What is Dr. Zubair Khalid's research focus?

Dr. Zubair Khalid specializes in molecular virology, mRNA vaccine development, and computational biology, with a focus on avian pathogens like IBDV and Avian Reovirus.

Where is Dr. Zubair Khalid currently working?

Dr. Zubair Khalid is a Postdoctoral Research Associate at the University of Maryland (UMD), specifically within the Department of Animal and Avian Sciences.

Brain Labeling: Labeled Diagrams of Brain Anatomy

Name: Brain Labeling: Labeled Diagrams of Brain Anatomy
Creator: Dr. Zubair Khalid

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-09-20

Brain labeling is the practice of naming each visible structure on a diagram of the brain so that anatomy can be studied, compared, and tested. A complete labeled diagram of the brain identifies the cerebrum, cerebellum, brainstem, diencephalon (thalamus and hypothalamus), corpus callosum, and the frontal, parietal, temporal, and occipital lobes, and it does so from at least three standard planes: sagittal, lateral, and coronal.

This guide builds those labels from the ground up. It explains what each plane shows, how gray matter differs from white matter, where the cranial nerves attach, and how brain size, gyral complexity, and olfactory bulb development vary across dogs, cats, and ruminants. A self-test table at the end lets you cover the labels and quiz yourself.

This article is educational and is not a substitute for veterinary diagnosis or treatment.

Why Brain Labeling Matters in Veterinary Anatomy

A label is a claim about position. When you write "hypothalamus" on a sagittal section, you are stating that the structure sits below the thalamic mass and above the pituitary stalk, at the ventral floor of the diencephalon. When you write "corpus callosum" on the same section, you are stating that the structure arches over the lateral ventricles and connects the two cerebral hemispheres. Getting these positions right is the difference between a useful study diagram and a misleading one.

Veterinary students use brain labeling for three practical reasons. First, it anchors neuroanatomy to a spatial framework that survives across species, so a dog brain and a sheep brain can be compared structure by structure. Second, it supports lesion localization: a clinician who knows that the frontal lobe sits rostral to the cruciate sulcus can reason about which behaviors might change after a frontal injury. Third, it is the vocabulary of the neurological examination, since terms like "cerebellar" and "brainstem" carry specific functional expectations.

The same labeling logic applies across vertebrates. A cellular-resolution atlas of the larval zebrafish brain annotated 72 non-overlapping brain regions and used that annotation to build an inter-areal wiring diagram, which shows how far the labeling approach scales [1]. Quantitative neuroanatomical phenotyping in mouse embryos scores 106 parameters across coronal and sagittal planes, focusing on the cortex, corpus callosum, hippocampus, ventricles, caudate putamen, and cerebellum [2]. The structures you label in a dog or cat are the same structures scored in those studies.

The Three Standard Views Used for Brain Labeling

Every labeled diagram of the brain starts with a plane. The three you will use most are sagittal, lateral, and coronal.

Sagittal View

A sagittal section cuts the brain into left and right halves along the midline. A midsagittal section passes exactly through the midline and exposes structures that no other plane shows cleanly: the corpus callosum, the third ventricle, the thalamus, the hypothalamus, the midbrain, the pons, the medulla oblongata, and the cerebellar vermis.

The cerebellar vermis is the narrow midline strip of the cerebellum. In a fetal MRI study of mid-sagittal sections, the cross-sectional area of the cerebellar vermis increased steadily between 21 and 38 weeks of gestation, while the fourth ventricle showed a biphasic growth pattern, slow until about 30 weeks and then faster [3]. That study measured a human fetus, but the geometric relationship it describes, vermis dorsal to the fourth ventricle in the midline, holds in domestic mammals.

Lateral View

A lateral view shows the brain from the side. It is the best plane for labeling the surface lobes, because the frontal, parietal, temporal, and occipital lobes are all visible in profile. The lateral view also shows the lateral sulcus, the gyri and sulci of the cerebral convexity, the cerebellum, and the brainstem disappearing ventrally.

The lateral surface is where gyral complexity is easiest to appreciate. Gyri are the raised folds and sulci are the grooves between them. In a neonatal MRI study of 438 brains, functional and structural connectivity was consistently strongest between gyro-gyral regions and weakest between sulco-sulcal regions, which supports the view that gyri act as global information processing hubs while sulci serve as local functional units [4]. That is a functional argument for why the folds exist, not just a description of their shape.

Coronal View

A coronal section cuts across the brain from side to side, roughly perpendicular to the long axis. It is the plane that shows the lateral ventricles in cross-section, the corpus callosum as a band above them, the caudate nucleus and putamen beside them, and the hippocampus in the temporal lobe.

Coronal sections are standard in developmental phenotyping. The mouse embryo protocol uses coronal and sagittal planes together because each plane reveals structures the other hides [2]. In a study of the temporal stem, coronal sections of an MRI-based 3D tractography model revealed the layered organization of the inferior fronto-occipital fasciculus, uncinate fasciculus, anterior commissure, and Meyer's loop of the optic radiation [5]. If you want to label white matter tracts rather than surface lobes, coronal is often the most informative plane.

Labeled Structures: Cerebrum, Cerebellum, Brainstem, and Diencephalon

Cerebrum

The cerebrum is the largest part of the brain. It consists of two cerebral hemispheres joined by commissural fibers, the largest of which is the corpus callosum. The outer surface is the cerebral cortex, a sheet of gray matter folded into gyri and sulci.

The cortex is not uniform. A spatial transcriptomics study defined cortical layers by gene expression rather than by appearance and resolved laminar boundaries more accurately than traditional anatomy-based methods, including sublayer-like domains within layers L1, L3, and L6 and a molecularly distinct transition zone at the gray-white matter interface [6]. The same framework extended to macaque and mouse cortex [6]. For labeling purposes, the practical point is that the six-layer cortical plan is a real, measurable organization, and the gray-white boundary is a genuine transition zone rather than a sharp line.

Cerebellum

The cerebellum sits caudal to the cerebrum and dorsal to the brainstem. It has a highly folded surface of folia, a midline vermis, and two lateral hemispheres. Its role in coordination and balance is the reason cerebellar signs look different from cerebral signs.

Brainstem

The brainstem is the stalk connecting the cerebrum to the spinal cord. From rostral to caudal it comprises the midbrain, the pons, and the medulla oblongata. All cranial nerves except the olfactory and optic nerves attach to the brainstem. The brainstem also contains the precerebellar nuclei that relay information to the cerebellum, a system mapped in three dimensions in the rat using coordinate-based diagrams anchored to cyto- and myeloarchitectonically defined nuclear boundaries [7].

Diencephalon, Thalamus, and Hypothalamus

The diencephalon is the region between the cerebral hemispheres and the midbrain. Its two most testable structures are the thalamus and the hypothalamus.

The thalamus is a paired egg-shaped mass of gray matter in the dorsal diencephalon. It is a relay station: nearly all sensory pathways except olfaction synapse there before reaching the cortex. The thalamus also participates in motor and limbic circuits. In a study of minimal hepatic encephalopathy, regional gray matter volume increased in the right lateral geniculate thalamus and left pulvinar medial thalamus, which illustrates that thalamic subnuclei can be measured individually [8].

The hypothalamus lies ventral to the thalamus, forming the floor of the third ventricle. It controls autonomic function, body temperature, hunger, thirst, circadian rhythm, and pituitary regulation through the hypophyseal portal system.

Corpus Callosum

The corpus callosum is the largest commissure of the brain. It is a thick band of white matter that crosses the midline and connects matching regions of the two hemispheres. In the horse, the rostral cerebral artery supplies the rostromedial cortex and the corpus callosum, which reflects how intimately the commissure is embedded in the cerebral vascular territory [9]. The hippocampal formation is classified relative to the corpus callosum as precommissural, supracommissural, or retrocommissural, a naming system that shows how central the callosum is as an anatomical landmark [10].

Labeled Lobes of the Cerebrum

Frontal Lobe

The frontal lobe is the rostral portion of each hemisphere. It contains motor cortex and regions involved in planning, decision-making, and social behavior. In the horse, the rostral cerebral artery supplies the rostromedial cortex, and the middle cerebral artery supplies the lateral and dorsolateral cortical surfaces [9].

Parietal Lobe

The parietal lobe lies caudal to the frontal lobe and dorsal to the temporal lobe. It processes somatosensory information and integrates sensory input with spatial awareness. The superior longitudinal fasciculus and arcuate fasciculus connect the temporal and frontal lobes through the parietal region, and their three-dimensional relationship to the middle cerebral artery has been mapped in cadaveric and tractography studies [11].

Temporal Lobe

The temporal lobe sits ventral to the lateral sulcus and lateral to the brainstem. It houses auditory cortex and, medially, the hippocampal formation. The retrocommissural portion of the hippocampal formation forms part of the floor of the temporal horn of the lateral ventricle and part of the medial surface of the hemisphere, and it includes the hippocampus (Ammon's horn and the dentate gyrus), the subiculum, and associated white matter fibers [10].

Occipital Lobe

The occipital lobe is the caudal pole of each hemisphere and is the primary visual cortex. In the horse, the caudal cerebral artery supplies the occipital and caudal temporal lobes [9]. The sagittal stratum, a prominent white matter structure within the occipital and parietal lobes, contains the optic radiation plus additional fiber populations running in other directions, and it has an external and an internal layer joined and crossed by fibers from surrounding white matter [12].

Gray Matter Versus White Matter

Gray matter contains neuronal cell bodies, dendrites, and synapses. White matter contains myelinated axons bundled into tracts. In a labeled diagram, gray matter appears as the cortical ribbon and as deep nuclei such as the thalamus, caudate nucleus, and putamen. White matter appears as the corpus callosum, the internal capsule, the sagittal stratum, and the various fasciculi.

The distinction is functional as well as anatomical. A study of cerebral small vessel disease found reduced gray matter volume across the frontal, parietal, temporal, and occipital lobes as well as the cingulate cortex and cerebellum, with 597 genes significantly associated with that volume loss enriched in protein synthesis, RNA metabolism, intracellular protein transport, and protein homeostasis pathways [13]. White matter changes are measured differently, using diffusion metrics in normal-appearing white matter after lesion maps are subtracted [14].

The gray-white interface is its own labeled feature. Gene expression-defined cortical layers identified a molecularly distinct transition zone at the gray-white matter interface [6]. When you label a coronal section, that boundary deserves its own line.

Cranial Nerves and Their Basic Roles

Twelve pairs of cranial nerves emerge from the brain. They are numbered rostral to caudal, and each has a basic role that a labeled diagram should indicate at its attachment point.

Number	Name	Basic role
I	Olfactory	Smell
II	Optic	Vision
III	Oculomotor	Eye movement, pupil constriction
IV	Trochlear	Eye movement (dorsal oblique)
V	Trigeminal	Facial sensation, chewing
VI	Abducens	Eye movement (lateral rectus)
VII	Facial	Facial expression, taste, tear and saliva production
VIII	Vestibulocochlear	Hearing and balance
IX	Glossopharyngeal	Taste, swallowing, pharyngeal sensation
X	Vagus	Parasympathetic control of viscera, swallowing, vocalization
XI	Accessory	Neck muscles
XII	Hypoglossal	Tongue movement

Cranial nerves I and II attach to the cerebrum rather than the brainstem. The remaining ten attach along the midbrain, pons, and medulla. When you label a sagittal or lateral view, mark the attachment site rather than the target organ, because the attachment site is what the examiner localizes to.

Self-Test Table: Structure, Location, and Primary Function

Cover the right two columns and work down the left. Then cover the left column and name the structure from the description.

Structure	Location	Primary function
Cerebrum	Dorsal and rostral, two hemispheres	Sensory processing, motor control, cognition, behavior
Cerebellum	Caudal to cerebrum, dorsal to brainstem	Coordination, balance, motor learning
Brainstem	Midbrain, pons, medulla, connecting cerebrum to spinal cord	Cranial nerve attachment, arousal, vital reflexes
Diencephalon	Between hemispheres and midbrain	Relay and homeostatic control
Thalamus	Dorsal diencephalon, paired	Sensory and motor relay to cortex
Hypothalamus	Ventral diencephalon, floor of third ventricle	Autonomic control, temperature, hunger, thirst, pituitary regulation
Corpus callosum	Midline white matter band above lateral ventricles	Interhemispheric communication
Frontal lobe	Rostral hemisphere	Motor planning, decision-making, behavior
Parietal lobe	Dorsal, caudal to frontal lobe	Somatosensory processing, spatial integration
Temporal lobe	Lateral, ventral to lateral sulcus	Auditory processing, memory, hippocampal formation
Occipital lobe	Caudal pole	Vision

Comparative Veterinary Notes: Dogs, Cats, and Ruminants

Brain size, gyral complexity, and olfactory bulb development differ across species, and these differences change what a labeled diagram should emphasize.

Dogs have a highly developed olfactory system. The olfactory bulb is proportionally large, and the frontal lobe contains extensive olfactory-receptive cortex. A dog brain diagram should give the olfactory bulb its own label rather than folding it into the frontal lobe.

Cats have a brain of similar basic plan to the dog but with a relatively smaller olfactory bulb and a cerebral cortex that is also gyrencephalic, meaning it bears gyri and sulci. The visual and auditory cortices are well developed, consistent with the cat's predatory sensory profile.

Ruminants such as sheep and cattle have gyrencephalic brains with pronounced cortical folding and large olfactory bulbs. The horse is the best-documented large animal example in the recent literature: a detailed anatomical study of ten adult horse heads found a complete and symmetrical circle of Willis formed by internal carotid branches connecting the carotid and basilar systems, with the rostral cerebral artery supplying the rostromedial cortex and corpus callosum, the middle cerebral artery supplying the lateral and dorsolateral cortical surfaces, and the caudal cerebral artery supplying the occipital and caudal temporal lobes [9]. Minor variations appeared, including interhemispheric anastomoses in 60% of specimens, but the overall arrangement was consistent across all ten [9].

The practical takeaway is that the labeled structures are conserved, but their relative sizes are not. A diagram built for a dog will misrepresent the olfactory bulb of a cat and the cortical proportions of a ruminant.

Clinical Relevance, Limitations and Common Mistakes

Two pairs of terms cause most labeling errors.

The first is thalamus versus hypothalamus. The thalamus is dorsal and is a sensory and motor relay. The hypothalamus is ventral and is a homeostatic and endocrine control center. The mnemonic that works is positional: hypo means below, and the hypothalamus sits below the thalamus at the floor of the third ventricle. If you label the dorsal egg-shaped mass as hypothalamus, every downstream functional prediction you make will be wrong.

The second is ventricle versus cistern. A ventricle is a fluid-filled cavity inside the brain substance, lined by ependyma. A cistern is a fluid-filled space outside the brain substance, within the subarachnoid space. The fourth ventricle is inside the brain, between the cerebellum and the brainstem. A subarachnoid cistern surrounds the brain. A fetal MRI study measured the fourth ventricle as an internal cavity whose cross-sectional area grew slowly until about 30 weeks and then accelerated, while the cerebellar vermis grew steadily [3]. That is a cavity inside the brain, not a space around it.

A third common mistake is treating the gray-white boundary as a sharp line. Gene expression-defined cortical layers resolved a molecularly distinct transition zone at that interface [6], so a labeled diagram should show a zone, not a knife edge.

A fourth mistake is labeling the cranial nerve target rather than its attachment. The vagus nerve supplies thoracic and abdominal viscera, but on a brain diagram it is labeled where it exits the medulla.

This article is educational and is not a substitute for veterinary diagnosis or treatment. Individual animals need a veterinarian for any clinical concern.

Frequently Asked Questions

What is brain labeling?

Brain labeling is naming each visible structure on a brain diagram so that anatomy can be studied and tested. A complete set of labels covers the cerebrum, cerebellum, brainstem, diencephalon, thalamus, hypothalamus, corpus callosum, and the four cerebral lobes.

Which plane is best for labeling the corpus callosum?

The midsagittal plane is best because the corpus callosum arches across the midline and is fully exposed there. Coronal sections also show it clearly as a band above the lateral ventricles.

How do I tell the thalamus from the hypothalamus?

The thalamus is dorsal and the hypothalamus is ventral. The hypothalamus forms the floor of the third ventricle and sits below the thalamus.

What is the difference between a ventricle and a cistern?

A ventricle is a fluid-filled cavity inside the brain. A cistern is a fluid-filled space outside the brain within the subarachnoid space.

Which cranial nerves attach to the brainstem?

Ten of the twelve pairs attach to the brainstem. The olfactory and optic nerves attach to the cerebrum.

Why do dog brains have larger olfactory bulbs than cat brains?

Dogs rely more heavily on olfaction, so the olfactory bulb and olfactory-receptive cortex are proportionally larger. The basic labeled structures are the same in both species.

What does gyral complexity mean?

Gyral complexity refers to the number and folding pattern of gyri and sulci on the cortical surface. Gyri are the raised folds and sulci are the grooves between them.

Do all domestic mammals have the same brain lobes?

Yes, the frontal, parietal, temporal, and occipital lobes are present across domestic mammals. Their relative sizes and the prominence of the olfactory bulb differ by species.