Lab 2 - Mapping the Brain Mricron PDF

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Lab work for physiological psychology. ...

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PHYSIOLOGICAL PSYCHOLOGY I – PSYC 2900 Lab # 3 “Mapping and Navigating the Brain” Part 1: Histological atlases Two of the earliest methods of investigating brain function are stimulating the brain with electrical current, and recording the electrical activity produced by neurons, either as action potentials produced by individual neurons and axons, or slow (graded) potential s produced by populations of neurons. However in order to accomplish this, the electrodes need to be introduced through small holes in the skull, which means that it is not possible to visually guide the electrode. So how do neuroscientists proceed? A classical technique is to remove the brain of an experimental animal, organ donor, or deceased patient, harden it in formaldehyde so it retains its shape, and then cut it up into very fine sections, which are then mounted on glass slides. The instrument used to do the slicing is referred to as a microtome. The mounted slides can then be stained with tissue dyes to produce visual contrast between different types of tissue. Different stains will produce different contrast depending on what cellular materials absorb the stain – for example some dyes are taken up more by protein in the nucleus and cell body, and so tend to stain grey matter, while others are absorbed by lipid and tend to stain white matter. Brains can be sliced through any axis – coronal, axial or sagittal, but the important point is that the set of slides covering the whole brain can be inspected to visualize the internal structures of the brain at each slice. A complete set of such slides makes up a brain atlas. A fine example of such an atlas is the Human Brain Atlas that has been created by the Michigan State University. Fortunately for students of neuroscience, MSU has created and posted a digital version of this atlas. The URL for this website is: https://www.msu.edu/~brains/brains/human/ Open it now and take a look at the main page. Note that you can use it to view slices in the coronal, horizontal (axial) or sagittal planes. Clicking on a particular slice in the montage will open that slice for viewing. Note that you can choose between a grey matter and a white matter stain. Let’s see if we can find the following brain structures:

A.) The cerebral ventricles, including the lateral ventricles, the third ventricle, the cerebral aqueduct and the fourth ventricle Study questions: - Try looking through the brain using each of the slice orientations (coronal, sagittal, axial). Scroll through the views in each section so that you can examine the whole brain. (Note how different the shape of the ventricles looks in each of the views, and in each of the slices. This will help you go understand how to look at brain parts from different viewpoints.)

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Where are each of the ventricles these located in relation to the brain’s “primary vesicles” – the hindbrain, midbrain and forebrain? Which ventricle is associated with which brain region?

B.) The cerebellum and pons Study questions: - How is the cerebellum connected to the rest of the brain? Does it appear to have different parts? What does the cerebellum contribute to behaviour? Do the different parts make different contributions? What cranial nerves arise in the hindbrain? What do they control? C.) The Midbrain Study questions: - Which part of the ventricular system is associated with the midbrain? - Where are the tectum and tegmentum in relation to the above structure? - What does each of these parts of the midbrain contribute to the control of behaviour? D.) The Thalamus and Hypothalamus Study questions: - Can you find different nuclei in the thalamus? Are they connected to the cortex? Is there a plan in terms of what is connected to where? - Does the hypothalamus have distinct nuclei? What might these contribute to the control of behaviour? -What endocrine gland is connected to the hypothalamus? Why is this important for instinctive behaviour? E.) The Limbic system: The hippocampus, amygdala and cingulate cortex Study questions: - What does the amygdala do? What is it connected to? How is it related to mind and behaviour? - How did the hippocampus get its name? What is it connected to? How is it related to cognitive function?

F.) The Basal Ganglia Study questions: - What are the primary components of this system? - Are there inputs and outputs to these circuits? Where do they come from and go to? G.) The cerebral cortex Study questions: Can you locate the prominent fissures including the median longitudinal, sylvian, rhinal and calcarine fissures? - How about the central sulcus? - How do these relate to the lobes of the cerebral hemispheres? - Can you identify the including the corpus callosum, anterior and posterior commissures? What are these and what do they do? - Can you find the fornix? What system is it associated with? - How about the cingulum? - Where is the pyramidal tract and what does it do -------------------------------------------------------------------------------------------------------Note: You can check locations by toggling labels on and off in the section views. -

Part II – radiological atlases. As you can see, some pretty remarkable things can be done using deep brain stimulation using implanted electrodes. These electrodes are implanted stereotaxically, that is to say using frames anchored to the skull surface that permit electrodes to be positioned with precision. In the earlier days of neurosurgery, stereotaxic surgery was done using “landmarks” on the skull – reference points that were constant across patients and in a relatively fixed position in relation to the brain. Examples would be the hard palate, the ear canals or the bony ridge at the top of the eye socket. This only works for “typical” skulls, and can lead to errors for people with odd-shaped heads or skull deformations. Fortunately the advent of CT and MR scans enabled radiologists to actually “see into” the soft tissue of the brain, and to create radiological brain atlases that can be used to guide surgery with much more precision, at least in terms of knowing approximately where the electrode needs to go. Final decisions can then be made based on a detailed scan of the individual’s own brain. Would you like to know how to use a radiological atlas? You might find this interesting even if you don’t plan on doing any neurosurgery, because it will allow us to actually peer into the brains of living people, to see the brain structures that neuroscientists find so interesting. This will also help you to understand findings from the whole emerging field of cognitive neuroscience. An especially interesting tool in this area is

functional neuroimaging, where we can actually view the ways in which brain activation shifts from moment to moment as we engage in various cognitive tasks. This enables us to understand how the brain controls processes like attention, memory, and the various decisions we make in everyday life. It also enables us to investigate how brain disease and injury affects these computational processes, and to assess the effectiveness of drugs and other forms of treatment. In order to navigate radiological atlases, we will need to use some software tools… A program called MRICron is available on the Internet. This is a free download, available at: https://www.mccauslandcenter.sc.edu/crnl/tools

This link takes you to an index page – to download it to your own personal computer, click on Installation and follow the instruction for your system – note that there are both Windows and Mac versions. The instructions (on the website) are as follows: 1. Download the installer. (the third one down with the ending win.zip 2. Copy the zip file to your desktop 3. Unzip the file – this will install a folder on your desktop called WIN 4. Open that folder and click on MRICron (the one with the little coloured brain) – this will open the program For an introduction and general description of what MRICron does, go to the index page for MRIcron at: h t t ps : / / pe o pl e . c a s . s c . e du / r or d e n/ mr i c r on / ma i n. h t ml

and open the “introduction” tab. Exploring the brain with MRIcron This program is a visualization tool that allows you to import and manipulate structural and functional images collected from MRI scanners. It also has various templates and overlays that can be used in conjunction with actual data sets to measure areas of activation in functional neuroimaging, track and display white matter bundles in diffusion tensor imaging, and to measure and quantify the location and extent of brain lesions. For now, we are going to do something much simpler, which is to use it to explore the structure of the normal human brain.

MRI Cr onus e sas i n g l es u bj e c tt e mpl a t et h a tc a nbeu s e dt ol o c a t ei nd i vi dua lb r a i ns t r u c t u r e si nMNIs pac e , wh i c hus e sac o or di n a t es y s t e m, wi t ht h ez e r oc o or di n a t e si nX, Y, Zs pa c e( 0, 0, 0 )l o c a t e dne a rt he mi d s a g gi t a lp oi n to ft hea nt e r i orc ommi s s u r e . MRI Cr ona l s oc on t a i nsov e r l a y s-t r a ns pa r e nc i e st ha tc a nb eus e dt ol oc a t ei nd i vi dua ls t r u c t ur e s , s uc ha s Br od ma n n ’ sc yt o a r c h i t e c t on i cr e g i o nsa nds o mee xa mpl e soft a s k r e l a t e df unc t i on a la c t i v a t i o ns .

For today…………. Let’s start by opening a file. Select “file” from the list at the top of the page, then “open templates” from the drop-down menu. Let’s start with the file called “ch2.nii.gz”. Here is a structural MRI of the entire head Open MRICron and click on the “view” window – this will open a drop-down menu. Select “display”. By default the program will display the brain in three two dimensional planes, called axial, coronal and sagittal. By selecting one of these in the view menu, one of these will be enlarged. Which view is which? Note that there are blue crosshairs (this can be toggled off and on in the view menu). Clicking with the mouse will change the position of the crosshair. Try this. Note that when you click on one of the slices the view of on the other two views will change. Can you figure out why that is? Now click “File>open template” and select “ch2better.nii.gz”. What is different from the file you were just looking at? ______________________________________________________________________ Now it is time to see if we can find some of the internal structures in the brain that we have talked about in class. ________________________________________________________________

Now let’s see if you can locate some of these structures using the MRICron brain template. Let’s imagine you are a neurosurgeon and wanted to implant a recording or stimulating electrode in a brain structure to diagnose or treat a neurological condition such as epilepsy or Parkinson’s disease. Let’s implant our electrodes in: 1. hippocampus 2. the amygdala 3. the putamen 4. the anterior cingulate gyrus 5. the fornix

In order to locate these structures you would need a reference point. The midpoint of the anterior commissure in the sagittal plane is assigned coordinates 0.0.0, corresponding to the coordinates in the X, Y, and Z planes. To bring up the MNI coordinates, toggle “MNI coordinates” in the View window. Now enter the numbers 0,0,0 into the x, y, and z fields and watch what happens to the crosshair. Next try changing the numbers in each of the fields, one at a time. What happens? So which direction is which? Note that you can plug in both positive and negative numbers. Which direction on each axis is positive?...