3D Animation of Full Human Brain Anatomy and Function

In this comprehensive 3D animation we go over the anatomy of the brain in detail, from the lobes, gyri and sulci of the cortex, to the nuclei of the basal ganglia, white matter, parts of the brainstem, locations of the ventricles, commissures, and other structures. We look at the anatomy as well as physiology, input/output connections, function and importance of each structure. About 60 structures plus their substructures are shown and described in this half hour long animation.

This animation includes views and descriptions of the amygdala, angular gyrus, anterior commissure, basal ganglia, caudate nucleus, central canal of spinal cord, cerebellum, cerebral aqueduct, cerebrum, cerebral cortex, cingulate gyrus, commissure of fornix, corpus callosum, fornix, fourth ventricle, frontal cortex, globus pallidus, gray matter, hippocampus, hypothalamus, inferior colliculus, inferior frontal gyrus, inferior temporal gyrus, internal capsule, interventricular foramina, lateral geniculate, medial geniculate, medulla oblongata, midbrain, middle frontal gyrus, middle temporal gyrus, occipital lobe, orbital gyrus, pineal gland, pituitary gland, pons, postcentral gyrus, posterior commissure, precentral gyrus, prefrontal cortex, putamen, septum, stria terminalis, substantia nigra, superior colliculus, superior parietal lobule, superior temporal gyrus, supramarginal gyrus, thalamus, third ventricle, tuber cinereum, white matter, and others.




The pair of amygdala deep in the temporal lobes are part of the limbic system. They are almond shaped.  The amygdala are made up of the basolateral complex, the medial nucleus, the cortical nucleus, the central nucleus and the intercalated cell clusters.  The amygdala is larger in males.  They play a role in emotional responses, decision making, and processing of memory. This involves memories associated with emotional events.

Each amygdala has an independent memory system. The right amygdala is concerned with fear conditioning and declarative memory as well as in associating time and place with emotions. The amygdala are involved in memory consolidation.  It is the main structure involved in the fight or flight response.

Projections of the amygdala include the locus coeruleus, the hypothalamus, the nucleus accumbens, and the thalamus.  There is data showing that the left amygdala has a role in the reward system. It has also been linked to obsessive and compulsive bevavior, anxiety disorders, and PTSD.  The left amygdala develops first, while the right amygdala grows for a longer span of time.

Angular gyrus

The angular gyrus is in Brodmann area 39. It is posterior to the supramarginal gyrus in the parietal lobe, and close to the superior edge of the temporal lobe.  It is involved in complex language functions such as reading, writing and their interpretation. It sends visual information to Wernicke’s area. Its other functions involve attention, memory retrieval, and spatial cognition including distinguishing between left and right.

Anterior commissure

The anterior commissure is a white matter tract much smaller than the corpus callosum. It connects the two temporal lobes of the cerebrum in front of the fornix.   It is important in pain sensation and olfaction as it includes fibers from the neospinothalamic tract and olfactory tracts.

Basal ganglia

The basal ganglia is a group of subcortical nuclei on top of the midbrain. They include the dorsal striatum (caudate nucleus and putamen), the ventral striatum (nucleus accumbens and olfactory tubercle), ventral pallidum, the globus pallidus, substantia nigra and subthalamic nucleus.

They connect with the thalamus, brainstem, cortex and others.

Caudate nucleus

The caudate nucleus along with the putamen form the dorsal striatum, which is divided by the internal capsule. In each hemisphere, it forms a thick anterior part called the head which tapers to a body and narrow tail, giving it a C shape. The tail curves toward the front.  It is located on both sides of the thalamus.

It functions in associative and procedural learning, inhibitory control of action, and movement. There is a link between the caudate and sleep patterns. Movement functions include posture as well as speed of directed movements.

Neuronal connections from the caudate reach the substantia nigra and globus pallidus and it is innervated by neurons from the substantia nigra. The caudate has projections to the hippocampus and receives projections from the amygdala. There are data showing effects on emotion, hyperactivity, and drive.

Central canal of spinal cord

The central canal runs through the spinal cord.  It is filled with cerebrospinal fluid and it transports nutrients to the spinal cord. In the upper regions of the spinal cord it can be found in the anterior portion, later becoming more central and ultimately posterior. The widest part of the central canal is the terminal or fifth ventricle.


The cerebellum is located in the posterior underneath the cerebral hemispheres. The pons and medulla are anterior to it. It is part of the metencephalon. The actual name means “little brain”. Its made up of a gray matter cortex, deeper white matter with myelinated fibers, deep gray matter cerebellar nuclei inside the white matter, and a fluid filled ventricle.

The cerebellum is made up of two hemispheres and a protruding midline vermis (worm in Latin).  The white matter is called the arbor vitae or tree of life due to its appearance when sectioned. The cortex is made up of a continuous layer of tissue folded repeatedly although it appears as parallel grooves on the surface.  The gyri of the cerebellum are called folia.

The lateral cerebellum is called the cerebrocerebellum and the medial cerebellum is called the spinocerebellum. The cerebellum is divided into three lobes- anterior above the primary fissure, posterior below the primary fissure, and flocculonodular below the posterior fissure.

The cerebellum is associated with movement, including motor learning, timing, coordination and precision as well as language and attention. The cerebellum receives input from sensory systems of the spinal cord. Neurons most commonly found in the cerebellum include Purkinje and granule cells. There are 3 important axon types in the cerebellum, mossy fibers, climbing fibers and parallel fibers.

Cerebellar peduncles

Three pairs of cerebellar peduncles connect the cerebellum to the nervous system.

Superior cerebellar peduncle-connects to the cerebral cortex

Middle cerebellar peduncle-connects to pons

Inferior cerebellar peduncle-output to reticular formation and vestibular nuclei


cerebral aqueduct

The cerebral aqueduct is found ventral to the cerebellum and dorsal to the pons. Also called the Sylvian aqueduct, it contains CSF and connects the third and fourth ventricle.  The gray matter around the aqueduct is called the periaqueductal gray.


The cerebrum or telencephalon is the largest part of the brain. It contains not only the two cerebral hemispheres made up of an outer cortex of gray matter and inner white matter but also subcortical structures such as the basal ganglia, hippocampus and olfactory bulb. The cerebrum is involved in voluntary motor actions, sensory perception, memory and thoughts. The cerebrum develops from the prosencephalon.

Cerebral cortex

The cerebral cortex is the outer gray matter layer of the cerebrum and is made up of two hemispheres.  The 2 cerebral hemispheres consist of depressions or sulci and elevations or gyri.  It is partially separated by a deep longitudinal fissure.  The medial longitudinal fissure separates it into the two hemispheres.

The cortex can be divided into the frontal, parietal, occipital and temporal lobe. The cortex includes primary sensory areas which receive sensory information and association areas.  The frontal lobe includes Broca’s area responsible for production of language and the temporal lobe includes Wernicke’s area responsible for speech comprehension.

choroid plexus

The choroid plexus is a plexus of cells that produce and secrete cerebrospinal fluid.  It also acts as a blood/CSF barrier.  It is made up of a core of capillaries and connective tissue surrounded by cuboidal epithelial cells.  Every one of the four ventricles contains a choroid plexus.

cingulate gyrus

The cingulate cortex includes the whole cingulate gyrus and can be found medially in the cerebral hemispheres above the corpus callosum.  It is part of the limbic system.  It functions both in respiratory control, executive function, as well as learning, memory and emotions.

commissure of fornix

The commissure of fornix is formed by fibers left and right fornix bundles.

corpus callosum

The corpus callosum, which translates into “tough Body”, is a thick nerve tract that connects the two cerebral hemispheres. It can be found below the cerebral cortex crossing the midline. The corpus callosum is the largest white matter body with several hundred million axons. It can be divided into the rostrum, the genu, the body and the splenium. The corpus callosum allows for communication between the two hemispheres of the cerebrum.


The fornix is a part of the limbic system and is an output of the hippocampus. It starts on each side in the hippocampus as fimbria hippocampi and continue as the crura or posterior pillars. At the commissure of fornix the fibers meet forming the body.  Around the anterior commissure the body divides again into the anterior pillars or columns which continue on to the mamillary bodies. The fornix is important in establishing episodic memories and fornix damage leads to problems with spatial memory.

fourth ventricle

The fourth ventricle carries cerebrospinal fluid and can be found extending from the aqueduct of Sylvius to the obex in the caudal medulla. It is at the level of the pons. The cerebellar peduncles form the sides of the fourth ventricle. The rhomboid fossa is the floor of this ventricle. The fourth ventricle has a diamond shape in cross section. The CSF flows into the fourth ventricle through the cerebral aqueduct.

frontal cortex

The frontal cortex as the name suggests can be found at the anterior of each cerebral hemisphere. It is separated from the parietal lobe by the central sulcus and from the temporal lobe by the lateral sulcus. The premotor as well the primary motor cortex are found in the frontal cortex.

globus pallidus

The globus pallidus which is part of the basal ganglia, translates into “pale globe”.  There are two parts: The pars externa and pars interna. It projects mainly to the substantia nigra and thalamus and functions in regulation of voluntary movement, through inhibitory action, whereas the cerebellum provides excitatory action.  It receives inputs from the caudate and putamen.

gray matter

Gray matter which consists of cell bodies includes the basal ganglia including the nucleus accumbens, caudate nucleus, putamen, and substantia nigra as well as the surface of the cerebrum and cerebellum, thalamus, hypothalamus and brainstem nuclei.  It is gray colored due to the color of neuron cell bodies as opposed to white matter which appears white due to the color of myelin.


The habenula is a cell mass on the side of the third ventricle located above the thalamus. It is called the crossroad between the basal ganglia and the limbic system.


The hippocampus, or seahorse in latin, is part of the limbic system and can be found as a pair, one on each side, by the floor of the lateral ventricle.  The parahippocampal gyrus conceals the hippocampus.  It is made up of the hippocampus itself and the dentate gyrus, which is surrounded by hippocampal gray matter.

The name cornu ammonis or ram’s horn is given to it because of its shape as shown in cross-section.  The abbreviation CA given to its parts including CA1, CA2, CA3 and CA4 come from this name.

The hippocampus takes part in storing of explicit memory, such as information about objects, places and people. This is done through long term potentiation.  Hippocampal damage is seen in dementia such as Alzheimers disease. It is also affected in schizophrenia and PTSD.

The three major pathways in the hippocampus include the mossy fiber pathway, the schaffer collateral pathway and the perforant fiber pathway. Input comes from the entorhinal cortex.  Outputs include the entorhinal cortex and the prefrontal cortex.  It is modulated by dopamine, serotonin and norepinephrine.  The hippocampus is one of the few brain regions where new nerve cells are born.


The hypothalamus is part of the limbic system and is found under the thalamus.  The name hypothalamus means “under chamber”. The hypothalamus links the nervous system and the endocrine system via the pituitary. Therefore it has a neuroendocrine function.  It works to control sleep, hunger, body temperature and activities of the autonomic nervous system.  The hypothalamus synthesizes and secretes hormones which control the pituitary gland.  Its connections include the reticular formation, brainstem, amygdala and septum.  Other functions of the hypothalamus include controlling defensive behaviors.

inferior colliculus

The inferior colliculus is located over the trochlear nerve and below the superior colliculus.  It is a large main nucleus of the auditory pathway in the midbrain where auditory pathways converge.  It also functions in spatial localization through hearing as well as a integration station and switchboard.  Its inputs include the auditory cortex and brainstem nuclei.  The name inferior colliculus means lower hill.  Inputs include several brainstem nuclei.

inferior frontal gyrus

The inferior frontal gyrus, a part of the prefrontal cortex, is the location of Broca’s area, responsible for speech creation and language processing.

Inferior temporal gyrus

The inferior temporal gyrus is the lowest of the gyri of the temporal lobe.  It is separated from the middle temporal gyrus by the inferior temporal sulcus.  The occipital temporal sulcus separates it from the fusiform gyrus.  It is involved in visual stimulus processing on the level of object recognition based on form and color.

internal capsule

The V shaped internal capsule is a white matter structure that separates the caudate nucleus and putamen and also the caudate and thalamus from putamen and globus pallidus.  It contains ascending and descending tracts connecting the cortex.  The bend in the V of the internal capsule is called the Genu.  It has an anterior limb and a posterior limb.  Much of the internal capsule is the corticospinal tract which carries information from the primary motor cortex to motor neurons in the spinal cord.

interventricular foramina

The interventricular foramina, also called the foramina of Monro, are channels which connect the right and left lateral ventricles to the third ventricle.  Cerebrospinal fluid flows through the interventricular foramina into the third ventricle.  They contain a choroid plexus in their walls which produces CSF.

lateral geniculate

The lateral geniculate is a small thalamic nucleus located at the end of the optic tract.  It is a visual pathway relay center.  Information from the eye and optic tract goes through the lateral geniculate on its way to the primary visual cortex.  The lateral geniculate has 6 layers of neurons.

lateral ventricle

There are two C shaped cerebrospinal fluid filled lateral ventricles.  They stretch from the inferior horn of the temporal lobe all the way down to the third ventricle.  They can be divided into three horns and a body.  The frontal horn can be found in the frontal lobe of the brain while the occipital horn enters the occipital lobe. The lateral ventricles are the largest of all the ventricles.

medial geniculate

The medial geniculate body is made up of several nuclei. Its part of the auditory system.  The MGB is a relay between the inferior colliculus and the auditory cortex.

medulla oblongata

The medulla oblongata is part of the brainstem.  Medullary pyramids contain the corticospinal and corticobulbar tracts.  The swellings or olives are due to the inferior olivary nuclei.  The medulla connects higher brain levels to the spinal cord.  The medulla functions in involuntary actions. Its autonomic control includes heart rate, respiration, sleep and heart rate.


The midbrain is the anterior part of the brainstem.  The dorsal side of the midbrain is the tectum, which means roof.  The tectum has 4 colliculi or bumps on its surface.  The tegmentum is the floor and is ventral to the cerebral aqueduct.  Its involved in homeostasis.  Superior colliculi process visual information and inferior colliculi process auditory information.  It functions in functions in alertness, sleep, temperature regulation, hearing and vision.

middle frontal gyrus

The middle frontal gyrus is found between the superior and inferior frontal sulci.  It has a role in the reorienting of attention.

middle temporal gyrus

The middle temporal gyrus is located in the middle of the temporal lobe.  It has been linked to accessing word meaning while reading, figuring out distance, and recognition of known faces.

occipital lobe

The occipital lobe of the cerebral cortex is named after the occipital bone and is the smallest lobe of the cortex.  It is located above the temporal and below the parietal lobe.  The occipital lobe includes the visual cortex, mainly Brodmann area 17 or V1.  It also includes V2 or the ventral stream, which is a secondary visual cortex.  Underneath the occipital lobe is the tentorium cerebelli which divides the cerebellum from the cerebrum.  The lateral occipital sulcus separates occipital gyri.

orbital gyrus

The orbital gyrus can be found on the inferior surface of the frontal lobe.  This area of the front lobe rests on the orbital plate of the frontal bone.  There are 4 orbital gyri- the posterior, lateral, medial and anterior.

optic chiasm

The name optic chiasm comes from the greek for crossing. It is X shaped.  It can be found under the hypothalamus and is where the optic nerves cross.  Fibers from the medial part of the retina cross over here but fibers from the lateral half of the retina stay ipsilateral.  It is located in the chiasmatic cistern and is encircled by the circle of willis.

optic tract

The optic tract is found in a pair and is an extension of the optic nerve.  It conveys information to the contralateral half of the visual field.  Axons of the right and left optic tracts synapse at the lateral geniculate nucleus.

pineal gland

The pineal is a small endocrine gland which is not paired.  The name comes from the shape of the gland, which looks like a small pine cone.  It produces melatonin, a serotonin derived hormone, that modulates sleep cycles.  The pineal can be found where two of the halves of the thalamus meet behind the third ventricle and is part of the epithalamus.

pituitary gland

The pituitary is an endocrine gland located at the bottom of the hypothalamus.  Hormones secreted here control blood pressure, temperature regulation, sex organ function, thyroid function, pain relief and water regulation.  The posterior pituitary is connected to the hypothalamus by the pituitary stalk.  The pituitary has an anterior, intermediate and posterior lobe.


The word pons comes from the Latin for bridge.  It is in the brainstem between the midbrain and the medulla.  Within it are tracts that carry sensory signals up and other signals down.  In the rear it is made up of two pairs of cerebellar peduncles. The middle cerebellar peduncle connects the pons to the cerebellum.

It is located in front of the cerebellum.  It has two major divisions- the ventral pons and the tegmentum.  The pons contains several cranial nerve nuclei including the vestibulocochlear nucleus, facial nerve nucleus, nucleus abducens and the motor nucleus of the trigeminal nerve.  It is part of various autonomic functions such as arousal, sleep regulation, equilibrium, and muscle tone.

postcentral gyrus

The postcentral gurys is located at the anterior parietal lobe. It includes Brodmann areas 1, 2, 3.  It is where the primary somatosensory cortex can be found.  It is the location of neurons that integrate sensory information from distinct parts of the body.  In front of it is the central sulcus. In the back of it is the postcentral sulcus.

posterior commissure

The posterior or epithalamic commissure is a white matter tract which connects the two hemispheres of the cerebrum.  It crosses the midline dorsally of the cerebral aqueduct.  It forms one of the stalks that attach the pineal gland to the wall of the third ventricle.  The posterior commissure connects language processing centers of the two hemispheres.

precentral gyrus

The precental gurys is Brodmann area 4. It is located at the rear of the frontal lobe just before the central sulcus. It has a diagonal orientation and is continuous with the postcentral gyrus.  Behind it is the postcentral gyrus.  This is the location of the primary motor cortex involved in execution of voluntary motor movements and skeletal muscles.

prefrontal cortex

The prefrontal cortex can be found in the anterior frontal lobe.  It is where executive function is carried out and high level filtering.

meaning acceptable behavior, predicting outcomes, determination of good and bad, working toward a goal.  It receives connections from brainstem arousal systems.


The putamen is a round structure that is a part of the basal ganglia.  Together with the caudate nucleus it forms the dorsal striatum.  To the medial of it lies the globus pallidus.  It functions in regulation of movement and is connected to the globus pallidus and substantia nigra.  The putamen is affected in Parkinsons disease where involuntary muscle movements occur.  Together with the globus pallidus it is known as the lentiform nucleus as they appear like a lens like shape.


The septum pellucidum is a membrane between the two cerebral hemispheres.  It separates the lateral ventricles and encloses the fifth ventricle.  It stretches from the corpus callosum to the fornix.

stria medullaris of hypothalamus

It is part of the epithalamus and is a horizontal ridge on the medial surface of the thalamus.

stria terminalis

The stria terminalis or the terminal stria is a bundle of fibers from the amygdala to the septal nuclei, hypothalamus and thalamus.  It runs across the lateral wall of the intra ventricular surface.  It marks the separation between the thalamus and caudate nucleus.

Substantia nigra

It is a long nucleus in the midbrain, however its functionally a part of the basal ganglia.  The substantia nigra plays roles in regulation of movement and muscle tone.  There are two parts in the substantia nigra: the substantia nigra pars compacta and the substantia nigra pars reticulata.

The substantia nigra pars reticulata is more anterior and contains GABAergic neurons.  The Substantia nigra pars compacta is very populated by dopaminergic neurons.  In Parkisons disease, the pars compacta degenerates.  Both parts receive input from the caudate and putamen whereas the pars reticulata sends information outside the basal ganglia.

superior colliculus

The superior colliculus can be found on top of the midbrain and is a paired structure.  It is a multi sensory structure.  Some of its functions include directing eye movements, head turns, and shifts in attention.

superior parietal lobule

The superior parietal lobule includes Brodmann area 5 and 7.  Its functions include spatial orientation.  It receives visual input and sensory input.

superior temporal gyrus

The superior temporal gyrus is located in the temporal lobe below the lateral sulcus.  It includes brodmann area 41 and 42 and Wernickes area. It is the location of the auditory cortex and processing of sounds.

supramarginal gyrus

It is located anterior to the angular gyrus.  It is part of the somatosensory association cortex.  Its involved in the interpretation of tactile sensory data.


Its a gray matter structure in the forebrain.  It is found medially.  The thalamus is a hub for information relay.  It relays sensory signals, regulates alertness, arousal, sleep and consciousness.  Every sensory system utilizes the thalamus except for the olfactory system.  Its connected to the cortex by many thalamocortical radiations.

third ventricle

It is filled with CSF and found between the two halves of the thalamus.  It is narrow.  The epithalamus is behind it.

tuber cinereum

The tuber cinereum, sometimes called the pituitary stalk is a hollow eminence of gray matter.  It contains fibers going from the hypothalamus to the pituitary gland.  It is part of the hypothalamus.

white matter

White matter is found deep in the brain including the cerebellum and superficially in the spinal cord.  White matter is made up of axon bundles that connect gray matter areas.  Within the white matter one can find gray matter nuclei like brainstem nuclei and the basal ganglia.  The name comes from the color of fatty myelinated axons.


Click here for a 3d animation of human kidney structure and function.


Doc J

Dr. J has worked in biology all his life and holds several advanced degrees and certificates in biology, anatomy, scientific illustration, 3d animation and motion graphics. He has always had an interest in teaching others the wonders of biology using the latest advances in graphics, including visualization, digital microscopy, animation, illustration, VR and interactive media.

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