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12.4: Brain- Diencephalon, Brainstem, Cerebellum and Limbic System

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  • By the end of this section, you will be able to:

    • Identify the components of the diencephalon and describe their functions
    • Identify the structures of the brainstem and describe their functions
    • Describe the structure and function of the cerebellum
    • Identify the major structures of the limbic system and describe their functions


    The diencephalon is the one region of the adult brain that retains its name from embryologic development. The etymology of the word diencephalon translates to “through brain.” It is the connection between the cerebrum and the rest of the nervous system, with one exception. The rest of the brain, the spinal cord, and the PNS all send information to the cerebrum through the diencephalon. Output from the cerebrum passes through the diencephalon. The single exception is the system associated with olfaction, or the sense of smell, which connects directly with the cerebrum. In the earliest vertebrate species, the cerebrum was not much more than olfactory bulbs that received peripheral information about the chemical environment (to call it smell in these organisms is imprecise because they lived in the ocean).

    The diencephalon is deep beneath the cerebrum and constitutes the walls of the third ventricle. The diencephalon can be described as any region of the brain with “thalamus” in its name. The major regions of the diencephalon are the thalamus itself, the hypothalamus, the epithalamus, which contains the pineal gland, and the subthalamus, which includes part of the basal nuclei (Figure \(\PageIndex{1}\)). 


    The epithalamus forms the posterior roof of the third ventricle and houses the pineal gland, an endocrine gland responsible for the secretion of melatonin. Melatonin regulates day-night cycles. Nuclei within the epithalamus help relay signals to the limbic system and are involved in emotional responses to odors.


    The thalamus is a pair of oval-shaped structures that each contain a dozen nuclei, called thalamic nuclei. The thalamus covers the superior and lateral walls of the third ventricle. The right and left thalami are connected by a mass of gray matter called the interthalamic adhesion. All sensory information, except for the sense of smell, passes through the thalamus before processing by the cortex. Axons from the peripheral sensory organs, or intermediate nuclei, synapse in the thalamus, and thalamic neurons project directly to the cerebrum. It is a requisite synapse in any sensory pathway, except for olfaction. The thalamus does not just pass the information on, it also processes that information. For example, the portion of the thalamus that receives visual information will influence what visual stimuli are important, or what receives attention. The cerebrum also sends information down to the thalamus, which usually communicates motor commands. This involves interactions with the cerebellum and other nuclei in the brainstem. Inferior to the thalamus lies the subthalamic nucleus, which is part of the basal nuclei. The subthalamic nucleus connects various basal nuclei and modulate their activity.


    Inferior and slightly anterior to the thalamus is the hypothalamus, the other major region of the diencephalon. The hypothalamus is a collection of nuclei that are largely involved in regulating homeostasis. The hypothalamus is the executive region in charge of the autonomic nervous system and the endocrine system through its regulation of the anterior pituitary gland. Other parts of the hypothalamus are involved in memory and emotion as part of the limbic system. Two groups of nuclei called the the mammillary bodies are located on the posterior part of the hypothalamus and are important for episodic memory, which is the memory of every day events that you can recollect.

    Sagittally and inferior to the cerebral cortex lies the corpus callosum, diencephalon and brainstem.
    Figure \(\PageIndex{1}\): Midsagittal Section of the Brain. The diencephalon is composed of the thalamus, hypothalamus, and epithalamus and defines the walls of the third ventricle. The brainstem comprises three regions: the midbrain, the pons, and the medulla. Within the midbrain, the tectum is composed of the superior and inferior colliculi. (Image credit: ”Brain Midsagittal Section" by Chiara Mazzasette is a derivative from the original work of Daniel Donnelly and is licensed by CC BY 4.0)


    The midbrain and hindbrain (composed of the pons and the medulla oblongata) are collectively referred to as the brainstem (Figure \(\PageIndex{1}\) and Figure \(\PageIndex{2}\)). The structure emerges from the ventral surface of the forebrain as a tapering cone that connects the brain to the spinal cord. Attached to the brainstem, but considered a separate region of the adult brain, is the cerebellum. The midbrain coordinates sensory representations of the visual, auditory, and somatosensory perceptual spaces. The pons is the main connection with the cerebellum. The pons and the medulla regulate several crucial functions, including the cardiovascular and respiratory systems (such as heart rhythm or breathing rate). The reticular activating system is found in the midbrain, pons, medulla and part of the thalamus and controls levels of wakefulness, maintains consciousness, enables people to pay attention to their environments, and is involved in sleep patterns and regulating the sleep cycle.

    The cranial nerves connect through the brainstem and provide the brain with the sensory input and motor output associated with the head and neck, including most of the special senses. The major ascending and descending pathways between the spinal cord and brain, specifically the cerebrum, pass through the brainstem.


    The mesencephalon, one of the original region of the embryonic brain, becomes the midbrain, a small region between the thalamus and pons. The cerebral aqueduct passes through the center of the midbrain, such that these regions are the roof and floor of that canal. Indeed, the midbrain is separated into the tectum and tegmentum, from the Latin words for roof and floor, respectively. 

    The tectum is composed of four bumps known together as the corpora quadrigemina or colliculi (singular = colliculus), which means “little hill” in Latin. The superior colliculus is the superior pair and combines sensory information about visual space, auditory space, and somatosensory space. At this level, the nucleus for the oculomotor nerve (CN III) is found. The inferior colliculus is the inferior pair of these enlargements and is part of the auditory pathway (trochlear nerve, CN IV). Neurons of the inferior colliculus project to the thalamus, which then sends auditory information to the cerebrum for the conscious perception of sound.

    The tegmentum is continuous with the gray matter of the rest of the brainstem. The substantia nigra consists of basal nuclei with a black appearance due to melanin production. These nuclei control movement, emotional response, and the ability to experience pleasure and pain. Degeneration of the neurons within the substantia nigra is a hallmark of Parkinson disease.

    The midbrain is connected to both the cerebrum and the cerebellum. On the anterolateral surfaces of the midbrain, motor tracts called cerebral peduncles run from the cerebrum to the spinal cord. Moreover, the midbrain is connected to the cerebellum through the superior cerebellar peduncle (SCP), a bundle of myelinated axons.


    The pons is visible on the anterior surface of the brainstem as the thick bundle of white matter attached to the cerebellum. The name of the pons is derived from its connection to the cerebellum. The word means “bridge” and refers to the thick bundle of myelinated axons that form a bulge on its ventral surface. Those fibers are axons that project from the gray matter of the pons into the contralateral cerebellar cortex. These fibers make up the middle cerebellar peduncle (MCP) and are the major physical connection of the cerebellum to the brainstem (Figure \(\PageIndex{3}\)). Gray matter regions of the pons contain neurons receiving descending input from the forebrain that is sent to the cerebellum. The pons houses autonomic nuclei important for respiration. The pons is also involved in sensory and motor information of some cranial nerves and houses the nuclei for cranial nerve V to VIII.

    Medulla Oblongata

    The medulla oblongata is the region known as the myelencephalon in the embryonic brain. The initial portion of the name, “myel,” refers to the significant white matter found in this region—especially on its exterior, which is continuous with the white matter of the spinal cord. The anterior region of the medulla oblongata shows two longitudinal ridges called pyramids, which house motor projection tracts (Figure \(\PageIndex{2}\)). In the posterior region of the medulla oblongata, these pyramids cross to the opposite side at a point called the decussation of pyramids. Due to this crossing, each hemisphere controls motor responses of the opposite side of the body. Inferior to each pyramid, a nucleus called inferior olive, is located and functions as a relay point for information on proprioception coming from the spinal cord and going into the cerebellum. Indeed, the medulla oblongata send information to the cerebellum through tracts called inferior cerebellar peduncle (ICP) (Figure \(\PageIndex{3}\)). The medulla oblongata contains several nuclei that are associated with last five cranial nerves (CN VIII to XII). It also contains autonomic nuclei important for vital functions such as respiration, heart rate, and blood pressure, among others.

    Inferior view of brain. From anterior to posterior: eyes, optic nerves, brainstem and cerebellum.
    Figure \(\PageIndex{2}\): Inferior View of the Brain. The inferior view of the brain shows the brainstem, cerebellum and cranial nerves. From anterior to posterior, the midbrain, pons and medulla oblongata form the brainstem. The cerebral peduncles of the midbrain and pyramids and their decussation of the medulla oblongata are also visible. The pituitary gland is attached to the hypothalamus, as are the mammillary bodies. (Image credit: ”Brain Inferior View" by Chiara Mazzasette is a derivative from the original work of Daniel Donnelly and is licensed by CC BY 4.0)
    Pons and medulla oblongata are anterior and connected posteriorly to cerebellum through peduncles.
    Figure \(\PageIndex{3}\): Cerebellar Peduncles. The connections to the cerebellum are the three cerebellar peduncles, which are close to each other. The superior cerebellar peduncle projects into the midbrain. The middle cerebellar peduncle is the ventral surface of the pons. The inferior cerebellar peduncle arises from the medulla—specifically from the inferior olive, which is visible as a bulge on the ventral surface of the brainstem. (Image credit: "Cerebellar Peduncles" by OpenStax is licensed under CC BY 3.0)


    Basal Nuclei: Parkinson's Disease

    Parkinson’s disease is a disorder of the basal nuclei, specifically of the substantia nigra, that demonstrates the effects of the direct and indirect pathways. Parkinson’s disease is the result of neurons in the substantia nigra pars compacta dying. These neurons release dopamine into the striatum. Without that modulatory influence, the basal nuclei are stuck in the indirect pathway, without the direct pathway being activated. The direct pathway is responsible for increasing cortical movement commands. The increased activity of the indirect pathway results in the hypokinetic disorder of Parkinson’s disease.

    Parkinson’s disease is neurodegenerative, meaning that neurons die that cannot be replaced, so there is no cure for the disorder. Treatments for Parkinson’s disease are aimed at increasing dopamine levels in the striatum. Currently, the most common way of doing that is by providing the amino acid L-DOPA, which is a precursor to the neurotransmitter dopamine and can cross the blood-brain barrier. With levels of the precursor elevated, the remaining cells of the substantia nigra pars compacta can make more neurotransmitter and have a greater effect. Unfortunately, the patient will become less responsive to L-DOPA treatment as time progresses, and it can cause increased dopamine levels elsewhere in the brain, which are associated with psychosis or schizophrenia.


    Visit this site for a thorough explanation of Parkinson’s disease.


    The cerebellum, as the name suggests, is the “little brain”. Similar to the brain, the cerebellum contains an outer layer of gray matter, an inner layer of white matter and deep cerebellar nuclei (Figure \(\PageIndex{4}\)). The white matter of the cerebellum is called arbor vitae ("tree of life") for its appearance that reminds that of branches of a tree. The folds of the cerebellar cortex are called folia, which means "leaf".

    Cerebellum is shaped like an horizontal tree, growing from the pons.
    Figure \(\PageIndex{4}\): Cerebellum. The cerebellum is situated on the posterior surface of the brainstem. This lateral view of a section of cerebellum shows the deep white matter forming the arbor vitae, which means "tree of life", while the cerebellar cortex is superficial. Descending input from the cerebellum enters through the large white matter structure of the pons. Ascending input from the periphery and spinal cord enters through the fibers of the inferior olive. Output goes to the midbrain, which sends a descending signal to the spinal cord. (Image credit: "Cerebellum" by OpenStax is licensed under CC BY 4.0)

    The cerebellum is divided into regions that are based on the particular functions and connections involved. The midline region of the cerebellum, called the vermis, is involved in comparing visual information, equilibrium, and proprioceptive feedback to maintain balance and coordinate movements such as walking, or gait (Figure \(\PageIndex{5}\)). The vermis connects the two cerebellar hemispheres. Each hemisphere consists of two lobes, the anterior lobe and the posterior lobe, separated by the primary fissure. The lateral hemispheres are primarily concerned with planning motor functions through frontal lobe inputs that are returned through the thalamic projections back to the premotor and motor cortices. Processing in the midline regions targets movements of the axial musculature, whereas the lateral regions target movements of the appendicular musculature.

    Midsagittal section on the left and superior view on the right with vermis and hemispheres.
    Figure \(\PageIndex{5}\): Major Regions of the Cerebellum. The cerebellum can be divided into two basic regions: the vermis, which is the midline, and the hemispheres, which are lateral to the vermis. Each cerebellar hemisphere consists of two lobes. The anterior lobe (in purple) and posterior lobe (in green) are separated by the primary fissure. (Image credit: "Major Regions of the Cerebellum" by OpenStax is licensed under CC BY 3.0)

    The cerebellum is responsible for coordination of movement, alternating movement of arms and legs, balance, posture and gait. If the primary motor cortex of the frontal lobe sends a command down to the spinal cord to initiate walking, a copy of that instruction is sent to the cerebellum. Sensory feedback from the muscles and joints, proprioceptive information about the movements of walking, and sensations of balance are sent to the cerebellum through the inferior olive and the cerebellum compares them. If walking is not coordinated, perhaps because the ground is uneven or a strong wind is blowing, then the cerebellum sends out a corrective command to compensate for the difference between the original cortical command and the sensory feedback. The output of the cerebellum is into the midbrain, which then sends a descending input to the spinal cord to correct the messages going to skeletal muscles.

    There is also strong evidence of the cerebellar role in procedural memory. The two are not incompatible; in fact, procedural memory is motor memory, such as learning to ride a bicycle. Significant work has been performed to describe the connections within the cerebellum that result in learning.


    Cerebellum: Ataxia

    A movement disorder of the cerebellum is referred to as ataxia. It presents as a loss of coordination in voluntary movements. Ataxia can also refer to sensory deficits that cause balance problems, primarily in proprioception and equilibrium. When the problem is observed in movement, it is ascribed to cerebellar damage. Sensory and vestibular ataxia would likely also present with problems in gait and station.

    Ataxia is often the result of exposure to exogenous substances, focal lesions, or a genetic disorder. Focal lesions include strokes affecting the cerebellar arteries, tumors that may impinge on the cerebellum, trauma to the back of the head and neck, or MS. Alcohol intoxication or drugs such as ketamine cause ataxia, but it is often reversible. Mercury in fish can cause ataxia as well. Hereditary conditions can lead to degeneration of the cerebellum or spinal cord, as well as malformation of the brain, or the abnormal accumulation of copper seen in Wilson’s disease.

    Limbic System

    The limbic system is a collection of structures of the cerebrum and diencephalon involved in emotion, motivation and memory associated with emotions. Although still debated, the structures mostly recognized in this system are the cingulate gyrus, hippocampus, amygdala, olfactory structures, and various nuclei of the diencephalon. Here we will focus on the cingulate gyrus, the hippocampus and amygdala as major structures (Figure \(\PageIndex{6}\)). The cingulate gyrus is located in the longitudinal fissure, superior to the corpus callosum, surrounding the diencephalon. The cingulate gyrus focuses the attention to events that are emotionally important. The hippocampus is a nucleus shaped like a seahorse, hence its name. The hippocampus is essential in forming memories and storing them long-term. Lastly, the amygdala (or amygdaloid body) is connected to the hippocampus and is involved in multiple aspects of emotions, especially fear. It helps encoding memories based on the state of emotion that the person is in.

    Medial view of the brain with the limbic structures
    Figure \(\PageIndex{6}\): Limbic System. The limbic system regulates emotion and other behaviors. It includes parts of the cerebral cortex located near the center of the brain, including the cingulate gyrus and the hippocampus as well as the thalamus, hypothalamus and amygdala. The amygdala is inferior to the hypothalamus. (Image credit: "Figure 35 03 06" by OpenStax is licensed under CC BY 4.0)

    Concept Review

    The diencephalon includes the thalamus and the hypothalamus, along with some other structures. The thalamus is a relay between the cerebrum and the rest of the nervous system. The hypothalamus coordinates homeostatic functions through the autonomic and endocrine systems.

    The brainstem is composed of the midbrain, pons, and medulla. It controls the head and neck region of the body through the cranial nerves. There are control centers in the brainstem that regulate the cardiovascular and respiratory systems.

    The cerebellum is connected to the brainstem, primarily at the pons, where it receives a copy of the descending input from the cerebrum to the spinal cord. It can compare this with sensory feedback input through the medulla and send output through the midbrain that can correct motor commands for coordination. The cerebellum is an important part of motor function in the nervous system. It apparently plays a role in procedural learning, which would include motor skills such as riding a bike or throwing a football. The basis for these roles is likely to be tied into the role the cerebellum plays as a comparator for voluntary movement.

    The limbic system includes structures of the cerebral cortex and diencephalon that are responsible for emotion and memory. The main structures are the cingulate gyrus, hippocampus and amygdala.

    Review Questions

    Q. What level of the brainstem is the major input to the cerebellum?

    A. midbrain

    B. pons

    C. medulla

    D. spinal cord



    Q. Which region of the cerebellum receives proprioceptive input from the spinal cord?

    A. vermis

    B. left hemisphere

    C. flocculonodular lobe

    D. right hemisphere



    Critical Thinking Questions

    Q. Why do the anatomical inputs to the cerebellum suggest that it can compare motor commands and sensory feedback?

    A. A copy of descending input from the cerebrum to the spinal cord, through the pons, and sensory feedback from the spinal cord and special senses like balance, through the medulla, both go to the cerebellum. It can therefore send output through the midbrain that will correct spinal cord control of skeletal muscle movements.


    nucleus deep in the temporal lobe of the cerebrum that is related to memory and emotional behavior
    anterior lobe
    region of the cerebellum
    arbor vitae
    deep white matter of the cerebellum
    cerebellar hemisphere
    region of the cerebellum lateral to the vermis
    cerebellar nuclei
    regions of gray matter within the cerebellum
    region of the adult brain connected primarily to the pons that developed from the metencephalon (along with the pons) and is largely responsible for comparing information from the cerebrum with sensory feedback from the periphery through the spinal cord
    cerebral aqueduct
    connection of the ventricular system between the third and fourth ventricles located in the midbrain
    cerebral peduncle
    segments of the descending motor pathway that make up the white matter of the ventral midbrain
    cingulate gyrus
    a medial gyrus of each cerebral hemisphere that partly surrounds the corpus callosum and is part of the limbic system
    corpora quadrigemina
    four colliculi, two inferior and two superior, that sit on the posterior surface of the midbrain
    decussation of pyramids
    location at which corticospinal tract fibers cross the midline and segregate into the anterior and lateral divisions of the pathway
    region of the diencephalon containing the pineal gland
    gyri of the cerebellum
    gray matter deep in the temporal lobe that is very important for long-term memory formation
    major region of the diencephalon that is responsible for coordinating autonomic and endocrine control of homeostasis
    inferior cerebellar peduncle (ICP)
    input to the cerebellum, largely from the inferior olive, that represents sensory feedback from the periphery
    inferior colliculus
    half of the midbrain tectum that is part of the brainstem auditory pathway
    inferior olive
    nucleus in the medulla that is involved in processing information related to motor control
    interthalamic adhesion
    connection within the thalamus
    limbic system
    structures at the edge (limit) of the boundary between the forebrain and hindbrain that are most associated with emotional behavior and memory formation
    mammillary bodies
    small round bodies, located in the diencephalon, that are part of the limbic system
    medulla oblongata
    continuation of the spinal cord, forming the most inferior part of the brainstem
    middle region of the adult brain that develops from the mesencephalon
    middle cerebellar peduncle (MCP)
    large, white-matter bridge from the pons that constitutes the major input to the cerebellar cortex
    pineal gland
    endocrine gland located in the epithalamus that secretes melatonin, which is important in regulating the sleep-wake cycle
    part of the brainstem that connects the thalamus and medulla
    posterior lobe
    region of the cerebellum
    primary fissure
    a fissure of the cerebellum that marks the boundary between the anterior lobe and the posterior lobe
    sense of position and movement of the body
    segment of the descending motor pathway that travels in the anterior position of the medulla
    reticular activating system
    diffuse region of gray matter throughout the brainstem that regulates sleep, wakefulness, and states of consciousness
    substantia nigra
    nuclei within the basal nuclei; part of the motor pathway
    subthalamic nucleus
    small collection of neurons situated ventral to the thalamus
    nucleus within the basal nuclei that is part of the indirect pathway
    superior cerebellar peduncle (SCP)
    white-matter tract representing output of the cerebellum to the red nucleus of the midbrain
    superior colliculus
    half of the midbrain tectum that is responsible for aligning visual, auditory, and somatosensory spatial perceptions
    region of the midbrain, thought of as the roof of the cerebral aqueduct, which is subdivided into the inferior and superior colliculi
    region of the midbrain, thought of as the floor of the cerebral aqueduct, which continues into the pons and medulla as the floor of the fourth ventricle
    thalamic nuclei
    collection of neurons within the thalamus
    major region of the diencephalon that is responsible for relaying information between the cerebrum and the hindbrain, spinal cord, and periphery
    prominent ridge along the midline of the cerebellum that is referred to as the spinocerebellum

    Contributors and Attributions

    OpenStax Anatomy & Physiology (CC BY 4.0). Access for free at