Lab 5 - Atlases and overlays in MRICron PDF

Preview

Summary

Download Lab 5 - Atlases and overlays in MRICron PDF

Description

Lab #5: October 22 &24, 2019 Last week you learned how to locate structures in MNI space. In functional neuroimaging research, we frequently have the converse problem – that is, we may have an area of increased signal that corresponds to some task-related activation (defined as a set of MNI coordinates), but don’t know exactly which brain area is actually activated, since our images do not come with labels attached. In clinical casework, the problem is similar – we can see from the MR images where the brain damage or lesion is, but need to know what specific issues the patient might have as a result of the damage, or as a result of surgery or other intervention to treat the condition How are we going to solve this problem? The answer is to refer to atlases that have been created to depict certain structures in MNI space. In MRICron several of these are provided. For gray matter, two useful ones are: the aal.nii and the brodman.nii atlases. For white matter, two useful ones are: the JHU white matter labels.nii and the natbrainlab.nii atlases. Each of these depicts a set of structures that have been mapped on to MNI space and then colour coded. To use these atlases we need to first open an template, so begin by opening the ch2.better.nii image under the file>open templates button. How does this differ from the ch2.nii image? Next we are going to use the atlases as “overlays” in the MRICron software. To accomplish this, the next step is to add the atlas to our image using the Overlay>Add button. Let’s start by selecting the aal.nii overlay. What happens when you add the overlay to the background image? Try clicking on some of the coloured areas and see what happens. Does any useful information appear on the screen? The above atlas is useful in providing a name for structures that are located in MNI space, so that if you had observed a significant increase in activation in that area in a functional imaging experiment you could name the structure that was involved. However you will notice that the coloured cortical regions are relatively large. For research purposes we might wish to narrow down the localization somewhat, which is where the brodmann.nii atlas becomes useful. What do you suppose it depicts? Note that the brightness of both the overlay and background image can be adjusted within the Transparency on background and Transparency on other overlays using the Overlay button. (Note, you can superimpose more than one overlay on a given template, but that this can become visually confusing – for now I recommend that you use them one at a time)

1

OK, here is the assignment for this lab (Due October 29 &31) Part 1: (15 marks) For each of the following coordinates, identify the structure or region, as well as the template you used to locate that structure. Let’s start with some cortical areas. Identify each of the following by name and by its Brodmann number. 7, 68, 7 53, -13, 45 -46, 6, -34 41, -13, 13 7, -81, 13 Now let’s try some subcortical structures. Do these have Brodmann labels? Why or why not? Which overlay do you find most useful? 20, 3, 2 26, 1, -17 2, -38, -6 -25, 11, 4 29, -10, -19 Finally, let’s try locating some white matter structures. For this you are going to have to open a new overlay. Which one are you going to use? Here are your coordinates: 15, 8, 4 -34, 1, 0 36, -21 27 9, -24, -25 9, -43, 14 Part 2: (5 marks each X 3 = 15) Choose one structure from each of the above groups (i.e. cortical, subcortical, white matter), do some research on the internet, and write a brief description (500 words or less) as to what the structure contributes to behaviour and/or cognitive function. Cite your sources at the end of each description.

2

Supplement: For the keeners among you, here is an additional web-based resource: http://www.med.harvard.edu/AANLIB/home.html

This is the Harvard Atlas. It contains both an atlas of clinically normal brains, and a number of patient cases illustrating various forms of neuropathology. The most basic module is called “Normal anatomy in 3D with MRI and PET”. This is a brain volume similar to the template in MRICron that shows the brain in axial, sagittal and coronal slices. You navigate around it by moving the yellow arrows above each of the brain slices. Note that the levels of section do NOT correspond with coordinates in either the MNI system or the Taliarach atlas. It also has a module called “atlas of normal structure and blood flow” with subsections called “top 100 brain structures” and “can you name these brain structures?” This can be useful as a self-test, and in finding your way around the brain using MR images. -----------------------------------------------------------------------------------------------------------.

3...