Download DENT-OBHS 131 VirtualLab

Neuroscience
Virtual Gross Lab
James H. Baños, Ph.D. ([email protected])
Overview: Although some aspects of basic neuroanatomy have been covered in the classroom lectures,
learning anatomy is best accomplished using an interactive approach. This means that rather than passively
watching a presentation about where structures are located, you need an opportunity to explore and
manipulate the subject of study (in this case, the brain). For this course, we will use an online interactive
brain atlas that combines images of actual brains with fairly advanced 3-D reconstructions and animations
derived from magnetic resonance imaging data.
How the Lab Will Work: Consider this document to be a “lab notebook” that will guide you through the
various aspects of neuroanatomy you will be expected to know. It is divided into several sections. The first
will cover external features, including the blood supply from Dr. Nicholas’ lecture. These will be followed
by a set of links to 3-D images and animations to review the internal anatomy, and to serve as a reference for
the next sections, where you will view coronal and horizontal sections. The final section will provide an
introduction to the cranial nerves. Each section will contain structures you are responsible for knowing (in
bold), including explanations that help you find some of the structures and identify important relationships
between structures. You may want to print this document, so you can read the text while viewing the images.
You can also print the images themselves (or generate your own custom images to study from). Once you
complete a section, you are strongly encouraged to continue exploring the atlas to further familiarize yourself
with the structures. You may work on the lab in small groups of 3-4. In fact, discussion with a few
classmates can make the lab more interactive. Just be sure that you actually spend time exploring, rather
than just watching over someone’s shoulder as they click the links. If you have questions while completing
the lab, feel free to email me ([email protected]).
The Atlas: The atlas used in these labs is the University of Washington Digital Anatomist Interactive Brain
Atlas.
Getting the Most out of the Atlas: The main menu is a good starting point for you to explore. On many of
the pages, such as this one, there are buttons below the image that allow you to label all structures, outline all
structures, and quiz yourself. Note that you can also click on a structure and the name of that structure will
appear at the top of the page. Throughout the labs, you will also find custom links to images showing the
structures of interest, like this.
Viewing the 3-D Animations: Among the most helpful parts of the atlas are the 3-D animations showing the
relationships between various structures. These animations require a Quicktime viewer, or a Quicktime plugin for your browser. PCs with iTunes software should already have Quicktime installed. Quicktime is
standard on Mac computers, but can be easily downloaded for free for PC or Mac. The animations are
sometimes a bit slow to download, but worth the wait.
Part I: External Features
1. Lobes of the Brain
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Frontal, Parietal, Occipital, Temporal lobes [3-D Animation ; Right Hemisphere ; Left
Hemisphere]
2. Lateral Surface
 Lateral (Sylvian) fissure [Lateral View]. This is the major landmark in that it separates the frontal
and temporal lobes.
 Central sulcus (of Rolando) [Lateral View; Dorsal View]. This is a major landmark in that it
separates the frontal lobe from the parietal lobe and is the boundary between primary motor cortex
(the precentral gyrus) and primary somatosensory cortex (the postcentral gyrus).
 Precentral gyrus [Lateral View]. The precentral gyrus is primary motor cortex and will be discussed
in more detail in a future lecture.
 Postcentral gyrus [Lateral View]. The postcentral gyrus is primary somatosensory cortex and will
also be discussed in more detail.
 Precentral sulcus [Lateral View]
 Postcentral sulcus [Lateral View]
 Superior, middle, inferior frontal gyri [Lateral View]. Remember, a “gyrus” isn’t always a single
neat ridge, such as the middle frontal gyrus in that image. It can be hard to understand why anyone
would consider that to be a single gyrus. Remember that when you look at a the same part of the
brain in a coronal view, you’ll see the much deeper fissures that clearly define each of the three
frontal gyri.
 Parts of Inferior Frontal Gyrus (orbital, triangular, opercular) [Lateral View]. Note that the
triangular and opercular parts of the inferior frontal gyrus make up Broca’s area, which is the center
for expressive speech output. Receptive speech is associated with Wernicke’s area, which is a loosely
defined area of parietal/temporal lobe posterior to the sylvian fissure (not marked specifically in the
atlas).
 Superior temporal sulcus [Lateral View]
 Middle temporal sulcus [Lateral view]
 Inferior temporal sulcus [Ventral View]
 Superior, middle, inferior temporal gyri [Lateral View]. Like the frontal gyri, the temporal gyri
may not always look convincing from the outside, but when one makes a coronal cut, the distinction
is much clearer. The superior temporal gyrus is labeled in this image. Which are the middle and
inferior? Where are the temporal sulci and how do they compare to other sulci?
 Insula (or insular cortex) – The insula is an area of cortex (including sulci and gyri that is “hidden”
deep inside the sylvian fissure. In a gross brain, you can only see it if you pull the temporal lobe back
or dissect it away. For example, look at this image of the Cortex dissected to reveal the insula]. The
insula is viewed more easily in coronal and horizontal slices.
 Transverse temporal gyri (or Heschel’s gyrus) – These are primary auditory cortex and lie inside
the sylvian fissure. They are called the transverse temporal gyri because they run perpendicular to the
superior temporal gyrus, which runs the length of the temporal lobe (see Cortex dissected to reveal
superior aspect of temporal lobe). You can also see them on a horizontal slice at the right level.
However, when looking at a horizontal slice, remember that the sylvian fissure is not perfectly
horizontal, so although you are seeing a good bit of temporal lobe posterior to the transverse
temporal gyrus in this slice, you are seeing very little of the temporal lobe that is anterior to it (and
visible in the image of the dissection).
 Supramarginal gyrus (to locate, trace the sylvian fissure posteriorly to its termination) [Lateral
View]
 Angular gyrus (to locate, trace the superior temporal sulcus posteriorly to its termination) [Lateral
View]. Note that the together, the angular and supramarginal gyri form the inferior parietal lobule.
 Superior parietal lobule [Lateral View; Dorsal View]
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Intraparietal sulcus – Separates the inferior and superior parietal lobules [dorsal view]
3. Medial Surface
 Corpus callosum – The corpus callosum is the massive body of white matter pathways that
interconnect the two hemispheres. Morphologically it has four parts (anterior to posterior): rostrum,
genu, body, splenium. [Medial View]
 Fornix – The fornix is the white matter pathway that forms the output of the hippocampal formation
in the medial temporal lobes, and is therefore a crucial part of the limbic system. When looking at the
medial aspect of a brain, the fornix is the white matter pathway that arcs down underneath the corpus
callosum [Medial View]. In reality, the fornix is bilaterally represented. The two pathways come
together at the midline to form the small portion of the fornix we’re able to see on the medial aspect
of the brain (see 3-D image of the fornix and hippocampal formation). You’ll learn more about the 3D morphology of the fornix in an upcoming section.
 Anterior commissure – The anterior commissure is another white matter pathway connecting the
two hemispheres, although it is much smaller than the corpus callosum. The fornix actually arcs down
right onto the anterior commissure where its splits, sending some fibers anterior and some fibers
posterior. To find the anterior commissure, simply follow the arc of the fornix. On the 3-D image, the
anterior commissure looks like the “whisker” sticking out in both directions. Note how the fornix
splits on either side of it.
 Paracentral lobule (medial continuation of pre and postcentral gyri) [Medial View]
 Cingulate gyrus and sulcus – The cingulate is the gyrus that sits just superior to the corpus
callosum. [Medial View]. It is an important part of the limbic system, and we’ll see it again in
coronal slices.
 Parietooccipital fissure (or sulcus) -- Remember, there is no clear boundary between the occipital
and parietal lobes when looking at the lateral aspect of the brain, but from the medial aspect, they are
separated by a very deep and clear fissure. [Medial View]
 Calcarine sulcus – This is a very important sulcus, because its banks form primary visual cortex.
The portion of medial occipital lobe superior to the calcarine sulcus is the cuneus (which means
cone, or wedge). Below the calcarine sulcus is the lingual gyrus (no named because of its
resemblance to a tongue). [Medial View]
4. Ventral Surface
 Gyrus rectus (straight gyrus) [Ventral View; Medial View]
 Orbital gyri – As the name implies, the orbital gyri sit just above the orbits of the eyes. This cortex
is crucial to higher level behavioral regulation. [Ventral View]
 Parahippocampal gyrus – The parahippocampal gyrus is the medial most aspect of the inferior
temporal lobe. It contains the hippocampal formation. Note that if you traced the parahippocampal
gyrus back up and around (as in this image with the brain stem dissected off), it would seem to run
continuously with the cingulate gyrus. Both are, in fact, important parts of the limbic system.
 Occipitotemporal gyrus – The occipitotemporal gyrus falls between the hippocampal gyrus and
inferior temporal gyrus. [Ventral View; Medial view]. Note: the atlas divides it into medial and
lateral, but you will not be responsible for this level of detail.
 Collateral sulcus – Separates the parahippocampal gyrus and the occipitotemporal gyrus. [Ventral
View]
 Uncus – This is the medial“protrusion” of the temporal lobe. We will learn more about the clinical
significance of the uncus in future lectures (so know it well). [Ventral View; Medial view]
5. Arteries (including circle of Willis)
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Internal carotid artery [Ventral View; MR Angiogram]
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Middle cerebral artery [MR Angiogram; MCA Aneurysm]
Anterior cerebral artery [Ventral View; Medial View; MR Angiogram]
Posterior cerebral artery [Ventral View; MR Angiogram, note relationship to CN III]
Posterior communicating artery [Ventral view]
Anterior communicating artery [Ventral View]
Superior cerebellar artery (note relationship to CN III) [Ventral View]
Posterior inferior cerebellar artery (PICA) [Ventral View]
Anterior inferior cerebellar aretery (AICA) [Ventral View]
Vertebral artery [Ventral View]
Basilar artery [Ventral View; Sclerotic Basilar Artery]
6. Ventricles and Miscellaneous Structures
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Lateral ventricles [3-D]
Septum Pellucidum (thin membrane separating the lateral ventricles) [Medial View]
Interventricular foramen of Monroe [3-D; Medial View]
Third ventricle [3-D]. If you look at this medial view, the third ventricle isn’t specifically labeled,
but you can see it surrounding the thalamus.
Cerebral aqueduct [3-D; Medial View]
4th ventricle [3-D; Medial View; Dorsal brain stem with cerebellum removed]
foramen of Magendie (median aperture) [3-D; Medial View]
foramina of Luschka (lateral apertures) [3-D]. This is a difficult structure to locate and is not
specifically labeled in the atlas. Just know its approximate location, and that it is two lateral
apertures.
choroid plexus [Example in a medial view]. The choroid plexus produces CSF and can be found in
all of the ventricles, although most of it is in the lateral ventricles.
pineal body [Medial View]
infundibulum or pituitary stalk [medial view]. The pituitary gland itself is not visible because it
usually remains in the skull when the brain is removed. Note also the relationship to the optic chiasm.
This will have clinical significance discussed in future lectures.
optic chiasm [Medial View; Ventral View]
optic tract [Ventral View]
7. Diencephalon, Brain Stem
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Hypothalamus [Medial View]
Mammilary Bodies [Medial View; Ventral View]. The mammilary bodies are technically nuclei of
the hypothalamus, but since they are structurally distinct and have specific functional significance as
part of the limbic system, they are listed separately here.
Thalamus [Medial View; 3-D thalamus in relation to ventricles]. Note that the thalami “touch” at the
midline, although they are not functionally interconnected. This point of contact is called the massa
intermedia, and it accounts for the “ring” shape of the third ventricle.
Midbrain [Medial View] (Note that in this image the tectum and tegmentum are labeled separately,
but you don’t need to worry about this for now)
Cerebral peduncles (part of the midbrain) [Ventral View; Anterolateral view (some cortex
removed)]. The peduncles are the big “columns” of white matter pathways that support the cerebral
hemispheres.
corpora quadrigemina (includes superior and inferior colliculi) [Medial View; Dorsal brain stem
with cerebellum removed]
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Pons [Ventral View; Medial View]
Medulla [Medial View]
Pyramids (part of the medulla) [Ventral View; Anterolateral view (some cortex removed)]
Inferior Olive (part of the medulla) [Ventral View; Anterolateral view (some cortex removed)]
Cerebral peduncles (part of the midbrain) [Ventral View; Anterolateral view (some cortex
removed)]. The peduncles are the big “columns” of white matter pathways that support the cerebral
hemispheres.
Part II: 3-D Review of Internal Structures
The following links are meant to give you a chance to review the internal structure of the brain in 3-D before
you start looking at coronal and horizontal slices. If you understand the structures in 3-D, the slices will be
much easier. These are the main structures and systems you want to know first, although a few more will be
added when we look at the slices.
I.
Ventricular system
a. Ventricles in relation to the cortex
b. Ventricles with amygdala
II.
Diencephalon (thalamus/hypothalamus)
a. Thalamus in relation to lateral ventricles
b. Hypothalamus
III.
Basal Ganglia
a. Caudate nucleus in relation to lateral ventricles
b. Putamen
c. Caudate, putamen, and nucleus accumbens (The nucleus accumbens is located at the juncture
of the caudate and putamen, at the anterior part of the basal ganglia. It is pictured here in
yellow)
d. Globus Pallidus
e. Putamen and globus pallidus
f. Basal ganglia, all parts
IV.
Hippocampus (including fimbria and fornix)
a. Hippocampus, fimbria, and fornix in relation to ventricles
b. Hippocampus and amygdala
Part III: Coronal Sections
Now you’re going to “slice” a brain in coronal sections. Below is a list of structures you are responsible for
knowing in coronal slices. Below those is an image of the brain indicating the approximate location of each
slice, to be used as a reference. These images are followed by a series of links showing what each slice looks
like, along with a brief description of the “high points” of that particular slice. As would be the case if you
were slicing a real brain, the structures are not labeled. However, the images are interactive in that you can
click them to explore, identify, and outline structures. As you will notice, the links to slices below do not
cover all slices represented in the online atlas. You are encouraged to explore the other slices as well,
although most will be similar to the ones linked below.
Structures you are responsible for knowing in coronal sections:
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Corpus Callosum
Cingulate gyrus
Lateral ventricles
3rd Ventricle
4th Ventricle
Septum Pellucidum
Caudate nucleus (head, body, and tail)
Putamen
Nucleus accumbens
Globus pallidus
Thalamus
Hippocampal formation
Fornix
Anterior commissure
Claustrum
External capsule
Extreme Capsule
Insular cortex
Cingulate gyrus
Amygdala
Slice 1 – In this slice, we catch the anteriormost portion of the corpus callosum (the genu). We just see the
lateral ventricles, and note to the right we have just clipped the head of the caudate on the right side (a small
spot of grey next to the lateral ventricle). We also see the tips of the temporal lobes (i.e., the temporal poles).
Many of the structures on our list are not yet visible, however.
Slice 2 – In this slice, we are cutting the anterior aspect of the basal ganglia where the caudate and putamen
are beginning to separate into distinct structures. Note the faint beginnings of what will become the internal
capsule (anterior limb) between them. The body of the corpus callosum is still visible. Below it we see the
septum pellucidum, which is the thin membrane separating the lateral ventricles. Also note above it the
cingulate gyrus, which we’ve seen on a midsaggital view.
Slice 3 – Here we see further differentiation of the caudate and putamen, with a more pronounced internal
capsule (anterior limb) visible. Note that at the inferior aspect of where they connect is the nucleus
accumbens. You also see the beginning of a couple of new structures that are helpful to learn with the basal
ganglia (morphologically, not necessarily functionally). Lateral to the putamen is a thin white matter
pathway called the external capsule. Lateral to that is a thin strip of grey called the claustrum. Lateral to the
claustrum is the extreme capsule. The claustrum is labeled in this atlas, although the external and extreme
capsule are not. You will see these structures in successive slices along the length of the basal ganglia. We
have also clipped the optic chiasm, just a bit of the hypothalamus, and third ventricle. We are well into the
temporal pole, but have not yet reached the amydala (which should be the first major temporal lobe structure
we encounter as we keep moving posteriorly).
Slice 4 – Here we see the caudate and putamen fully separated, with the globus pallidus visible medial to the
putamen. We have cut the anterior commisure such that it is clearly visible, as are the columns of the fornix
(which come right down to the anterior commissure). We are approaching the anterior end of the temporal
horn of the lateral ventricles, so the amygdala is visible.
Slice 5 – Here we still see the various parts of the basal ganglia clearly. We can still see hypothalamus, and
are not posterior enough to see the thalamus just yet. The amygdala is still visible. The interesting thing in
this slice is that we are just posterior to the anterior commissure, so you can see the columns of the fornix
where they are arcing down to the anterior commissure (at lower part of the septum pellucidum).
Slice 6 – In this slice, we have cut perfectly through the intraventricular foramen of Monroe, so you have a
perfect view of the lateral ventricles “emptying” into the third ventricle. It’s a bit difficult to find, but we
have clipped just a bit of the anterior thalamus. This lets us know that we are probably in the area of the genu
of the internal capsule and will soon be transitioning into the posterior limb. Note that part of the amygdala is
still visible, although we are starting to open the temporal horn of the lateral ventricles.
Slice 7 – Now we start to see some significant changes as new structures are visible. We have a good view of
the thalamus. The caudate, putamen, and globus pallidus are still visible, although they are not so prominent.
The temporal horns of the lateral ventricles are clearly visible, as is the hippocampus. The hippocampus here
actually looks a bit like a seahorse (especially on the left), which is where the name comes from. It often
looks more like an indistinct jelly roll. Down to the bottom right, we have clipped part of the cerebral
peduncle. You can see the descending and ascending white matter pathways fairly clearly.
Slice 8 – This slice offers another great view of the ascending and descending white matter pathways passing
through the cerebral peduncle and pons.
Slice 9 – This slice is much more posterior. Basal ganglia, thalamus, etc are no longer visible. However, you
can see the posteriormost aspect of the hippocampus, including the fornix on each side moving to the
midline. Note also that we can see the 4th ventricle.
Part IV: Horizontal Sections
Horizontal sections should be easier now that you’re familiar with coronal sections. The structures are more
or less the same. Some have a similar appearance (e.g., the basal ganglia) but look a bit more elongated in
horizontal sections. You’ll also be better able to see the relationship among the basal ganglia, thalamus, and
internal capsule.
Structures you are responsible for knowing in horizontal sections:
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Corpus callosum
Lateral Ventricles
3rd ventricle
Caudate nucleus
Putamen
Nucleus accumbens
Globus pallidus
Thalamus
Internal capsule (anterior limb, genu, posterior limb)
Claustrum
External capsule (Not labeled directly, thin white band between putamen and claustrum)
Extreme capsule (Not labeled directy, thin white band between claustrum and insular cortex)
Insular cortex
Slice 1 – Beginning from the superior aspect of the brain, this first slice open the lateral ventricles. If you
look down into the ventricles, you can see the thalamus from above. At the anterior end of the ventricles, you
can find a very thin slice of the head of the caudate.
Slice 2 – As we move downward a bit, you clearly see the thalamus (posterior) and caudate (anterior). We
are still too high to see much of the putamen, although we see the upper edge of it on the right. We also see a
thin little strip of the claustrum. The external and extreme capsules are visible on either side of the claustrum
(just like the coronal sections), although they are not labeled here in the atlas. Note the fornix arcing upward,
inward, and forward.
Slice 3 – Here we again see the thalamus and caudate clearly. The putamen is also visible on each side,
offering some definition to the internal capsule (anterior limb, genu, and posterior limb). The globus pallidus
is still not yet visible, because it is smaller than the putamen. Note on the right (posterior aspect of the
ventricle) that we see the hippocampal formation. It looks similar to what we saw in coronal sections.
Remember, this is possible because it essentially curves upward along the temporal lobe (from anterior to
posterior).
Slice 4 – This section is probably the “classic” horizontal section in terms of showing the basal ganglia,
thalamus, and internal capsule. Note that you can still see the hippocampal formation.
Slice 5 – This is the level of the anterior commissure. Note that the caudate and putamen are once again seen
close to where they join, so just a bit further down we should find the nucleus accumbens (but not yet in this
slice).
Slice 6 – Finally, the caudate and putamen look very similar to the more anterior coronal slices. This is
where the nucleus accumbens can be located.
Part V: Introduction to Cranial Nerves
We have not yet covered the cranial nerves in any detail. For now, what you need to focus on is the name,
number, and anatomic location of each nerve. Function will be covered in the brain stem lectures. Below are
links to most of them in the online atlas, although not all are pictured. Below that is a simpler diagram to
help learn their locations. If you print it and cut the labels off, it can be used to make a simple set of flash
cards, which can be good starting point to learn the nerves. Note how they are more or less numbered in a
logical fashion as you travel from superior to inferior aspects of the brain stem. The important exceptions are
CNs XI and XII, which are in “reverse” order.
Cranial Nerves
I.
II.
olfactory – The actual nerve is not visible. It is essentially a bundle of little fibers passing
through the skull that is torn during brain removal. What you can see, however, is the olfactory
bulb and tract)
optic
Midbrain
III.
IV.
oculomotor – This nerve emerges from between the cerebral peduncles.
trochlear – smallest cranial nerve and only one to exit from dorsal brainstem
Pons
V.
VI.
VII.
trigeminal – large stump, on ventrolateral pons
abducens – at pontomedullary junction anteriorly
facial - at cerebellopontine angle (where the pons and cerebellum come together)
Medulla
VIII.
IX.
X.
XI.
XII.
vestibulocochlear - at cerebellopontine angle
glossopharyngeal – lateral superior medulla
vagus – directly caudal to IX
spinal accessory
hypoglossal – anterior surface of medulla