

Structure Input Projects to Function
Ventral posterolateral nucleus (VPL)
Ventral posteromedial nucleus (VPM)
Lateral geniculate nucleus
  • Vision
Medial geniculate nucleus
  • Hearing
Ventral lateral nucleus
  • Motor
Anterior nucleus
Dorsomedial nucleus
  • Part of the limbic system
    • Expression of affect
    • Behavior
    • Emotions
Intralaminar nuclei

Thalamic stroke causes contralateral hemiparesis and hemisensory loss, miotic and unreactive pupils, upgaze palsy with gaze deviation away from the side of the lesion, a phenomenon known as “wrong-way eyes”!


Limbic system

The limbic system is a collection of neuronal pathways from different anatomical parts of the brain that are responsible for feeding, emotions, memories, attention, and sexual behavior. It is composed of the hippocampal formation (includes the hippocampus, dentate gyrus, and the entorhinal cortex) mammillary bodies, amygdalae, cingulate gyrus, and the anterior thalamic nuclei.

Structure Location Characteristics
Hippocampal formation Hippocampus
Dentate gyrus
Entorhinal cortex
Mammillary bodies
  • Receives signals from the hypothalamus, cerebral cortex, and the olfactory cortex
  • Relays emotional reactions, especially to fear, aggression, and anxiety
  • Recognition of emotional facial expressions
  • Involved in decision-making
Cingulate gyrus
  • Above the corpus callosum bilaterally
  • On the medial surface of each hemisphere
Anterior thalamic nuclei

Papez circuit



The midbrain mediates visual and auditory reflexes. It contains the nuclei of the oculomotor nerve (CN III) and the trochlear nerve (CN IV).

Structure Location Characteristics
  • Contains sensory pathways and nuclei of cranial nerves
  • Involved in modulation of extrapyramidal motor function
Crus cerebri
Cerebral peduncles

Pretectal area

Cerebral aqueduct
Periaqueductal gray matter
Medial longitudinal fasciculus
Substantia nigra
  • Formed by two parts
    • Pars compacta (contains melanin) → dopamine↑ motor function
    • Pars reticularis → GABA↓ motor function
Central tegmental tract
Red nucleus

Dopaminergic pathways

These pathways are collections of neurons that release dopamine. They are not anatomically limited to the midbrain but involve some midbrain nuclei. Their dysfunction is implicated in some psychiatric diseases and they play a role as the target of antipsychotic drugs.

Pathway Location Characteristics Defect
  • Controls executive functions
  • Controls movement



Structure Location Function
Cochlear nuclei
Trapezoid body
Superior olivary nucleus
Corticopontine tract
Pontine nuclei
Locus coeruleus
Medial lemniscus
  • Pathway for proprioception
Lateral lemniscus
  • Relays cochlear input
Spinal lemniscus


Medulla oblongata

The medulla is an important structure located between the pons and the spinal cord. It contains autonomic centers that regulate autonomic functions such as circulation, respiration, and gastrointestinal activity. It contains centers for swallowing, sneezing, coughing, and vomiting. It is connected to the cerebellum via the inferior cerebellar peduncle.

Structure Characteristics
Nucleus gracilis and Nucleus cuneatus
  • Form the base of the medulla
  • Fibers in this region are uncrossed → cross at the pyramidal decussation
Lateral cuneate nucleus
Inferior olivary nucleus
Lateral reticular nucleus
Arcuate nucleus (medulla)

Solitary nucleus and tract

(nucleus tractus solitarius)

Area postrema

(vomiting center)


Ventricular system


There are four ventricles that are interconnected to each other. They contain cerebrospinal fluid (CSF), which serves as a fluid cushion and immunological reservoir.

Ventricle Anatomy
Lateral ventricles
  • Paired (right and left)
  • Located in the cerebral hemispheres
  • Drain into the 3rd ventricle via right and left interventricular foramina (of Monro)

Third ventricle

Fourth ventricle

Cerebrospinal fluid


Territory Main Branches Features of infarction

Basilar artery

Formed by the union of the two vertebral arteries



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