An overview of the abdomen and gastrointestinal tract

Overview of abdomen and GIT

The abdomen is rewarding to learn: it is perhaps more intuitive to understand than the thorax and neck, and being a large region containing large components, structures are easy to see. That said, it is still complex, and you can easily get overwhelmed when you first meet it. As with most areas of anatomy, a good learning strategy is to build a basic framework first, and then add in the details iteratively.

Conceptual framework

Regions: In terms of anatomical first principles, the abdomen is the space below the thoracic cavity that contains visceral organs, and the relevant musculoskeletal borders. Those borders include the diaphragm superiorly and the pelvic floor (= pelvic diaphragm) inferiorly.  This tells us something about the skeletal regions involved with the abdomen; given the position of the diaphragm, the abdomen includes the lower part of the thoracic skeleton as well as the lumbar skeleton, and given the position of the pelvic floor, the abdomen includes the pelvic spaces. This is a key concept, which leads to some (initially) counterintuitive observations; many of the important abdominal organs are located within the lower ribcage, and the ‘pelvic cavity’ is in reality the bottom end of the abdominal cavity as there is no tissue that separates the pelvic part of the cavity from the rest of the abdominal space. If you use the term ‘pelvic cavity’, you are referring to the lower part of the abdominal cavity (which is why some books refer to the abdomen as the abdominopelvis).


Layers: Taking the musculoskeletal tissues of the abdominal region to be the borders of the abdomen proper, then:

  • Most of the abdomen is taken up by a central cavity, which is itself mainly occupied by visceral organs. Around the organs in the cavity, the space is filled with serous fluid (the organs occupy so much of the cavity that the volume of serous-filled space is quite small).
  • The cavity is lined with a membrane, the peritoneum.
  • Between the peritoneum and the musculoskeletal ‘walls’ is a layer, the extraperitoneal space, that is filled with loose connective tissue (including fat) and fascia, some visceral organs, and various nerves and vessels.


Systems and organs: The abdomen houses three major visceral systems:

  1. The gastrointestinal tract (GIT; = digestive tract, alimentary canal, gut).
    • Most of the sections of the GIT are located in the abdomen;
      • The most distal part of the Oesophagus
      • Stomach
      • Small intestine
      • Large intestine
    • The abdomen also contains the accessory digestive organs (liver, gall bladder, pancreas)
  2. The renal-urinary system (metanephros)
    • Kidneys
    • Ureters
    • Bladder
  3. The reproductive system (mesonephros)
    • Gonads (although the testes become located outside the abdomen during development)
    • Uterus, Fallopian tubes, & Vagina
    • Prostate & Vas deferens

The other abdominal organs are:

  • The spleen (accessory circulatory organ)
  • The suprarenal glands (endocrine)

Also present are the components of the circulatory system (arterial, venous, lymphatic) and nervous system that supply the organs and tissues of the abdomen.


Abdominal cavity and peritoneum: One of the most obvious and important features of the abdomen is that it contains a large cavity. This ‘space’ is mainly filled with components of the gastrointestinal tract – even though it is described as a cavity, don’t imagine that it is some sort of empty space, as is tightly packed with various digestive organs. Any ‘space’ within the cavity that is not filled with this organs is filled with serous fluid, but the volume of that fluid-filled space is very small compared with the capacity of the abdominal cavity.

The abdominal/peritoneal cavity develops as the coelom and its purpose is principally to provide a space for the liver, the stomach, and 4-6 metres of gut; these are thus referred to as ‘intraperitoneal’ organs. Having a cavity (as opposed to loose connective tissue) allows room for the intestines to coil extravagantly during development, which in turn is required to allow 4-6 metres of gut to be contained in the abdominal region. It also allows some mobility for the stomach and intestine to expand and contract as they process food.

The cavity is lined with a thin membrane, the peritoneum. Around the front and the sides of the inside of the cavity, the peritoneum forms a lining that separates the abdominal cavity from the body wall (much like a bin-liner inside a bin). At the back of the cavity, however, the peritoneum is folded; these folds project into the abdominal cavity and enclose the intraperitoneal organs that lie within the cavity.

GIT fig1

Between the intraperitoneal organ and the edge of the cavity, these folds help to anchor and support the organs. If they contain significant blood supply and fat, they are termed mesenteries or mesocolons; if they contain mainly fat then they are called omenta; and if they contain little apart from the double payer of the peritoneal fold then they are called ‘visceral’ ligaments (not to be confused with the ‘real’ ligaments of the musculoskeletal system).

GIT fig2


A fundamental concept to understand is that there is a single layer of peritoneum involved with all of these structures. The lining of the abdominal cavity, the folds that make up the mesenteries, omenta, and visceral ligaments, and the peritoneum that surrounds the intraperitoneal organs, are all parts of a single layer of peritoneum. Where the peritoneum lines the abdominal cavity (i.e. where is adjacent to the body wall) it is termed the ‘parietal’ peritoneum, and where it lines the folds and the intraperitoneal organs it is terms the visceral peritoneum; but it is all one single, connected layer.


Intraperitoneal and extraperitoneal organs: if the purpose of the peritoneal cavity is to provide room for elongated bits of gut tube, then it follows that the intraperitoneal organs are going to belong to the GIT; sure enough, the stomach and most of the intestines are intraperitoneal. The other intraperitoneal organs are the liver, gall bladder, and spleen. All of the other visceral organs in the abdomen are extraperitoneal: the pancreas, suprarenals, kidneys, ureters, bladder, and reproductive organs, as well as the major vessels and nerves of the region.

As it develops, the guts forms a twist and elongates. It starts out being entirely intraperitoneal, anchored to the posterior wall of the abdominal cavity via the mesenteries. As it grows, however, some sections become secondarily directly attached to the posterior wall of the cavity: the duodenum, the ascending colon, and the descending colon. These parts are secondarily extraperitoneal. Most of the gut remains intraperitoneal. The stomach and the liver develop with a dorsal and a ventral mesentery, which end up as various ligaments of the lesser and greater omenta. The intestines have only a dorsal mesentery.

Git fig3


One last concept: the extraperitoneal organs that lie behind the posterior part of the cavity (i.e. against the posterior body wall) are termed retroperitoneal. This include the duodenum, pancreas, spleen, suprarenals, kidneys, ascending and descending colon, as well as the aorta and inferior vena cava and their major branches, and the main nerves derived from the lumbar plexus. The extraperitoneal organs that lie in the pelvic part of the cavity, underneath the peritoneum in the pelvis, are termed intraperitoneal and include the bladder, uterus, vagina, prostate, and rectum, the internal iliac arteries and veins and their major branches, and the nerves of the sacral plexus. Note that, when the bladder and uterus enlarge as part of their function (urine storage and pregnancy respectively), they protrude markedly into the peritoneal cavity.

GIT fig4a

 GIT fig4b

Simplified ‘sagittal’ section of abdomen, showing peritoneum and peritoneal folds (mesenteries, omenta, peritoneal ligaments) in pink, major abdominal organs in blue, and main arteries in red. Extraperitoneal tissues are indicated (green stipple). Note that the volume of the intraperitoneal cavity is much less that indicated in this diagram. Colour scheme is as for earlier figures, except that muscle+bone tissues are shown as grey dots.


Relations to surface anatomy: lying immediately under the diaphragm, the liver, stomach, and spleen are high up in the abdominal cavity and are almost entirely protected by lower part of the rib cage. The kidneys lie just below the ribs at the back. The pelvic organs are located within the true pelvis (i.e. much lower that the iliac crests, which are the top of the false pelvis). The rest of the space is taken up by the intestines. The transverse colon crosses across of the front of the abdomen high up, just below the sternum, and the colic flexures (where ascending and descending colons join to the transverse colon) are very high up, right under the diaphragm and also protected by the rib cage.

Physicians divide the abdomen (as seen from anteriorly) into regions to help diagnosis. There are two common schemes; a division into 9 segments, or a system of four quadrants (see lecture notes).

Gastrointestinal tract: major regions and blood supply: The GIT is subdivided into three regions:

  1. Foregut: oesophagus, stomach, first 2/3 of duodenum. The liver and pancreas are considered to be associated with this region.
  2. Midgut: last 1/3 of duodenum and the rest of the small intestine (jejunum, ileum), ascending colon, first 2/3 of transverse colon.
  3. Hindgut: last 1/3 of transverse colon, descending colon and sigmoid colon, rectum, anus.

These divisions are functionally significant (they are sites of different stages in the digestive process), but also reflect blood supply and perception of sensory information from the gut. In the thoracic cavity, the foregut is supplied by oesophageal branches from the aorta, whilst in the abdominal cavity it is supplied by the celiac trunk. Innervation is via the celiac ganglia and thence the celiac, hepatic and splenic plexuses.

The midgut is supplied by the superior mesenteric artery (‘SMA’), which branches extensively to supply the jejunum, ileum, caecum, ascending colon, and most of the transverse colon, as well as anastomosing with the celiac trunk via the inferior pancreaticoduodenal arteries and the inferior mesenteric artery via the marginal artery of the colon. Nerve supply is via the superior mesenteric plexus.

The hindgut is supplied by the inferior mesenteric artery (‘IMA’), which supplies part of the transverse colon, all of the descending and sigmoid colons, and the superior rectum. Nerve supply is via the inferior mesenteric plexus.



Nerves and vessels of the lower limb: the rule of 3

Sometimes we can use a little bit of knowledge of embryology, evolutionary history, or biomechanical function to gain some insight into some complex anatomy. Other times, we just need to remember one simple thing. Even just one number. Welcome to the nerves and vessels of the lower limb; to start off, you need to understand the major nerves and major arteries, and the your number that you need to remember is three.

We’ll start with nerves – specifically, the main nerves that supply motor innervation. There are three compartments in the thigh. There are three passages from the pelvis into the thigh: the femoral canal leads into the anterior compartment, the obturator canal leads into the medial compartment, and the sciatic foramen leads into the posterior compartment. If you spend 5 seconds looking at a skeleton, it becomes ridiculously obvious that those passages must lead into those compartments.

In a move of audacious obscurity, the nerve that runs through the femoral canal into the anterior compartment is called the femoral nerve. The nerve that runs through the obturator canal into the medial compartment is the obturator nerve. And the nerve that runs into the posterior compartment through the sciatic foramen is the sciatic nerve (ok, so the sciatic nerve is really a bundle of two nerves running together in one sheath, but we’ll stick with the 3 nerves / 3 passageways / 3 compartments story for now; it makes learning the initial framework much easier).

Nerves - thigh

Neither the femoral nerve nor the obturator nerve supply any motor innervation below the knee. All of the motor innervation to the leg and foot is via the sciatic nerve – or, more correctly, the tibial and fibular nerves. There are three compartments of the leg (= crus): posterior, lateral, and anterior. The tibial nerve innervates the posterior compartment, exiting the popliteal fossa between the heads of gastrocnemius and travelling in the deep part of that compartment. The fibular (= peroneal)  nerve exist the popliteal nerve inferior-laterally, wrapping around the head of the fibular and then splitting into a nerve that innervates the lateral compartment, and a nerve that innervates the anterior compartment. Proximal to that split, it is called the common fibular nerve. The first branch, innervating the lateral compartment, doesn’t have to travel far from the popliteal fossa so it is called the superficial fibular nerve. The branch that goes to the anterior compartment has to go somewhat further so it is called the deep fibular nerve.

Nerves - leg

The foot also has three main motor nerves innervating dorsal and plantar intrinsic muscles. The deep fibular nerve supplies the anterior compartment of the leg, then runs in front of the ankle to supply the dorsal foot. The superficial fibular does not provide any motor innervation to the foot (although it does supply sensory innervation). Tibial nerve, after innervating the muscles of the posterior compartment of the leg, runs through the tarsal tunnel (behind the medial malleous) and enters the plantar tissues of the foot; it then splits into the medial and lateral plantar nerves, which between them innervate all of the ventral (plantar) intrinsic foot muscles (i.e. All of the intrinsic foot muscles except Extensor Digitorum Brevis, which is innervated by deep fibular nerve).

Nerves - foot

Three is also a good number to remember for the arteries. In the thigh, the femoral artery runs into the anterior compartment through the femoral canal (it sits next to the nerve underneath the inguinal ligament). Likewise, the obturator artery runs through the obturator canal into the medial compartment. There is (usually) no large artery next to the sciatic nerve; the third major artery of the thigh is a large branch off the femoral, called the deep femoral artery (profunda femoris). The profunda femoris actually supplies most of the muscles of the thigh via its three perforating branches;  the quads, the hamstrings, and even a good part of the adductors (the obturator artery is pretty small). The femoral artery has some small branches as it descends the thigh particularly to sartorius), but mostly it is concerned with supplying the tissues of the knee and below.

LL Arteries

It doesn’t make much sense to run an artery across the front of the knee, so the femoral artery moves medially from the anterior compartment to the posterior compartment, entering the popliteal fossa through the adductor hiatus and thence becoming the popliteal artery. It gives off some genicular branches to the knee, and then runs into the posterior compartment of the leg. High up, it splits into an anterior tibial and a posterior tibial artery; the anterior tibial runs through the interosseus space above the membrane, and then supplies the anterior compartment of the leg. The posterior tibial artery runs down the posterior compartment, deep to gastrocnemius and soleus, and its supply of the posterior compartment is helped by a lateral branch that runs behind the fibular in the posterior compartment; the fibular artery. There is no separate artery of the lateral compartment – it is supplied by perforating branches of the fibular artery.

Much like the nerves, the dorsal foot is supplied by a continuation of the artery in the anterior compartment; the anterior tibial artery enters the foot medial to the Extensor Digitorum Longus tendons and becomes the dorsal pedal artery. The posterior tibial artery runs through the tarsal tunnel, next to the  tibial nerve behind the medial malleolus, and splits into the medial and lateral plantar arteries to supply the ventral foot.

So the number of the lower limb is three. Three major arteries and three motor nerves in the foot (with very similar locations and names). Three motor nerves in the leg – one for each compartment), and three major arteries: two posterior, one anterior, none lateral. Just remember that there is one tibial nerve, and two tibial arteries, and you’ll get the names right. Finally, in the thigh, there is a motor nerve for each of the three compartments, but there are two major arteries in the anterior, one in the medial, and none in posterior. Once you are comfortable with that basic framework, then you can add on the cutaneous nerves and the smaller arterial branches.

Cranial Nerves: a starter

Learning the cranial nerves is one of those rites of passage for students of anatomy; they are seen as complicated, difficult, and arranged without any rhyme or reason. Medical students have come up with various complex (and unrepeatable) mnemonics in an effort to try to tame this nest of anatomical vipers. The ‘cranial nerve week’ is often viewed with trepidation by teachers and students  alike.

This is a shame, because with a little bit of embryology the cranial nerves actually make a lot of sense. Yes, there is some detailed information, but the basic framework of cranial nerves is not hard to grasp.

To ‘get’ cranial nerves, you need to understand 3 basic things about the head and neck:

  • The cranial nerves are (mainly) peripheral nerves of the head and throat.  As such, they innervate head tissues that lie outside of the braincase, and they innervate the throat. They are not concerned with the brain or the ‘vertebral’ part of the neck.
  • The tissues innervated by the cranial nerves are:
    1. The special sensory organs: nose, eyes, ears.
    2. The somatic muscles of the head: extra-ocular muscles, and muscles of the tongue.
    3. The pharyngeal arches (the visceral part of the head and neck) and associated tissues
  • Head segments in front of the ear (pre-otic) are innervated by one cranial nerve per segment, whilst head segments behind the ear (post-otic) are innervated by one cranial nerve for multiple segments.
CN diag.png
Tissues innervated by cranial nerves: special sensory capsules (green), head somites (red), and pharyngeal arches (dark blue). CNS structures of head  and neck shown in light blue.

Understanding this, we can group the 12 cranial nerves into three groups:

  1. The cranial nerves that collect sensory information from the olfactory, optic, and vesitibulo-cochlear sensory apparatus: the Olfactory (CNI), Optic (CNII), and Vestibulocochlear (CNVIII) nerves. These can grouped as the ‘special somatic sensory’ cranial nerves
  2. The cranial nerves that innervate the somatic muscles of the head. There are three pre-otic sets of muscles that form the extra-occular muscles, each innervated by  their own nerve: Oculomotor (CNIII), Trochlear (CNIV), and Abducens (CNVI). The post-otic somites form the tongue muscles, and are innervated by a single motor nerve, Hypoglossal (CNXII).
  3. The pharyngeal arches are innervated by five cranial nerves. The first three arches each get their own nerve: the first arch (jaw) is innervated by Trigeminal (CNV), the second (stapes-styloid-hyoid) by Facial (CNVII), and the third arch (back of the tongue/top of the throat/hyoid) by Glossopharyngeal (CNIX). The fourth and sixth arches (most of pharynx, all of larynx) are innervated by Vagus (CNX), with some help (to some neck muscles) from Accessory (CNXI).

CN diag 2

Note that the third group of cranial nerves do some multi-tasking; they innervate:

  • Skin of the face (General Somatic Afferent).
  • Glands of the head (General Visceral Efferent – these are all parasympathetic fibres).
  • Muscles and mucosal tissues of the pharyngeal arches (Special Visceral Efferent, General Visceral Afferent).
  • Taste (Special Visceral Afferent).


Thus we get the following summary:

Cn table


This can be expanded to include the specific tissues innervated by each nerve:


CN table 2

Once you are comfortable with that basic framework of the cranial nerves, then have a look at how their nuclei and columns (General Somatic Efferent, Special Visceral Afferent, etc)in the brainstem are organised:

Lower limb muscles 2: thigh and leg

Thigh muscles and leg (crus) muscles are the lower limb equivalents of the arm (brachium) and forearm muscles. If you compare the thigh and arm muscles, focusing on their embryological compartments and action at the knee/elbow:

Thigh vs arm mm table

then it is clear that the Quadriceps and Triceps are equivalent (dorsal muscles, extensors of the mid-limb joint). The Hamstrings are doing the same thing as the Biceps and Brachialis muscles in the arm: located ventrally, flexing the mid-limb joint. Even the Adductors have an equivalent in the arm, Coracobrachialis, which like most of the medial thigh muscles works to adduct the proximal limb joint and does not work on the mid-limb joint.

The reason why these similarities are not always obvious is because of the way that the limbs rotate differently to move from their embryological orientation to the Anatomical position. The upper limb is simply adducted so that the dorsal side lies posteriorly, whilst the lower limb is adducted, extended, and medially rotated – three sets of 90 degree rotations which result in the dorsal side of the leg being held anteriorly. Equivalent muscles such as the Triceps and Quadriceps end up on opposite sides of the Anatomically positioned limbs, and so their actions across the proximal limb joints look opposite; long-head of Triceps extends the shoulder, whilst rectus femoris of Quadriceps flexes the hip. Likewise, Biceps brachialis is a flexor (and adductor) of the shoulder, but the Hamstrings extend the hip. But once you get down to their actions on the mid-limb joint (knee and elbow), the similarities in these dorsal and ventral muscles become clear.

There are some differences between the limbs, of course, and beyond their different rotations  during development this is largely a result of the locomotory demands upon the lower limb. Overall, the lower limb is stronger and more muscular than the upper, with strong fascia and more aponeurotic attachment of muscle. Quadriceps is much larger than Triceps (and even gets  an extra head), and the hamstrings are also larger than their brachial counterparts. One of the most obvious differences is that the Adductors of the thigh are large enough to warrant their own anatomical compartment, whilst their upper limb counterpart has become so small that it is grouped with the elbow flexors and often forgotten. This shrinking of the Coracobrachialis is one of the most obvious examples of the consequences of human bipedality; the Coracobrachialis in a quadrupedal monkey is much larger, almost the size of the Adductors.

The table above shows a couple of extra muscles of the thigh that do not have equivalents in the arm. The first one, Sartorius, is interesting: it can be used to help stabilise the knee in full extension (standing with the knees locked), but as soon as the knee is flexed by the hamstrings it becomes an additional flexor of the knee. It also flexes the hip, and being a long, parallel-fibred muscle, it is capable of very rapid shortening; this makes it well suited for rapidly flexing knee and hip, thereby raising the foot, during the recovery stroke of running. The second muscle, Gracilis, is the one part of the adductor set that does cross the knee joint. There is no muscular counterpart in the upper limb, but in other primates the large Coracobrachialis often has a thin muscular head that crosses the elbow and this confirms the evolutionary similarities between the Adductors and Coracobrachialis.

Looking at a diagrammatic cross section of the thigh and arm, we can see some of those similarities and differences:

Thigh vs arm mm diag

The thigh has more muscles (it’s stronger), and those muscles are much bigger than those of the arm (again, it is stronger). We can also see another important feature; the dorsal extensor compartment of the thigh is huge, occupying about 3/4 of the space, whilst the extensor compartment of the arm occupies about half, sharing more evenly with the flexor compartment. This asymmetry of dorsal/ventral muscle compartments is seen throughout the leg; the hip extensor is much larger than the flexor, the ankle flexors are much larger than the extensors, and this is directly related to the biomechanics of the lower limb. Propulsion is produced by a combination of hip extension, knee extension, and ankle flexion, and the requisite muscles are much larger so they can act together to produce this power stroke. Conversely, the muscles that produce the recovery stroke – hip flexors, knee flexors, ankle extensors – are much smaller. The general purpose usage of the arm means that the extensors and flexors are more closely balanced in size.



Distal limbs

Looking below the knee, the similarities between the leg (crus) and forearm (antebrachium) are still strong (although they are not always obvious). Recall the diagrammatic summary of the forearm muscles (this diagram is explained here:

Forarm mm

When we compare the long muscles of the leg to this, then we can see some clear similarities:

  • There are a set of  ankle stabilisers that are equivalent to the wrist stabilisers (green)
  • There are superficial (red) and deep (blue) flexors and extensors of the digits.

Forearm vs leg mm

There are also some muscles (black font) which do not have clear equivalents between the limbs. Brachioradialis of the forearm has no counterpart in the leg. The large muscles of the calf, Gastrocnemius and Soleus, have no clear counterparts in the forearm; this makes some functional sense, as Gastroc. and Soleus insert onto the heel bone (calcaneal tuberosity) and play an important role in powering locomotion. There is no equivalent of the heel in the wrist.

After allowing for these large ankle flexors, the two flexor compartments are largely similar. There is a small superficial muscle that doesn’t appear to do much and is disappearing from human populations (Plantaris = Palmaris Longus), a deep flexor of the hallux (Flexor Hallucis Longus = Flex. Pollicis Longus), and a deep flexor of the other digits (Flexor Digitorum Longus = Flexor Digitorum Profundus). The forearm muscle that is missing in the leg is Flexor Digitorum Superficialis; as we will see later, this muscle has not so much disappeared but moved – it has become shorter and is now an intrinsic muscle of the foot. This means that the deep extrinsic flexor of the digits is now the only long digital flexor present, so its name has been changed from Flex. Digit. Profundus to Flex. Digit. Longus.

The extensor compartments are also similar, but again with less muscles than in the forearm.  Extensor Digitorum Longus is equivalent to the superficial extensors of the forearm, Extensor Digitorum and Extensor Digiti Minimi (without the separate muscle belly to the little toe). But the deep muscles of the forearm are much reduced in the leg. Extensor Hallucis Longus is present as an equivalent of Ext. Poll. Longus, but given that the hallux does much less abduction than the thumb, the absence of  an equivalent muscle to Abductor Pollicis Longus might not surprise us. However, the equivalents of Extensor Indicus and Extensor Pollicis Brevis are present in the lower limb; as with Flexor Digitorum Superficialis, they have become shorter and are now intrinsic foot extensors (which we will look at later).

There are some odd things about the leg, which are hard to explain but need to be remembered. The first is that Flexor Hallucis Longus and Flexor Digitorum Longus originate from the opposite sides of the leg to the digits they act on: FHL originates from the fibular side and acts on the hallux (a tibial digit), whilst FDL does the opposite. Their tendons cross over in the foot. I do not know of a good reason to explain this, but it is a very consistent pattern. The other peculiar feature of the leg is the lateral compartment: this contains two muscles, Fibularis Longus and Fib. Brevis. From innervation (via the Common Fibular Nerve), the lateral compartment (along with the anterior) is a dorsal compartment of the leg, but the tendons of these muscles run  behind the ankle joint and work as flexor-stabilisers of the  ankle, equivalent to Flexor Carpi Ulnaris (which is a ventral muscle).  Again, it is not clear why this happens.

One last muscle of the leg remains. High up,  behind the knee joint, there is short, oblique muscle that lies deep in the popliteal fossa, named Popliteus. Like Anconeus in the arm, it is a posterior stabiliser of the mid-limb joint and is sometimes grouped with the thigh muscles (as Anconeus is often grouped with the arm muscles). Popliteus is a deep ventral muscle, however, and Anconeus is a superficial dorsal muscle, so we shouldn’t think that these are developmentally equivalent.

Lower limb overview, and hip muscles

In many introductory anatomy courses, the lower limb (that’s the leg* to most people) is presented after you’ve been taught the anatomy of the arm. This is a useful approach: the human upper limb is a fairly generic example of the mammalian version of the pentadactyl limb, and if you needed to teach the comparative anatomy of forelimbs in animals as diverse as bats, moles, horses, and dolphins you could do worse than use the human anatomy as a basic anatomical model. The forelimbs in all these species is simply a modified version of the basic pattern we seen in the human upper limb. To some degree, this is also true of the human lower limb; it shares the same underlying pattern, with some modifications that can be understood in terms of its specialised locomotor biomechanics.

* In anatomy, the ‘leg’ refers strictly to the part of the lower limb between the knee and the ankle. (i.e. the calf and  shin). To everyone else, it’s the whole lower limb. This is one of the few instances where anatomical terminology has taken a perfectly good English word and redefined it to mean something different to its common usage (the other example is ‘arm’). It is both confusing and annoying, especially since the discipline usually avoids doing this; where a precise term is needed, it is usually coined using latin and/or greek roots to produce a new word.  Redefining common English words is something that happens often in Physics and Engineering, but Anatomy is usually better than that.

First, let’s start with the similarities (bones and joints):

  • Both limbs are attached to the axial skeleton via a limb girdle
  • There is a single long bone proximally, then a pair of long bones, then rows of 3-4 short bones, finishing in 5 digits
  • In both limbs, the proximal joint (shoulder/hip) is a ball and socket joint, and the mid-joint (elbow/knee) is essentially a hinge. The metacarpal/metatarsal-phalangeal joints are ellipsoidal and the interphalangeal joints are hinge joints.
Skeleton_antomical position 1
Human postcranial skeleton, showing the limbs held in the Anatomical Position. Note that the pollex and hallux – which are each digit 1 of their limb – are held on the lateral and medial sides of the limb respectively.

These similarities be come even more obvious if both limbs are visualised in the embryological position (easy to do for the upper limb; somewhat harder for the lower!).

Skeleton_embryological position 1
Human postcranial skeleton, with the limbs held in the Embryological Position (please do let me know if you can still do this — for most people, the last time you did this you were in utero!). The similarities between the limbs are clear; the radius and tibia line up, as do the pollex and hallux. Flexion of the limb joints is a movement towards the ventral surface in this position, while extension is a dorsal movement. To get into the anatomical position, the upper and lower limbs are rotated differently: the upper limb is simply adducted, whilst the lower limb is adducted, extended, and medially rotated. This results, for example, in the anterior compartment of the thigh (named after its location in the anatomical position) being built as a dorsal compartment in the embryo.

Doing this, it is clear that:

  • Flexion of limb joints is a ventral movement (extension is movement in the dorsal direction). Notably, in the embryological position, the mid-limb joints (elbow and knee) flex in the same direction.
  • The radius and tibia are seen to be equivalent (homologous) bones.
  • The first digits (pollex and hallux) line up as the digits closest to the head (cranial) side of the hand/foot (these homologous digits end up on opposite sides in the anatomical position).
  • The lesser tuberosity and trochanter (of the humerus/femur) both ‘point’ towards the head, whilst the greater tuberosity/trochanter project dorsally.

Although the  similarities between the limbs are striking, there are also some differences:

  • The pelvic girdle is a large, robust, made of three fused bones, and joined strongly to the sacral vertebrae. In contrast,  the pectoral girdle is made from two comparatively gracile bones that are not fused and which are  only weakly joined to the axial skeleton.
  • The range of movement at the proximal ball and socket joint is large at the shoulder, much less so at the hip.
  • Instead of an olecranon at the elbow, there is a large sesamoid bone at the knee
  • Of the distal long bones, only the tibia contacts the femur proximally, but both the fibula and tibia contact the tarsals. In the upper limb, both radius and ulna contact the humerus, but only the radius contacts the carpals.
  • Three carpal bones contribute to the (wrist) radio-carpal joint, but only one tarsal (the talus) to the ankle.
  • Still with the distal limb joint, the wrist is biaxial (ellipsoidal), but the ankle is uniaxial (hinge).
  • The forearm can pronate/supinate, but the leg (calf+shin) cannot.
  • The carpals are small, with minor movements between them. The tarsals are large, capable of a large range of motion (inversion/eversion of the foot), and form a strong arch structure.
  • The fingers are long, but the toes are short. In the hand, the first digit is strong but is shorter than the other fingers; in the  foot, the hallux is robust and usually the longest digit.

Many of these differences relate (unsurprisingly) to the different biomechanics of each limb; the lower limb is specialised for some reasonably complex locomotor biomechanics, but the human upper limb is used minimally for locomotion and it mainly a general-purpose tool for manipulation. We’ll look at these links between anatomy and biomechanics later.

Muscles: I think the easiest way to learn the muscles is to group them by region:

  1. Hip muscles
  2. Thigh muscles
  3. Leg (shin and calf muscles)
  4. Intrinsic foot muscles

The muscles are grouped by the location of the main muscle belly. For example,  some thigh muscles work across the hip joint, others across the knee (some do both), but the main mass of these muscles is located in the thigh.

We’ll look at the hip muscles first. These are a bit simpler than the shoulder muscles: recall, when learning the shoulder muscles, they can be grouped into three functional categories:

  1. Muscles that move/stabilise the pectoral girdle: Trapezius, Rhomboids, Levator scapulae, Pectoralis minor, Serratus anterior. These muscles act between the girdle and the axial skeleton – they do not attach to the humerus and therefore do not act on the shoulder (glenohumeral) joint
  2. Shoulder stabilisers: the four rotator cuff muscles (Supraspinatus, Infraspinatus, Subscapularis, and Teres minor).
  3. Shoulder prime movers: the big muscles that move the humerus at the glenohumeral joint: Pectoralis major, Deltoid, Latissimus dorsi, Teres major.

Unlike the shoulder, the pelvic girdle is firmly attached to the axial skeleton and so we don’t need muscles to hold it in place. Thus, the hip muscles consist basically of two groups: small deep stabilisers, and large prime movers. All of these muscles work across the hip joint.

The prime movers of the hip are large, powerful muscles and they attach to the large iliac blades (the function of the iliac blades is essentially to provide muscle attachment).  The blades are angled so that their anterior surface (iliac fossa) faces forwards and slightly medially, whilst the posterior surface (gluteal fossa) faces backwards and laterally. The muscle that arises from the iliac fossa – Iliacus, helped by Psoas major from the lumbar region – runs across the front of the hip joint, inserts onto the lesser trochanter of the femur, and therefore acts as an flexor of the hip.

Conversely, the three gluteal muscles are positioned within the gluteal fossa to act as hip extensors and abductors. Gluteus maximus originates in the lower half of the fossa, runs behind the hip joint, inserts onto the posterior femur (at the gluteal tuberosity) and the iliotibial band (ITB), and works as a powerful extensor of the hip. The ‘deep glutes’, Gluteus medius and Glut. minimus, originate from higher up on the fossa, run laterally above the hip joint, and insert onto the top of the greater trochanter: these attachments allow them to work as hip abductors.

The deep stabilisers (six muscles) lie in two locations:

  1. Four muscles lie deep in the inferior part of the gluteal fossa, deep to Gluteus maximus and inferior to Glut. med and Glut. min.: Piriformis, the two Gemelli, and Quadratus femoris.
  2. Two muscles lie on either side of the obturator foramen: Obturator internus, and Obturator externus.

All of these muscles insert onto the greater trochanter, the intertrochanteric ridge, or the trochanteric fossa at the back of the femur; thus, their action (in addition to active stabilisation of the hip joint) is to laterally rotate the femur at the hip. This provides the most common name for this group, the ‘deep lateral rotators’.

There are two other muscles to be aware of that act on the hip joint. These are smaller than the big prime movers, and are located right at the top of the thigh, so they are sometimes grouped with the thigh muscles. They are both at the front of the thigh. One originates from the pectineal line on the superior pubic ramus, and runs in front of the hip joint to insert high on the medial aspect of the femoral shaft: this is Pectineus. It can help adduct and flex the hip, but it is also providing active stabilisation at the front of the hip joint (recall that the deep stabilisers are mainly at the back of the joint).  The other muscle arises from the front of the iliac crest, just behind the ASIS, and runs laterally down to the front of ITB, just in front of where Gluteus maximus attaches onto the ITB from behind. Its job is interesting: as Glut. max. acts on the ITB (which is part of the fascia lata of the thigh), this smaller muscle tenses the ITB to hold it tight so that Glut. max. doesn’t pull the ITB backwards under the skin. All of the force developed by Glut. max. is therefore used to extend the femur against the hip, rather than moving the fascia lata around. The name of this smaller muscle at the front is thus Tensor fasciae latae.

So we can summarise hip muscles:

Hip muscles table.png

Cranial Nerves: principles

(If you are new to cranial nerves, then try this starter for a very basic overview.)

In humans, the cranial nerves are the first dozen nerves of the peripheral nervous system. As their name suggests, they are located at the head end of the animal. Where the spinal nerves connect to the CNS at the spinal cord, the cranial nerves connect directly to the brain, and although there are some basic similarities between cranial nerves and their spinal counterparts, there are some important differences and quite a lot of extra detail. As students of head and neck anatomy, you need to understand them.

  • Edits: 24/10/2017 for some typos, and a footnote concerning CN I and II
  • 19/10/2017 to include figures and update notes on the categories of cranial  nerve nuclei).


Grey matter  nuclei in the Central Nervous System

In order to do this, we need to understand the fundamental pattern of how peripheral nerves connect to the CNS, and the spinal nerves are actually a good model for this. As we’ve seen earlier, the sensory nerves enter the spinal cord via the dorsal roots, while the effector nerves leave via the ventral roots. All of these nerves connect directly to the grey matter in the centre of the cord; the sensory nerves to the projection of grey matter on the dorsal surface (the dorsal horn), the effector nerves to the projection on the ventral surface (the ventral horn). Connections within the grey matter are further organised so that somatic and visceral neurons are grouped together into grey matter nuclei. If you look at a cross section of the spinal cord, those nuclei always line up as follows: the Somatic Sensory most dorsally, then the Visceral Sensory nuclei, then the Visceral Motor nuclei, and then finally and most ventrally, the Somatic Motor nuclei. The spinal cord is of course bilaterally symmetrical, so there are a pair of each nuclei, one on each side.  This pattern is repeated along the entire length of the spinal cord.

CN Fig 1 Spinal cord nuclei

That same pattern is also present in the brain stem; make a cross section of the medulla or pons, and you will find the nuclei lined up in the same order. But in the brainstem, we have some additional nuclei that relate to some ‘special’ features of the head; the special senses (smell, sight, hearing and balance, and taste), and the special motor pathways involving the skeletal muscles of the pharyngeal arches. Specifically, there are two additional types of special sensory nuclei: one Special Somatic sensory group (the vestibulocochlear nuclei are a good example), and a Special Visceral sensory group (which deal with taste sensory input).  And, because we have pharyngeal arches in the head and neck, we also have a set of nuclei for the motor nerves that go to the skeletal muscles derived from these pharyngeal arches. Another name for the pharyngeal arches is branchial arches (note the “n”; these are not brachial, which relates to the anatomy of the arm), and so these nuclei are sometimes called branchiomeric. Because the pharyngeal system is a special part of the visceral system, these are known as Special Visceral motor nuclei; they lie in between the normal, or ‘general’, visceral motor nuclei and the general somatic motor nuclei on the ventral margin of the brainstem.

Note that, as the ventricles in the brain are larger than the central canal of the spinal cord, the edge of the grey matter has in effect rotated slightly so that the most dorsal nuclei are actually dorso-lateral, and the most ventral are ventro-medial.

CN Fig 2 Brainstem nuclei

We now have seven grey matter nuclei on each side of the brain stem, instead of the four present in the spinal cord. With the additional nuclei, the official terminology changes to accommodate the extra ones. The four nuclei that are the same as the ones in the spinal cord are known as General nuclei, whilst the three that are in the head only are Special. This gives us:

  • The nuclei for the special sensory capsules are Special Somatic Afferent (the nasal, optic, and otic capsules are derived from somatic tissues). These nuclei lie most dorso-laterally in the brain stem*.
  • The nuclei for the somatic sensory nerves are thus General Somatic Afferent, to distinguish them from the special ones.
  • The nuclei for the taste receptors are Special Visceral Afferent; these are situated between the GSA and the GVA columns.
  • The nuclei for the visceral sensory nerves are the General Visceral Afferent.
  • For the visceral effector nerves – in the brain, these are all parasympathetic nuclei – we have General Visceral Efferent nuclei.
  • The branchiomeric motor nerves, which innervate the muscles derived from the pharyngeal arches, are connected to the Special Visceral Efferent nuclei.
  • Finally, the somatic motor nerves connect to the General Somatic Efferent nuclei (these are situated most ventromedially on the brain stem).

[* Strictly speaking, this map of the cranial nerve nuclei applies to cranial nerves III to XIII, as Cranial Nerves I and II belong to the forebrain, i.e. they are rostral to the brainstem. Remember that the brainstem is located in the mid- and hindbrain. CN I and CNII are grouped with CNVIII in the scheme below because these three innervate special sensory capsules derived from somatic tissues. My advice is to not worry about this when you are learning the cranial nerves themselves – in which case the scheme presented below works well – but be aware of this detail if/when you need to know the details of the cranial nerve nuclei in the brainstem.]

Another difference between these nuclei in the spinal cord versus the brainstem: the grey matter nuclei run as continuous columns along the spinal cord, with spinal nerves regularly coming off the cord at each vertebral segment. In the brainstem, however, the cranial nerve nuclei are much less continuous; if you map them on a longitudinal section then most of the nuclei appear as distinct regions along the length of the pons  or medulla (the exceptions are the nuclei for the vagus/accessory, the hypoglossal, and especially the trigeminal).

One final difference before we look at the cast of cranial nerves: in the spinal cord, the somatic sensory and visceral sensory nerves connect to their grey matter nuclei via the dorsal roots, and the visceral and somatic effectors leave via the ventral roots, but all the nerves come together in a single mixed spinal nerve (for that segment) before splitting into the rami.

CN Fig 3 psinal nerve

With the cranial nerves, however, the Special Sensory Afferent nuclei form their own nerves and they never share. Similarly, the General Somatic Efferent nuclei form their own nerves and never share (with one exception). The other five nuclei – the General Somatic Afferent, Special Visceral Afferent, General Visceral Afferent, General Visceral Efferent, and Special Visceral Efferent – are the ones that can share a nerve together, similar to the situation with all of the spinal nerves. As the Special Visceral Efferent nuclei relate directly to the pharyngeal arches, these ‘mixed’ cranial nerves end up being organised around the ancestral/ embryological gill arches; more on that below.

This pattern of sharing/not sharing results in 3 basic types of cranial nerves:

  1. Cranial nerves to the special sensory capsules, derived from Special Sensory Afferent nuclei. There are of these: Olfactory (CN I), Optic (CN II), and Vestibulocochlear (CN VIII).
  2. Cranial nerves to the somatic muscles, which are derived from the somites of the head. There are four of these: Oculomotor (CN III),  Trochlear (CN IV), Abducens (CN VI), and Hypoglossal (CN XII).
  3. Lastly, the cranial nerves that contain a mix of the other nuclei. These can contain one or more of GSA, GVA, GVE, or SSE (none of the cranial nerves contain nerves from all of these nuclei, but most contain nerves from at least a couple). Since they contain the branchiomeric motor nuclei, these five  ‘mixed’ cranial nerves line up with pharyngeal arches; at the front, Trigeminal (CN V), then  Facial (CN VII), then Glossopharyngeal (CN IX), and then Vagus and Accessory (CN X & XI). Note that Accessory is, as its name suggests, in effect an additional part of the Vagus nerve that carries only Special Visceral Efferent neurons.

CN Fig 4 three CN types

The 12 cranial nerves

With these principals in mind, we can then map out our three groups of cranial nerves. This is easiest to map out on an embryo, so we start with a basic diagram of the neural tube that will form the Central Nervous System in the head and neck in early embryogenesis. At this stage of development, we can also clearly see the pharyngeal arches.

CN Fig 5.1 brain segments

The three pairs of special sensory capsules are located in the head like so:

CN Fig 5.2 sensory capsules

We also have the somites of the head, which will develop into somatic muscles. These appear next to the neural tube.

CN Fig 5.3 somites

With all these in place, we can list the cranial nerves the supply those structures. Our first group are the cranial nerves to the special sensory capsules (Special Somatic Afferent); CN I (Olfactory), CN II (Optic), and CN VIII (Vestibulocochlear):

CN Fig 5.4 Special Sensory CNs

The next group are the nerves that supply the somites. In front of the ear, each somite is supplied by its own nerve, i.e. CN III (Oculomotor), CN IV (Trochlear), and CN VI (Abducens). Behind the ear, the occipital somites are supplied by one large nerve, the Hypoglossal (CN XII).

CN Fig 5.5 Somatic Motor CNs

The third and final group are the five cranial nerves that supply the pharyngeal arches (and other things). The first arch is supplied by CN V (Trigeminal); this arch becomes the jaws and part of the middle ear, so motor supply to those structures is done by the Trigeminal. The second arch is supplied by CN VII (Facial); this includes structures behind the jaw such as the hyoid and the styloid, but also includes a bunch of muscles that originate behind the ear and migrate forwards to form the facial muscles. Recall that the Facial nerve emerges from the skull behind the jaw joint.

CN Fig 5.6 mixed branchiomeric CNs

The third arch is supplied by CN IX (Glossopharyngeal): this arch forms various soft tissues at the back of the oral cavity/top of the pharynx. Finally, the fourth and sixth arches are supplied by one nerve, CN X (Vagus), similar to how the post-occipital somites are all supplied by one nerve. These arches form, among other things, the cartilages of the larynx. Vagus also supplies the parasympathic nerves to the thorax and abdomen, so there is a large vagal trunk that travels down to the thorax within the carotid sheath. Vagus is also assisted by the Accessory nerve (CNXI), which does some of the branchiomeric motor supply to some large muscles of the neck and shoulder (trapezius and sternocleidomastoidus).

Each of these five nerves in this ‘pharyngeal’ group of cranial nerves carries branchiomeric (Special Visceral Efferent) axons. But these nerves are mixed, so they carry GSA, SVA, GVA, and GVE fibres as well. Not all of them carry all of these. If we look at the parasympathetic fibres (General Visceral Efferent)

CN Fig 5.8 parasympathetics GVE

we can see that Facial, Glossopharyngeal, and Vagus carry these fibres, but Trigeminal does not (Accessory doesn’t either – but it only has Special Visceral Efferent fibres). The parasympathetics also give us the single exception to the rule that the somatic motor cranial nerves never share; Oculomotor includes General Visceral Efferent fibres that it carries to the eye.

As you might expect, General Somatic Afferent fibres are present with each arch. Note that the Ophthalmic (V1) and Maxillary (V2) parts of the Trigeminal only contain GSA fibres, while the Mandibular (V3) contains GSA and SVE fibres. Most general somatic sensory innervation of the head is via Trigeminal, but the Facial, Glossopharyngeal, and Vagus do small amounts.

CN Fig 5.9 somatic sensory GSA

There are no General Visceral Afferent fibres with the first and second arches, but they are present in the others:

CN Fig 5.10 visceral sensory GVA

Finally, we have the special sensory nerves from the taste receptors, the Special Visceral Afferents. These are located on the mucosa of the tongue: this is evidently built from the second, third, and fourth arches because these fibres travel along the Facial, Glossopharyngeal, and Vagus nerves:

CN Fig 5.11 taste visceral sensory SVA

Different textbook versions

The cranial nerves are often presented to students as a long list of complex names, without the evolutionary/developmental framework (outlined above) that allows you to understand them. As such, the different innervation by each nerve seems to be random, and learning them is difficult. To try and simplify the process, some texts reduce the categories of nerve/nuclei types from the seven groups presented here. Although this sounds like a good idea in principle, this requires grouping some of the types together into a joint category, and there is a lack of consistency in how different types get blended together. As a result, trying to marry the scheme presented in one textbook with the scheme presented in another can be very confusing.

Having spent some years trying to work out what different books/websites/lecture notes mean when they are talking about this topic, what follows is a brief guide to making sense of the sometimes contradictory information out there.

  • Scheme 1: 7 types of cranial nerve nuclei and nerve fibres. This is the scheme used here, and by Gray’s Anatomy (the ‘big’ version, currently in its 41st edition). It’s actually a slight simplification, but I think it passes Einstein’s test of explanation (“make it as simple as you can, but no simpler”). I’m happy to discuss those simplifications.
  • Scheme 2: 6 types. You see this a lot; usually, it’s done by merging the GVA and the SVA neurons into a single category, so that taste is no longer a special sense and is part of the visceral sensory system. The anatomical basis for this is quite legitimate; the nuclei for both GVA and SVA are located in the same large grey matter column of the medulla, the solitary nucleus. The only potentially confusing thing about it that taste is widely described as a special sense, but this scheme does not accord it that status.
  • Scheme 3: 6 types. Some books take a more functional approach and merge the special senses, so that taste is grouped with smell, sight, and hearing/balance. The Gray’s ‘for Students’ edition uses this scheme. I’m not a fan of this approach because (a) the SVA columns are not located anywhere near the SSA columns, and (b) using this approach merges our first and third categories of cranial nerves explained above; this essentially destroys our evo-devo story of cranial nerves and takes us back to rote-learning long lists. I don’t like lists.
  • Scheme 4: 5 types. You can go from 7 to 5 a few different ways. One approach is to merge all four of the visceral nuclei into two groups, a visceral sensory and a visceral motor, so that GVA and SVA get lumped together, as do GVE and SVE. I don’t mind this; it allows us to  keep the evo-devo story with the three types of cranial nerves, so it might not be a bad way to first introduce the topic. This is the scheme that I first learnt and it made sense to me at the time. The main issue will be if you ever have to understand the nuclei in the brainstem, which will then require an explanation of special visceral afferents and efferents, but it’s not a bad scheme to start off with.
  • Scheme 5: 5 types. You can also do a few funky things like merge SVA with SSA, and SVE with GSE. The rational for this is that you are (a) treating all of the special senses as one group (see scheme 3 above), and (b) treating all of the motor nerves to skeletal muscle in the head and neck as a single motor group. As discussed above, I’m not a fan of this approach because it is impossible to group the cranial nerves into any of the three evo-devo categories used above, and takes us back to rote learning long lists; from that perspective, this scheme is even worse than scheme 3. By masking the relationship between the cranial nerves and the pharyngeal arches (branchiomeric muscles  are treated as the same as somatic muscles), it obscures one of the most interesting and useful features of head and neck anatomy.








The Central Nervous System

The Central Nervous System (CNS) is a hollow tube situated along the dorsal axis of the animal. Its basic function is to integrate sensory information (which arrive via sensory neurons), and coordinate responses (via effector neurons). It does this through a large number of interconnections within the CNS itself.

Most animals move forwards. In the same way that a car windscreen faces forwards so that you can see what’s coming, the primary visual and other special senses are placed at the front of the animal, in a structure we call the head. These sensory organs continuously collect incoming information: to process it, the front part of the CNS, located in the head, is enlarged into a brain.

Brains are pretty amazing structures. The human brain is quite impressive, as the numbers show:

• 20 billion : neurons in cerebral cortex
• 100 billion : neurons in the brain
• 5000 billion : glia cells
• 60 trillion : synapses in cerebral cortex
• 10,000 : synapses per neuron
• 180,000 km : length of fibre tracts
• 250,000 neurons per minute: max rate of neuron growth (early gestation)
• 60 per minute: loss of neurons from neocortex

Like the spinal cord, the brain has specialist regions, which can be summarised as follows:

CNS organisation-regions

Brain vesicles table

White matter, grey matter

When sectioned, the CNS is made of two types of tissue: white and grey. The white matter is made of nerve axon fibres, i.e. the parts of the neurons that are wrapped in myelinated sheaths (it’s the myelin that makes it look white). The grey matter is where the synapses occur; the grey colour comes from the cell bodies of many thousands of neurons lying side by side. This means that the grey matter is where the information processing happens, whilst the white matter are the neuron tracts conveying information from one part of the CNS to another.

In the spinal cord, the grey matter lies in the middle of the cord, surrounded by white matter tracts. There are about 10 major tracts; each tract is a bundle of millions of axons heading towards the same region. Some of these are afferent, taking information towards the brain, i.e., carrying sensory information; whilst others are efferent, taking information from the brain to the peripheral effectors. The names of each tract look complicated, but the names tell you where the tract is coming from, and where is it going. Hence:
• The spinothalmic tracts take information from the spinal nerves to the thalamus (they are afferent/sensory)
• The trigeminothalmic tracts take information from the trigeminal nerve to the thalamus (afferent/sensory)
• The spinocerebellar tracts take information from the spinal nerves to the cerebellum (afferent/sensory)
• The corticospinal tracts take information from the cerebral cortex to the spinal nerves (efferent/motor)
• The tectospinal tracts take information from the tectum to the spinal nerves (efferent/motor).

You can see from the name of the tract whether it is a sensory or a motor tract. The majority of afferent fibres go to the thalamus, and are then relayed to the appropriate areas of the cerebrum (usually the sensory cortices of the parietal lobes).

Grey matter in the spinal cord: grey matter columns are areas where specific groups of neurons synapse before heading towards the PNS. The afferent neurons arrive into the spinal cord via the dorsal root, so synapse in the dorsal horn. The efferent neurons leave via the ventral root, so they synapse in the ventral horn. The visceral neurons lie more in the centre line, whilst the somatic neurons synapse on the tips of the relevant horns.

Fig: Grey matter columns in dorsal and ventral horns:

In the telencephalon, the different parts of the cerebral hemispheres show highly regionalised grey matter connections. The cerebral cortex (i.e. the parts on the outside of the tube in the telencephalon) gets a lot of attention when talking about brain function, and it does do a lot:
• conscious and subconscious processing of information
• assessment and planning of action
• initiation of motor responses
• storage of long term memory

But there are some deeper parts of the cerebrum, in conjunction with structures in the diencephalon and mid-brain, that perform important functions:
– Basal nuclei: responsible for fine tuning motor activity and connecting involuntary responses
– Limbic system: moderates arousal, fear, aggression, hunger – the basic ‘urges’. Also important in processing short term memories.

These systems are often shown as deep, twisting structures somewhere within the brain. They are made of grey matter nuclei in the forebrain (both the telencephalon and the diencephalon) and midbrain. Mostly, they lie deep to the cerebral cortex, although they do involve a couple of deep, infolded parts of the cortex.

The twisted architecture is confusing, but actually follows the growth of the telencephalon. You can see how this works by looking at the shape of the ventricles; visualise the limbic system and basal ganglia lying on the edge of each lateral ventricle, deep within the cerebral hemispheres. Now coil the lateral ventricles like a set of rams horns (which is actually how the cerebrum grows); the resulting twisted spiral shape describes the ventricles, the basal ganglia, and the lateral ventricles. The interesting thing about understanding how the shape of these structures relate to the growth of the telencephalon is that the temporal lobes are, topologically, the most anterior parts of the brain, rather than the frontal lobes; this is somewhat counter-intuitive.

That is a very basic summary. The brain and spinal cord are incredibly complex – by far the most complex anatomical system – but when first learning  anatomy, most health students do not have to worry about too much of that complexity and a basic overview is enough. Most courses teach the cranial nerves before going into a more detailed account of brain neuroanatomy; an overview of the cranial nerves is provided in the next entry.

Nervous system: basic organisation

The Nervous System is the wiring that allows animals to respond to their world. Like muscle tissue, nerves are unique to animals, and both rely on changes in polarity across the cells membranes to function. Nervous tissue is one of the 4 major tissue types that you develop as an embryo (muscle is another; connective tissues and endothelial tissues make up the rest).

In a big complex animal like a human, the nervous system has a lot to do. It needs to detect information about your external environment; threats and hazards, food and water, mates and competitors, and anything else of relevance. It also needs to detect information about your internal environment; temperature, hydration, food levels, injury, blood pressure, and a myriad others. It must transmit this information to a central processing system, where the information can be assessed – consciously or subconsciously – and responses organised as appropriate. Those responses might involve the release of secretions from a gland, or a complex and precise sequence of muscle activation. Even a basic activity like picking up a pencil involves about 100 muscles all over the body, and the degree of coordination required is computationally very complex. Your nervous system does all of this for you, mostly without you having to think.

Because it’s complex, we can study the nervous system by organising it into different categories and subunits. A common approach is to recognise a central part which does much of the processing, aptly named the Central Nervous System (CNS), and then a series of nerves that convey information between the CNS and other parts of you. These latter nerves are often known as the Peripheral Nervous System (PNS).

The CNS is basically a hollow tube of nervous tissue, surrounded and filled by a special fluid (cerebrospinal fluid, or CSF), and enclosed by a special set of membranes called the meninges. The CNS tube lies on middle axis of the body; in vertebrates, it is situated dorsal to the gut tube and the major blood tube. Because you are essentially a segmented animal, the different parts of the CNS connect with a series of peripheral nerves that innervate each segment. The peripheral nerves that connect the CNS to the head are called Cranial Nerves, and connect to the CNS via holes (foramena) in the skull bones. The peripheral nerves connecting to the rest of the body meet the CNS in between the bones of the spine column, and are thus known as Spinal Nerves.

The CNS is important, but nervous tissue is delicate, so the body protects it well. The head part of the CNS is of course the brain, and it is completely enclosed by the skull bones. Behind the head, the CNS is the spinal cord, and it is almost completely enclosed by the vertebrae; the spinal cord lies within a spinal canal and is well protected by bone.

Another way to help us organise and understand the nervous system is to consider the tissues being innervated. Recall that a fundamental distinction is made between the somatic and visceral tissues; as such, there are somatic nerves and visceral nerves. An important feature of nerve axons is that they only carry impulses in one direction; this gives us another way of organising. Nerves that carry information from the sensory organs to the CNS are sensory nerves (also known as afferent nerves), whilst nerves that convey impulses from the CNS to the effector muscles and glands are effector nerves (also known as effector nerves, or even just motor nerves).

In the body, the somatic tissues – skeletal muscle, bone, and other connective tissues – lie towards the outside of the body, whilst the visceral tissues lie mostly within the thoracic and abdominal cavities. As such, we find visceral nerves heading towards the body cavity, and somatic nerves towards the outer musculoskeletal parts. The somatic nerves relay precise sensory information that we can process consciously as required; we are immediately aware of a pin prick on the skin, both that it has happened, and exactly where it is, thanks to how the somatic sensory nerves work. We can also plan and execute a precise motor response, thanks to the somatic effector nerves. The visceral nerves work a little differently, however, especially in the thorax and abdomen. Recall that these are the ‘vegetative’ parts of the animal, and are under a much greater degree of involuntary control that are the somatic tissues. As a result, the visceral sensory and effector nerves are not only quite distinct to the somatic nerves anatomically, but also differ in how they work.

The visceral nerves help control, for example, the precise activities of the gut as it processes food, but this information is mainly processed in the enteric nervous system and very rarely does your CNS need to get involved. Normally, you are not consciously aware of what your gut is doing. Only if something goes wrong might the visceral sensory nerves relay pain information to the CNS; and even then, it is a diffuse ‘gut pain’, which lacks the precise information about location that your somatic sensory nerves always provide; gut pain is generally experience as a discomfort located around the belly button, no matter where in the 6 metres of your gut the pain is actually located.

The visceral effector nerves work differently to their somatic counterparts as well. Somatic effector nerves activate skeletal muscles – hence, their alternative name of ‘motor’ nerves – but visceral effector nerves work on smooth muscle, cardiac muscle, and glands. The essence of somatic motor nerves is simple: they activate their target muscle, and when they stop activating, the muscle relaxes. The visceral effectors are more complicated; some of them speed up the action of their target tissues, whilst others slow them down, and the normal running of the visceral organs is a fine tuned balance between these two sets of effector nerves. The ‘speed up’ effectors are called the sympathetic nerves, and the ‘slow down’ effectors are called the parasympathetics.

That is the general pattern of somatic vs visceral parts of the nervous system. Two further things to note about these for now:
1. Whilst most of the visceral tissues lie within the body cavity, there are some tissues embedded within the somatic musculoskeletal parts: the smooth muscles of the blood vessels that control vasodilation/vasoconstriction, the smooth muscle that erects the body hairs in response to cold (or fear), and the sweat glands in the skin. These have visceral nerve innervation; curiously, they are controlled only by sympathetic nerves. The parasympathetic system is restricted entirely within the body cavity.
2. As mentioned previously, the classic ‘vegetative’ parts of the visceral system are the organs of the thorax and abdomen. In the head and neck, things get a bit more complex; the nasal, oral, pharyngeal and laryngeal regions are embryologically derived from visceral tissues, but much of these are under conscious control. A special part of the visceral nervous system, the branciomeric nerves, deal with these; they essentially act in a very similar way to the somatic motor neurons, and are contained within the cranial nerves. They will be dealt with later.

In the spine, peripheral sensory nerves enter the spinal cord via dorsal roots, whilst effector nerves leave the spinal cord via the ventral roots. The cell bodies of the peripheral sensory nerves are contain within a ganglion in the dorsal root. Immediately outside the bony spinal canal of the vertebrae, the roots join to form a single spinal nerve; as this nerve contains sensory and effector neurons, it is known as a mixed nerve. The neurons are then organised into somatic and visceral parts; the visceral nerves travel a short distance to a ganglion that lies immediately lateral to the vertebral body, connecting to it via a white (well myelinated) communicating ramus. From there, most of the nerves travel alongside the spinal column in a large connecting nerve trunk; because these nerves are mainly sympathetic fibres, it is known as the sympathetic trunk. When the visceral nerves approach their target tissues, they move from the trunk to an autonomic plexus, before travelling the last part of their journal piggy-backing on the major arteries and veins that are also travelling to those tissues. Visceral sensory neurons do the journey in reverse. This is the typical pattern in the thorax and abdomen. The parasympathetics often arrive by a different route, via the last part of the vagus nerve (called the vagal trunk), or via sacral nerves; they meet up with their sympathetic counterparts are the relevant autonomic plexus before travelling to their targets with the vascular tissues.

For those sympathetic neurons that are headed to the ‘somatic’ parts of the body – to innervate blood vessels, hair papillae, or sweat glands – the journey is a little different. They travel to the ganglia in the sympathetic trunk, via the white communicating rami, along with the other visceral nerves. From there, however, they travel back to the spinal nerve via a different communicating ramus (the grey one), and thence to their targets.

For the somatic nerves, the journey is usually less complex. If they are innervating the epaxial muscles (or their associated bones, connective tissues, and overlying skin), they get their via the dorsal ramus of the spinal nerve. If they are destined for the hypaxial tissues then they travel via the ventral ramus. The dorsal and ventral rami divide just after the dorsal and ventral nerves join together, just outside of the spinal canal, and close to where the white and grey communcating rami attach; the spinal nerve is not a single nerve for very long. The only complication with the somatic nerves are the plexuses of the ventral rami, located in the neck and in the lumbar-sacral regions; these allow some cross connection of the ventral rami prior to innervating the anterior neck muscles, the upper limb, or the lower limb.

The nervous system and the vertebrate body plan: a (very) basic summary

It’s sometimes easier to understand the human body plan by going back to our roots, i.e. when you were a fish.

1_body plan - fish

The early anatomists made a basic division between the parts of the body that are under voluntary control, and the parts that are not (involuntary).

They considered the voluntary parts to be animal, and the involuntary parts  to be vegetable. This is what we mean when we say that someone is in a vegetative state; that only the involuntary parts (heart, lungs, guts, kidneys, etc) are working.

The modern names for these are somatic and visceral. Your visceral organs are all those parts in the body cavity (that work involuntarily), while the somatic parts are the muscle and bone that are built from the embryonic somites.

2.2_somatic vs visceral

Note that the gills (pharyngeal arches) are actually the visceral parts of the head and neck. Unlike the visceral components of the thorax and abdomen, these are often under voluntary control. This wasn’t clear to the first anatomists, so the ‘visceral = involuntary = vegetative’ connection really only applies to the thorax and abdomen.


A fundamental division within the somatic system is the muscles (and associated bone, connective tissue, skin etc) that develop dorsal to the spinal column,  and those that develop ventral to it. The dorsal muscles are called epaxial, and the ventral ones are hypaxial.

3_Somatic - epaxial vs hypaxial

In a fish, the epaxial and hypaxial muscles are about the same size. In humans (and all other mammals) the epaxial part is smaller than the hypaxial. The epaxial muscles in humans are the intrinsic muscles of the back (and neck), whilst the hypaxial muscles are everything else: intercostals, abdominals, diaphragm, limb muscles, and anterior neck muscles.


The nervous system controls all of these parts: somatic and visceral, epaxial and hypaxial. The divisions of the nervous system reflects these parts.

The basic organisation of the nervous system is into:

  • CNS (Central Nervous System): brain and spinal cord
  • PNS (Peripheral Nervous System): cranial nerves and spinal nerves

4.1_Nerves - CNS

The spinal nerves come off the spinal cord at each vertebral segment. Each spinal nerve is formed from two roots leaving the spinal cord; a dorsal root, that contains sensory neurons, and a ventral root, which contains motor neurons. The two roots join together as soon as they leave the spinal canal, forming a mixed spinal nerve.

That spinal nerve then immediately splits into two rami. The dorsal ramus supplies the epaxial muscles and associated tissues, while the ventral ramus supplies the hypaxial tissues.

4.2_Nerves - CNS + PNS 1 - spinal nerves


The other part of the PNS is the cranial nerves. These supply various structures, mainly in the head. Some of the cranial nerves supply the pharyngeal arches; from front to back: V, VII, IX, X+XI.

4.3_Nerves - CNS+PNS 2 - ANS

The most posterior pharyngeal arch tissues  in the throat  (or most inferior in humans) are supplied by the vagus nerve (cranial nerve X). The vagus also send a branch – the vagus trunk – to make up one part of the Autonomic Nervous System, which supplies the involuntary visceral organs  in the thorax and abdomen.

The Autonomic Nervous System (ANS) has two components; the sympathetic nerves (which speed things up, e.g increase heart rate), and the parasympathetic nerves (which slow things down).

4.4_Nerves - CNS+PNS 2 - cranial nerves

The sympathetic  nerves come from the spinal nerves via the sympathetic trunk

The parasympathetic nerves come from the vagal trunk, which is the last (and largest) branch of the vagus nerve, and the pelvic nerves.


This is a very simplified account.  The nervous system is a complex thing to learn, however, so it is worth starting with a fundamental understanding of its basic components.