BrainVoyager Brain Tutor Practical

BrainVoyager Brain Tutor Assignments

Student Name:

Background

Brain Tutor is a program designed to allow you to view an MRI scan of a healthy human brain, both
represented as slices in three standard orientations (coronal, sagittal, and transverse) and as a 3D
rendering of the cortical surface. You can use it to explore brain structures and to learn to find your
way around both slice views and surface views of the brain. Please download and install the program
(make sure that you download brain tutor, not brain voyager).

Note: Brain tutor is free to download for use on your own computer!
Go to http://www.brainvoyager.com/, then go to Downloads, and find information on how to install
BrainVoyager Brain Tutor for your operating system (if it doesn’t show up: scroll down). As of
October 2023, Brain Tutor can be installed through the Windows Store (for Windows 11), Mac App
Store (for macOS) or the Apple Store (for iOS / iPadOS). Just search for Brain Tutor in the Store, and
click install/get. There are even Apps for your smartphone available but these are not recommended.

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Please start Brain Tutor after successful installation (collaborate with another person if the program
does not run). The program consists of three panels – an Atlases List (on the left, this panel may be
hidden. You can show/hide it by clicking on the three lines in the top left corner), and two view
windows: a Volumes panel (left), which shows brain volumes in three planes (sagittal, coronal, and
transverse), and a Surface panel (right), showing the 3D surface of the brain. Finally, you can find the
Tools bar in the top right corner. An important tool for this assignment is the ROI Description box,
which you can call by clicking on the symbol with the three horizontal lines.

In the Volumes panel, you can zoom in on each of the planes (sagittal, coronal, transverse), by
clicking the corresponding icons at the bottom of the panel.

In the Surface panel, you can use the buttons at the bottom to hide or show the head, and to toggle
both the left and right hemispheres, and subcortical structures on and off independently. You can
change how the head is sliced open by using the Mesh Slicing tool: click the top icon on the tools bar,
and adjust the transverse, coronal, and sagittal slicing. You can adjust the viewpoint (i.e. zoom in and
out, rotate) with the Viewpoint Navigator tool (second icon in toolbar).

Finally, under Atlases, you can change which structures are listed by selecting either the brain’s
Lobes, Gyri, Sulci, Subcortical areas, or Tracts. It is also possible to display Brodmann areas (defined
cytoarchitectonically) or Functional areas that have been defined functionally using fMRI. Click the
name of an area, and that area will be highlighted in the Volume and Surface panels. You can select
multiple brain structures list simultaneously, by holding the Ctrl key (for mac, perhaps try another
key) and clicking the names of the structures you want to highlight. You can also click on the brain in
the Surface panel to highlight what area that is (if available in the currently selected list; the selected
brain structure should be highlighted with a color). The ROI Description box (which you can call
through the Tools bar) gives you more information about the selected brain structure.

Use Brain Tutor to answer most assignment questions; Feel free to use any other sources as well
(textbooks, Wikipedia, etc).

Note: a brain can be navigated using different coordination systems. Brain tutor uses the Talairach
coordinates. However, other coordinate systems also exist, like that from the Montreal
Neurological Institute and Hospital (MNI). For a coordinate converter, see:
https://bioimagesuiteweb.github.io/webapp/mni2tal.html

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Assignments

- In the Atlases List, select Lobes. Click on each of the lobes that are listed on the left to highlight
them in the Volumes and Surface panels. Notice how a description appears in the ROI Description
Box. What is the name of the sulcus dividing the frontal lobe from the parietal lobe (inspect the other
options in the Atlases List)?

Central Sulcus

- Now select the Functional atlas from the Atlases List. Notice how the panel on the right changed to
now show functional areas defined by fMRI experiments. Again, clicking on an area highlights that
area in the Volume and Surface panels and shows information about that area in the ROI Description
Box. Select the Broca area. To get an idea of where this area is with respect to the skull, click the right
button at the bottom of the Surface panel to superimpose the head on the brain model. Use the
Mesh Slicing box in the Tools bar to (de)select Sagittal and Coronal slicing. To change the slicing of
the skull, you can either move the crosshair in the Volume panel around with your mouse, or you can
use the sliders in the Mesh Slicing tool. Where is Broca’s area in the head (describe a part of your
head)?

It is on the left side, above your ear, a little to the front.

- Notice how Broca’s area is highlighted in both the Surface panel (on the right) and Volume panel
(on the left). If you click around in the Volume panel you can see so-called Talairach coordinates
change in the TAL Coordinates box within the Volume panel. Roughly what are the Talairach
coordinates of Broca’s area?

Coördination points: -52, 14, 15

- To find out what Talairach coordinates are, look it up in Wikipedia. According to the Wikipedia page,
what is the structure at the origin [0,0,0] of the Talairach coordinate system? To answer this
question, modify the TAL coordinates in the Volume panel and then match the Sagital mesh to the
SAG volume panel using the mesh slicing tool. Next, inspect the Tracts in the Atlases List while the 3D
subcortical regions are shown in the surface panel. Which directions are x, y, and z? Also see
https://bioimagesuiteweb.github.io/webapp/mni2tal.html for a useful tool.

Fornix tract. X is van links naar rechts, voor naar achter is Y en onder naar boven is Z.

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- To bring a scan into Talairach coordinates, the origin is set to the structure from the previous
question, and then the brain is rotated such that the structure at [0,-24,0] is brought into the same
transverse and sagittal slices. What is the name of this second structure (use Wikipedia or another
internet source, because this tract cannot be shown in BrainTutor)? Why do you think these two
structures were chosen to define the coordinate system?

Posterior commissure. Handig want het is in het midden.

- What are the proper terms for navigating around the brain? Connect the following directions.

1 Up, towards the top of the skull Anterior/Rostral

2 Down, towards the spine Medial
3 Front, towards the face Posterior/Caudal
4 Back, away from the face Superior/Dorsal
5 Inwards, towards the midline Lateral
6 Outwards, towards the ears Inferior/Ventral

- Find the name of the structure at Talairach coordinates [2,-2,24]? What is the function of this
structure?

Corpus Callosum allows the transferring of inputs from one hemisphere to the other. Involved in
several motor, perceptual and cognitive function.

- If you look for this structure in the Surface panel in Brain Tutor, you will see that it is cut in this
graphical representation (Hint: Click on it with the Gyri-list open in the Atlases List panel)

Cingulate gyrus.

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- Look for the Calcarine Sulcus by selecting the Sulci Atlas from the Atlases List. In which lobe is this
area, and in which Brodmann area?

Occipital, BA17

- What is the more common name of this functional area?

Calcarine Fissure

- A patient has a lesion at Talairach coordinates [41,-30,-12]. What functional area is this, and what
problems might this patient experience (inspect the functional areas in the Atlases List)?

Fisum Form Face, perception of faces and recognising identity. Ja kan mensengezichten niet meer
herkennen.

Look for the primary motor area M1 (this area is not labeled in Brain Tutor, so use other resources).
This area includes one gyrus and one side of one sulcus. Which gyrus and which side of which sulcus?

Achterkant van de Precentral Sulci, Precentral Gyrus.

Neurons in this area are organized into a map, known as the motor homunculus. In Brain Tutor, you
can highlight the area responsible for moving the hands. With respect to this area, where might you
find neurons controlling the legs and feet (use the Latin terms that you used to label the numbered
directions earlier)? What about neurons innervating the face?

Legs and feet: 32, -10, 58 hands: 32, -17, 63. Dus de Y verlaagd een beetje en z verhoogd. Voor de
face: X kleuin beetje omhoog en Z iets lager.

- Find the primary auditory cortex. In which gyrus is this located, and which Brodmann areas does
this include?

Superial temporal gyrus, BA 22.

- Go to Talairach coordinates [0,3,-17] in the Volume panel. This puts the crosshair on a small white
structure. Explore what this structure connects to by looking through adjacent slices (only inspect the
Tracts if you cannot find this out). What structure is this?

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- Explore the functional properties of different areas in each of the four lobes. Roughly speaking,
what deficits might you expect in patients with damage in the following areas? (Tip: look at what
Brodmann areas are in these regions and what their associated functions are.)

Prefrontal cortex:

Occipital lobe:

Ventral part of the temporal lobe:

Anterior part of the temporal lobe:

Superior temporal gyrus:

Postcentral gyrus:

- The hippocampus is a cortical structure that is very important for memory. This structure is listed in
the Subcortical atlas. At which Talairach coordinates can you find the left hippocampus?. The
hippocampus is difficult to recognize in 2D pictures of the brain. To practice, follow the highlighted
outline of the hippocampus in the different views (sagittal, coronal, transverse/axial). Then click on
the thalamus first in the sagittal view, then slowly move in lateral and inferior directions in the
coronal view until you find the left hippocampus.

- What do you think the white dots are that are visible in the transverse slices of the neck (e.g. at
[-25,-23,-115])?

- In the coronal slice at y=9 and around z=6, you see two dark subcortical structures in each
hemisphere, separated by white matter. These structures are part of the basal ganglia. What is each
of these structures called, what are they called together, and what is the name of the white matter
tract separating them? Use the Subcortical atlas and the following website to answer this question:
http://www.neuroanatomy.ca/regions.html

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- A third part of the basal ganglia is visible in the Transverse slice (axial) as a blob centred on [-17,-
4,4], just posterior to the two structures identified in the previous question. This third part is darker
than the surrounding tissue but not as dark as the two previously identified structures. What is the
name of this third structure?

- The basal ganglia include other, smaller structures that are difficult to see in this MRI image. One of
these is critically involved in Parkinson’s disease. What area is this?

- The thalamus has numerous important roles in the brain; one is as a relay station for incoming
sensory information, for example from the eyes and ears, to the cortex. Find the thalamus in Brain
Tutor and give its Talairach coordinates. How is it positioned relative to the following nearby
structures? Make sure to use appropriate terms (e.g. more superior to, more lateral to, etc).

Talairach coordinates:

Position compared to midbrain:

Position compared to corpus callosum:

Position compared to striatum:

- In the slice at z=0, you see substantial white matter heading from the thalamus towards the
posterior part of the brain in both hemispheres. What is the name of this tract, and what kind of
information does it convey (note that this tract cannot be shown in Brain Tutor)?

- Look up the region of the brain that responds to taste, particularly disgust. In which gyrus is this
region located, and how would you describe its location with respect to the brain’s four main lobes?

- The brain is surrounded by cerebro-spinal fluid (CSF). There is also CSF on the inside of the brain, in
a network of four ventricles. The first two are known as the lateral ventricles. What are the most
anterior and posterior coronal slices in which the lateral ventricles are visible?

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- Find the third ventricle. What structure forms the edge of this ventricle on the lateral side?

- Find the fourth ventricle. This ventricle is bounded on the anterior side by part of the brainstem.
Which part? And what is the name of the large structure forming the boundary on the posterior side?
What is the function of this structure?

- When you scroll through sagittal slices in the Volume panel, you see what seems like a shadow pass
through the image around slice x=0, between the two hemispheres. This is the Cerebral Falx, an
extension of the tough outer membrane covering the brain. What is the name of this membrane?

- Feel free to explore other areas of the brain using Brain Tutor! There is a lot of information available
to help you make sense of what is localized where in the brain. Also, you might find it interesting to
see how other features appear on MRI, such as teeth, the tongue, the nasal cavity, the eyeballs, etc.