General Neuroscience

Basics of Neuroscience VI: An Introduction to Neuroanatomy

Alexander Skvortsov


Like most complex organ systems, the nervous system is composed of many parts. One can consider the brain on the scale of hemispheres, regions, neural circuits, individual neurons, or even on molecules. In previous editions of Basics of Neuroscience, we have considered the cellular composition of the brain, neural communication (both intracellular and extracellular), processes of strengthening of neural connections, and the process of addiction. As you might noticed, these topics mainly concern the brain on a cellular scale. To better understand the processes of the human nervous system, one must be able to connect cellular processes to a larger picture of neuroanatomy. This month’s article shall discuss the anatomy of the central nervous system.


Directional Terminology

Before discussing the anatomical structure of the brain, it is important to first understand formal directional terminology used by scientific professionals in various medical, research, and clinical fields. These terms are used to describe relative location of a point.

Anterior (rostral) - A directional term used to indicate location towards the front of the brain

Posterior (caudal) - A directional term used to indicate location towards the back of the brain

Lateral - A directional term used to indicate location towards a side of the brain

Dorsal - A directional term used to indicate location towards the top of the brain

Ventral - A directional term used to indicate location towards the back of the brain

Superior - A directional term used to indicate location above that of a reference point

Inferior - A directional term used to indicate location below that of a reference point

Medial -A directional term used to indicate location at the midpoint of the brain




Observation of the Central Nervous System

    In order to label, divide, and categorize the brain, we must first understand how to properly observe it. The central nervous system, henceforth referred to as the CNS, is composed of the brain and the spinal cord, and is contained within the cranial cavity and the spinal canal, respectively. Upon death of an individual, blood flow to the brain ceases, triggering a breakdown of neurons. To counter this deterioration, scientists perform a process known as fixation, which essentially stabilizes the structure of the brain, generally either by freezing or through the use of a formalin solution.

    After the brain has been successfully fixated, researchers proceed to separate it in order to observe internal regions. In a standard separation, the cerebellum is separated from the cerebrum and spinal cord. The cerebrum and cerebellum are then dissected separately. Three main types of cuts are used to accomplish this dissection. Horizontal cuts section the brain into horizontal slices from top to bottom. Coronal cuts divide the brain into vertical slices done perpendicularly to the longitudinal cerebral fissure (the primary division between the two cerebral hemispheres). Sagittal cuts are vertical slices done parallel to the longitudinal cerebral fissure. The Mid-Sagittal cut, which is also known as the medial cut, is a special plane of view which separates the cerebral hemispheres along the longitudinal cerebral fissure.

    Upon cutting the brain, one can notice its relatively bland coloration. Unlike one could assume from the many colorfully labeled diagrams so often found in textbooks, the brain can be described as a mixture of white and gray. Gray regions of the brain, primarily known as gray matter, such as the outer cerebral cortex and the many internal nuclei, are mainly composed of dendrites and somas and handle most of the computational processes described in Basics of Neuroscience III, while white regions, conventionally referred to as white matter, consist mostly of axons.


Anatomical Division

    We can visualize the division of the central nervous system-- the brain and spinal cord-- in several different ways. An informal approach simply separates the brain into the brainstem, cerebrum, spinal cord, and cerebellum. The cerebrum can then be divided into 2 hemispheres.

    A more formal approach to anatomical division, however, takes use of latin terminology. The brain as a whole, is referred to as the Encephalon. The Encephalon is then divided into two major regions known as the Prosencephalon, or forebrain, and Rhombencephalon, or hindbrain.

    The Prosencephalon can be further divided into the Telencephalon, which contains the cerebral cortex, and basal ganglia, and the Diencephalon, which contains the Thalamus and Hypothalamus,  as well as the third ventricle. The Rhombencephalon is divided into the Mesencephalon, which contains the midbrain, Metencephalon, which consists of the pons and cerebellum, and Myencephalon, which consists of the medulla oblongata.

    While the latin approach is considered more formal, convenience often brings neuroscientists to use the more casual classification of basic neural regions.

    In addition to the inner composition, the brain is covered throughout by three levels of meninges called the Dura Mater, Arachnoid Mater, and Pia Mater. The Dura Mater is very tough, thick, and mostly opaque. The Arachnoid mater is a thinner, inner layer which can be compared to a spidersilk-resembling material. Finally, the Pia mater is the most delicate covering and directly adheres to the brain. The Pia Mater contains many of the blood vessels on the surface of the brain.  


Cerebral Hemispheres

    The Prosencephalon, conventionally known as the forebrain, is the region generally associated with the cerebrum. The forebrain encompasses most of the brain, with the exception of the midbrain, brainstem, and cerebellum. For the most part, the forebrain can be divided into two cerebral hemispheres with relative ease by cutting along the longitudinal cerebral fissure: the major division between the two hemispheres. However,  this is not to say that the two hemispheres are symmetrical, either structurally or functionally.

    The adult human brain is generally lopsided, with the left hemisphere slightly larger than the right. In terms of function, the left brain is traditionally associated with logical, computational, factual, and language-based thinking. The right brain, on the other hand, is associated with creative processes such as art, music, holistic thinking, and and imagination. Keep in mind, however, that this association is one of dominance, not one of monopoly. Although one lobe of the brain may be more involved in a given process than another, it is important to remember that, for the most part, both lobes are involved in a given process. A mistaken belief in hemisphere-process monopolization has led to the common perpetuated myth of hemispheral dominance, or that some people have a stronger/larger/etc hemisphere, resulting in increased talent regarding a certain process. This is simply not true, as most processes the hemispheres work in tandem, with some slight unbalance. Cerebral hemispheres are closely linked by a bundle of white matter known as the corpus callosum.




    Throughout the brain, an observer can find cavities known as ventricles. In a functioning environment, these ventricles are generally filled with a transparent, colorless fluid called Cerebrospinal fluid, or CSF for short. CSF can be found inside ventricles, as well as surrounding the brain and spinal cord. CSF constantly re-circulates through the brain, and is produced by ependymal cells on a structure called the choroid plexus, which can generally be found inside ventricles. Functions of the CSF include protection and suspension of the brain inside the cranium, chemical stability, and glymphatic cleaning (see Vol 1 Issue 3, The Necessity of Sleep).

    The ventricular system contains 4 primary ventricles, each lined with choroid plexus, the subarachnoid space, various cisterns and sulci on the brain, and the central canal of the spinal cord. Two of the ventricles compose a system called the lateral ventricular system- they form an arc shaped area located directly inferior to the corpus callosum, and are divided by a thin membrane known as the septum pellucidum. Below the lateral ventricular system is the third ventricle and extending through the brainstem is the fourth ventricle. The ventricles are connected to each other by a system of passages called the foramina.


Cerebral Lobes

    The dorsal surface of the prosencephalon is covered entirely by the 4 cerebral lobes: the Parietal, Temporal, Occipital, and Frontal lobes. The external cerebral lobes consists of 2 main regions: a 6-layered sheet of gray matter known as the cortex, and a thicker layer of white matter. In addition to these 4 external lobes, there also exists an insular cortex which is located below temporal lobe external lobes.

    The Temporal lobes are located on the lateral sides of the brain, are divided from the main corpus of the cerebrum by the Sylvian fissures, and are primarily a center for processing of auditory information. The temporal lobe also contains structures important for memory, such as the hippocampus and amygdala. For more information on how the hippocampus and amygdala are involved in memory, see Basics of Neuroscience IV. A very important part of the Temporal lobe is Wernicke’s area, which plays a key role in speech interpretation.

    The Occipital Lobe is located at the posterior of the brain and is the primary processing center for visual input to the brain. It includes different visual areas, including V1 (which responds to lines of different orientations) and increasingly complex visual processing areas. This region is connected with several higher brain regions, including V4 (which is linked to color perception) and V5 (which is linked to visual motion)

    The Parietal lobe is located at the superior- medial surface of the brain, posterior to the frontal lobe, and is very important for somatosensory functions, such as the integration of pain, temperature, and mechanoreception. It is also involved in spatial coordination and language interpretation. A very important area of the parietal lobe is the somatosensory cortex located at the anterior of the parietal lobe, which serves as a central integration center for somatosensory information.

    The frontal lobe is a cortical area located at the anterior part of the brain that is responsible for an extremely diverse set of functions. In short, the frontal lobe is responsible for the integration and analysis of sensory information and the subsequent executive decisions. These include a multitude of decisions ranging from choices and suppression of socially unacceptable behaviors to  voluntary movement; the motor cortex located towards the posterior of the frontal lobe also makes the frontal lobe responsible for initiation of movements.

    The Insular Cortex is a relatively small, hidden cortical area contained within the Sylvian fissure. While the exact functions of the insular cortex are largely unknown due to lack of comprehensive research, it has been linked to pain, basic emotions, desires, and various social emotions.


Deep Brain Nuclei

    There exist 2 primary systems of deep brain nuclei located beneath the cortex: the basal ganglia and the limbic system.  

    The basal ganglia is a complex system of interconnected deep-brain nuclei located inferior to the cerebral cortex.  The system is involved in various functions primarily concerning motor planning and coordination, but also including emotion, motor learning (also known as procedural memory), and behaviors. The Basal Ganglia receives direct input from the cortex, and communicates back through the thalamus.

    The largest component of the basal ganglia system is the striatum, a compound nucleus composed of the dorsal and ventral striatum, which can further be divided into the putamen and caudate, and the nucleus accumbens and olfactory tubercle, respectively. The striatum is the primary recipient of input signals from the cortex. Other components of the basal ganglia include the globus pallidus, which is primarily composed of inhibitory GABA-ergic neurons and the ventral striatum, which is a key center of pleasure processing and consists of the nucleus accumbens and olfactory tubercle.

The_Limbic_System_and_Nearby_Structures_-_John_Taylor (1).jpg


    The limbic system, although often confused with the basal ganglia, performs a critically different set of tasks, mainly pertaining to emotion, endocrine function, and self-preservation. The limbic system has been conventionally referred to as the “feeling and reacting brain,” in contrast to the cortex being the “thinking brain,” as the limbic system is a more reflexive, primitive part of the brain. The largest and most significant parts of the limbic system are the amygdala, hippocampus, hypothalamus, and limbic cortex.

    The hippocampus, as mentioned in Basics of Neuroscience V, is highly linked with memory creation and consolidation, especially concerning declarative (explicit) memory. Some areas of the hippocampus are partially responsible for other types of memory, such as short-term memory. The hippocampus is responsible for the encoding and retrieval of memories, but not in the storage -- lesions in the hippocampus affect the formation of new memories rather than existing ones, as seen in the revolutionary case of HM, a patient who had his medial temporal lobe (which contains the hippocampus) removed, resulting in extreme anterograde amnesia (See anterograde amnesia, Vol 1 Issue 4). The hippocampus can be divided into the three-layered dentate gyrus, the spiral hippocampal body, which is conventionally divided into four areas, referred to as C1-4, and an area called the subiculum.

    The amygdala is also highly involved with memory, primarily linking memory to strong, mostly negative, emotions. As a matter of fact, the amygdala is considered to be the primary region associated with primal, self-preservation emotions, such as fear. This makes sense from an evolutionary perspective, as it allows the brain to link various past negative experiences to unpleasant emotions, thus leading the organism to avoid these experiences. For this reason, the amygdala has reciprocal connections to most other brain regions. The amygdala is a very diverse complex that can be further divided into 13 sub-nuclei.

    The hypothalamus is an area that functions primarily as a liaison between the brain and the endocrine hormonal system, as well as to regulate some major areas of human behavior such as sleep. The hypothalamus contains several nuclei that regulate sleep including the suprachiasmatic nucleus- the main driving force of circadian rhythms (for more information see our article on how sleep works (Vol 1, issue 3)). In addition, the hypothalamus is the most sexually dimorphic areas in the brain. The hypothalamus processes its primary task, regulation of the endocrine system, through communication with the pituitary gland; either directly with the posterior pituitary or indirectly with the anterior pituitary.Additionally, the hypothalamus contributes to regulation of autonomic systems (various unconscious processes) using pathways through the brainstem and spinal cord. The hypothalamus almost exclusively regulates temperature, osmosity, hunger, and the aforementioned  sleep cycles and processes.

    A final major area of the limbic system is the limbic lobe, an arc shaped region of the brain that spans both hemispheres and is located dorsal to the corpus callosum. Two major areas of the limbic lobe are the cingulate gyrus and the parahippocampal gyrus. The cingulate gyrus is strongly linked with many human functions such as emotion, judgement, motivation, reasoning, and pain.


Brainstem and Cerebellum

    Extending below the cerebrum is a group of structures known as the brainstem, which join the cerebrum and the spinal cord. Considered to be some of the first neural areas to have evolved, the parts of the brainstem primarily regulate various autonomic functions such as breathing, blood pressure, heartbeat, and sleep. For purposes of brevity, this section will focus exclusively on the following structures of the brainstem: the thalamus, pons, and medulla oblongata.

    Located on the extreme superior region of the brainstem is a double-lobed structure known as the Dorsal thalamus, or more conventionally as the thalamus. The executive function of the thalamus is sensory relay; all sensory signals pass, either directly or indirectly, through the thalamus. The thalamus consists of a variety of nuclei which send afferent signals primarily to cortical areas of the brain, in which sensory information is processed, analyzed, and compounded.

    Connected superior to the spinal cord is a structure resembling an inverted frustrum called the medulla oblongata. The medulla oblongata serves as a connection between the spinal cord and the cerebrum, and thus serves as a primary relay center for somatosensory information, as well as for the mass of motor signals descending into the somatic nervous system. In addition to this, the medulla oblongata serves as a base for 5 of the 12 cranial nerves which innervate the head and neck. The most important function of the medulla is controlling autonomic functions of the body (basic unconscious processes), such as breathing, heart rate, etcetera. These functions are fulfilled by a neural area called the reticular formation, which is mostly contained within the posterior medulla, although there is some overflow to the Pons.

    The Pons is a structure directly superior to the medulla that bulges out from the brainstem, structurally resembling an “adam’s apple”. The pons is quite similar to the medulla as it serves as a relay between the spinal cord and brain, performs as a base for several cranial nerves, and contains the superior region of the reticular formation, thus aiding in various autonomic processes. In addition, the pons plays an important part in the functions of sleep and arousal.

    Another extremely important part of the brain is the cerebellum: a bi-lobed structure, of which the outside surface slightly resembles a cauliflower and can be found at the anterior of the brain inferior to the occipital lobe. The cerebellum functions primarily in terms of movement coordination and optimization. An important part of this function is that movement does not originate in the cerebellum, but rather is coordinated and optimized there - instructions for movement originate in the motor cortex of the frontal lobe. The cerebellum is directly responsible for coordination of movements and motor learning, and works with the vestibular system in order to preserve balance. The cerebellum can be divided into several distinct structural areas, namely the cerebellar cortex and the cerebellar deep nuclei. The cerebellar cortex is mainly responsible for processing and integrating data from the various somatosensory systems including the cerebral cortex and the thalamus. An especially interesting aspect of the cerebellum is its histology: The cerebellum is home to one of the most beautiful neurons in the brain- the purkinje cell. The Purkinje cell is a neuron with extensively branching dendrites; in fact, there can be over 100,000 connections to a single Purkinje cell. Purkinje cells receive an immense volume of input from thousands of small granule cells also located in the cerebellar cortex, and after comprehensive calculation and analysis, relay the resulting information to cerebellar deep-brain nuclei, where it is then processed. These deep-brain nuclei then perform final coordinations and communicate through the spinal cord and the somatic nervous system the branch of the PNS that organizes voluntary movements) the movement command to muscle fibers throughout the body.


  1. Taylor, John. General Science. Taylor Electronics. Archived from the original on 9 June 2013. Retrieved on 27 March 2014.

  2. Midline cut section of the brain. [Digital image]. (2013). Retrieved November 2, 2016, from;sa=view;id=13786

  3. Motor and Sensory functions [Digital image]. (n.d.). Retrieved November 2, 2016, from

Alexander Skvortsov

Alexander Skvortsov

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