Subcortical structures

Thalamus

The thalamus is the largest subcortical structure. It acts as a relay center between the brainstem and cerebrum. The thalamus is comprised of 12 nuclei–anatomically, nine of them are grouped into anterior, medial, and lateral nuclei, while the remaining three form laminar sheets that separate these groups. Functionally, they can be classified into three groups: relay nuclei, intralaminar nuclei and the reticular nucleus. 

Two of the lateral thalamic nuclei, the lateral and medial geniculate bodies, are together called the metathalamus. Geniculate bodies are the sensory relay nuclei. The medial geniculate body is an auditory relay station, while the lateral geniculate body is the optic relay station. The thalamic nuclei are in charge of an entire spectrum of body functions, such as relaying sensory and motor signals and regulating consciousness, sleep, and alertness.

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Epithalamus

The epithalamus is the posterior part of the diencephalon. It is located posteroinferior to the thalamus and consists of the pineal body, stria medullaris and habenular trigone. Historically, the pineal gland was considered to be the third eye because of its connections to the visual system. But we now know that pineal gland function is to control the sleep-wake cycle (circadian rhythm) by releasing the sleeping hormone, melatonin. The pineal gland’s connections with the visual system provide information about the time of the day based on how much light there is. Darkness triggers melatonin secretion. 

The stria medullaris is a bundle of white matter connecting the hypothalamus and habenular trigone. The habenular trigone is a triangular area found in front of the superior colliculus which provides fibers to the pathway connecting the basal ganglia and the ventral brainstem. This pathway enables initiation and control of movements.

Subthalamus

The subthalamus is found ventral to the thalamus. It consists of the subthalamic nucleus, the zona incerta (of Forel) and the peripeduncular nucleus. 

The subthalamic nucleus is functionally part of the basal ganglia, it participates in the control of motor activity. The role of the zona incerta remains unknown. It relays fibers between a wide range of CNS regions, and is thought to play a role in activities such as motor integration and the accuracy of body movements. The peripeduncular nucleus has rich connections with the limbic system and is believed to play an important role in controlling sexual behaviour.

Learn more about the subthalamus anatomy and other diencephalon structures in our study unit.

Hypothalamus

Inferoanterior to the thalamus is the hypothalamus. It is a part of the diencephalon that maintains endocrine and autonomic functions. By controlling many important mechanisms related to survival, such as food and fluid intake, sleeping, metabolism, and body temperature, the hypothalamus enables a state of physiological equilibrium (body homeostasis). 

Structurally, the hypothalamus is composed of 13 nuclei. Anatomically they are arranged anteroposteriorly into three groups: anterior (preoptic and supraoptic), middle (tuberal), and posterior (mammillary). Hypothalamic nuclei can also be divided in mediolateral zones according to their proximity to the third ventricle:

• Periventricular – controls the release of hormones from the anterior pituitary lobe
• Medial – regulates the autonomic nervous system, release of hormones from the posterior pituitary lobe and circadian rhythms 
• Lateral – controls emotions due to its connections with the limbic system, and regulates feeding and sleep-wakefulness

The hypothalamus controls survival mechanisms through special pathways called the hypothalamic axes. The axes project from the hypothalamus to the pituitary gland, and from the pituitary gland towards target organs. There are three main axes:

• Hypothalamic-pituitary-adrenal axis mediates the stress response
• Hypothalamic-pituitary-thyroid axis regulates metabolism intensity
• Hypothalamic-pituitary-gonadal axis regulates reproduction

It’s notable that every axis goes through the pituitary gland (hypophysis). This is because the hypothalamus and pituitary gland are intricately linked. Hypothalamic axons link the hypothalamus with the posterior pituitary whilst a collection of blood vessels called the hypophyseal portal system connects the hypothalamus to the anterior pituitary. 

Hypothalamic axons project from the hypothalamus to the posterior lobe of the pituitary gland (neurohypophysis). These axons transport neurohormones (oxytocin, antidiuretic hormone/vasopressin) produced by the hypothalamus to the neurohypophysis; where they are stored, and released into the circulatory system when needed.

The hypophyseal portal system acts to transport hypothalamic "releasing" hormones to the anterior lobe of the pituitary gland (adenohypophysis). Hypothalamic hormones are synthesized by the hypothalamus and act to control the secretion of hormones, such as thyroid-stimulating hormone and adrenocorticotropic hormone, produced by endocrine cells of the adenohypophysis. This is why the hypothalamus is colloquially referred to as the master of the master, as it both produces hormones itself and also controls the production and release of hormones from the pituitary gland. 

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Hippocampus

The hippocampus is an often used synonym for what is officially called the hippocampal formation in anatomy. It plays an important role in long term memory storage and spatial navigation.

The hippocampal formation continues on the parahippocampal gyrus, as it dives into the medial temporal lobe. The hippocampal formation consists of the dentate gyrus, hippocampus and subiculum. It may sound confusing to say that the hippocampus is part of the hippocampal formation, as we know these terms are often used as synonyms. However, in its narrowest meaning the anatomical term hippocampus actually refers to the part of the hippocampal formation found between the dentate gyrus and subiculum. 

So, the dentate gyrus, hippocampus and subiculum together form the hippocampal formation which is named for its shape, a seahorse. The formation has two parts: head and tail, although some sources describe three parts (head, body and tail). The head refers to the wider anterior part, while the tail continues posteriorly. 

The hippocampal formation communicates with many different parts of the brain through its major output called the fimbria, which later becomes the fornix. The fornix projects from the hippocampus to the mammillary bodies of the hypothalamus. These connections are important for creating long-term memory. If a person had an injury that affected the hippocampus function, they would be unable to create new memories (anterograde amnesia) after their injury.

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