Table of Contents
CMA Methodology Overview 3
A Guided Tour of CardViews 4
Cortical Parcellation - Getting Started 10
Dorsal Axial View 12
Medial Sagittal View 15
Lateral Sagittal View 18
Ventral Axial View 23
Coronal View 25
Nodes and Planes 26
Coronal Series I 28
Coronal Series II 33
Coronal Series III 37
Axial Series 41
Midsagittal Series I 47
Midsagittal Series II 51
Lateral Sagittal Series I 54
Lateral Sagittal Series II 58
Parcellation Labels 63
White Matter Parcellation 85
Generating Volumetric Data with XVol 87
Creating 3D Models with SegSurf 89
CardViews General Functions Summary 92
CardViews Parcellation Functions Summary 96
Sulci Definitions 102
Parcellation Units Definitions 105
Atlas of the Parcellated Brain 106 Cortical Parcellation - Method and Utilization 1 Center for Morphometric Analysis Version 2 ; May 2004
Nikos Makris, M.D., Ph.D. David N. Kennedy, Ph.D. James Meyer, M.D.
Andrew Worth, Ph.D. Verne S. Caviness Jr., M.D., D. Phil.
Larry Seidman, Ph.D. Jill Goldstein, Ph.D. Camille Macpherson Jason Tourville
Scott Rauch, M.D.
Barbara Glode, M.A. Jennifer Koch
George Papadimitriou Joseph J. Normandin Nicole Cullen
Denise Boriel, M.A., M.S. Heather A. Sanders
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CMA Methodology Overview
The CMA methods of analysis comprise general segmentation, cortical parcellation, subcortical parcellation, and white matter parcellation. These methods of analysis subserve volumetrics and
human brain mapping.
Volumetrics is a science dealing with brain structure measurements as well as algebraic relations that relate these volumes (Caviness, 1999). Because of their comprehensive and quantitative nature, our methods of analysis provide a set of volumes that can be used for statistical analysis of covariance and modeling (Cereb. Cortex, Kennedy, 1998), thus enabling characterization of normative data as well as comparisons with disease data sets.
Human brain mapping
The principle aim of our system provides a basis for brain function and metabolic activity mapping by determining a finite and specific set of quantifiable regions of interest or parcellation units.
The methods of general segmentation, cortical and subcortical parcellation, and white matter parcellation are designed in the context of a neural systems approach (namely, the motor system,
perceptual (somatosensory, visual, auditory, gustatory, olfactory) systems, nociceptive (pain) system, cognitive (attention, executive, memory, visual/spatial, language) systems, and the affective (limbic) system). These methods may help elucidate basic questions in neuroscience, such as the relationships between cytoarchitectonic fields, cerebral connections, and neural functions. Cortical Parcellation - Method and Utilization 3 Center for Morphometric Analysis Version 2 ; May 2004
A Guided Tour of CardViews
CardViews, short for cardinal views, is a program that creates visual images of the brain in the coronal, axial, and sagittal planes and displays them all on the same screen. This makes it easy to cross-reference a point you are not sure about. CardViews is used for segmentation and parcellation of the brain.
Type the following line at the prompt of any workstation in the "Cave":
cardviews 1110 2
The computer will "think" for a moment and then begin to load brain images corresponding to the second scan of subject 1110 in the lab's image database. The program that you are loading is called CardViews. The images that you see are actual magnetic resonance images from a real person. Aligned on the right side of the screen are the CARDinal VIEWS used in general anatomical study: coronal, as if the person is facing you; sagittal, as if you are staring right into their right ear; and axial, looking from the spine toward the top of the head (axial seems like a top-down view, but it's really bottom-up).
The left side of the images in any cardinal view is the right side of the brain.
The way the images were obtained allows CardViews to illustrate any area of the image in the three cardinal planes. Through the use of projection lines, any area can be cross-referenced to help determine sulcal boundaries, extent of gray matter areas, vasculature, nerves, etc. To see a quick illustration of this, single-click with the left mouse button on the rectangles called "auto trans" and "Projection." This will bring up crosshair lines. Now move the pointer to the large central image and double-click the left mouse button on any area of the image. You will see the other views change to show the intersection of the crosshairs in the other two planes. Experiment by double-clicking around the central image and watch the other views transform their images. The horizontal line in the central image shows the axial plane. The vertical line shows the sagittal plane.
There are slice numbers in the corner of each view. If you look above the central image you will see the same numbers next to the abbreviations "COR", "SAG", and "AXI." As you double-click around the central coronal image, you'll see the sagittal and axial numbers change to reflect the position of the projection lines.
In general, you will work with brains that have 64 or 128 coronal slices with 256 slices in the sagittal and coronal planes. The slice numbers referenced by the projection lines are listed next to COR, SAG, and AXI. The arrow buttons next to the numbers are another way to change slices. A single-click on any of the smaller images will bring it to the central window.
Single-click with the left mouse button on the word "Quit" at the top left of the CardViews window. This is how you quit the program. Start it up again like you did at the beginning (type "cardviews 1110 2"). Notice that Cardviews starts with the middle slice of the coronal plane (in this case slice 32 of a 64 slice brain) and that the slice 128 in both of the other two planes.
You can adjust the brightness and contrast of the screen to enable easier viewing. You will adjust the screen to many different levels of brightness and contrast depending on which structures you are Cortical Parcellation - Method and Utilization 4 Center for Morphometric Analysis Version 2 ; May 2004
segmenting. To change the brightness and contrast, click in the central image box with the middle mouse button. Now move the mouse around. You should see the brightness of the image changing. Click the middle mouse button again while in the image box. This will set the image brightness and contrast. Play around with this feature for a bit. Notice that if you click in the lower right hand corner of the image box, and slide the mouse upwards, you will increase the brightness of the screen. If you then slide the mouse to your left, you will decrease the contrast of the screen. Watch how the outside of the brain seems to be larger or smaller depending on the brightness of the screen. Also note how the gray and white matter appear to "bleed" together as the contrast is decreased. After you're done, set the brightness/contrast to a level where you can see the edge of the brain without the white and gray bleeding together. Your cursor will be approximately two-thirds up in the image box, underneath the word AXI.
The exact position of your cursor will vary depending on which computer you are sitting at, so if your cursor isn't here, that's okay!
The Three Cardinal Views
Cardviews will display a sulcal line in all three planes. Make sure the "auto trans" button is on by single clicking on it (auto trans allows you to scroll through the three views with the up and down arrows next to the COR, SAG, and AXI slice numbers). If it is active, there will be a thick white line around the box. Move the mouse to the central image and single-click the right mouse button. You will see the words "NAV draw_mode" and something in green just above the central image. Draw a giant "X" across the coronal image: single-click the left mouse button at the top-left of the image and again at the bottom-right; single-click the right mouse button to exit from draw mode; initiate draw mode again by single-clicking the right mouse button; similar to before, left-click once at the top-right corner of the image and once at the bottom-left; then right-click to exit draw mode. If all went well, you should now have a green-colored " X" across the coronal slice.
Click on the sagittal image on the right side of the screen. This will bring the sagittal image to the central image screen. Now click in the up arrow next to the word SAG. You will notice some green dots move. As you continue to press the up arrow, you should notice the dots moving further apart. This is because you are moving laterally to the edge of the brain, and the dots are getting further apart as you approach the side of your "X." Click in the down arrow key to move medially. Eventually you will pass the center of the brain, and move laterally towards the right side of the brain. The dots will start to move further apart as you approach the other end of the "X."
Next click on the axial view to move this view to the center of your screen. Hit the up arrow next to the number by the word "AXI." You will again see the green dots come closer and further apart. These correspond to your "X." This demonstration was to help you understand how the different views are connected to one another, and how sulci lines appear in different views.
When you're done playing, quit cardviews. Then restart the program as you did before. When the NAV screen appears, turn on "auto trans." You are ready for the next section of the tour.
CardViews Four Modes
There are four modes in CardViews: NAVigation, SEGmentation, REView, and Tile Display. The buttons to change modes are just below "Quit." NAV mode is used to draw sulcal lines (for parcellation) and boundary lines that help to determine where one structure ends and another begins. SEG mode is used for segmenting structures and editing outlines. REV mode is used to Cortical Parcellation - Method and Utilization 5 Center for Morphometric Analysis Version 2 ; May 2004
label the outlines and check for errors. Tile Display presents you with a larger series of brain slices which allows you to easily follow a structure through multiple slices. It can also be used to draw sulci lines, check for labeling errors, and compare the outlines from different segmentors.
So far you've been playing around in NAV mode. NAV mode is used for parcellation and to assist in segmentation. You will draw and save lines called sulci lines in this mode. Notice the word OVERLAY at the bottom of the screen, under the central image. Next to it is written the path where your sulci files are stored. You don't need to know what this means (that's what computer techs are for) but you should see 1110_2 written somewhere in this line. That indicates that you are working on brain 1110 scan 2. Below this line is the word "Prefix." You will save your sulci lines with your own personal prefix. To do this, first click on the line next to the word "Prefix." Enter your 3 initials, followed by the letter s. For example, if your name is John Frank Brown, you would enter jfbs. Then hit return. When you hit return, you should see the Sulci File line change. Your prefix now appears next to 1110_2. You are now ready to draw sulci lines.
To draw a sulci line, you will follow the same procedure you did previously to draw the "X." First enter draw mode by clicking the third mouse button. Then click where you want the line segment to begin with the first mouse button. Click at another point to draw a segment. Click somewhere else. You should have a line with 2 segments. Continue to play with the drawing feature. After you've finished drawing your line, make sure you hit the third button to exit draw mode and return to base mode. You can re-enter draw mode to reinitiate drawing in a different area.
To get rid of a line you don't like, click on it while you are in base mode. This will turn the line black. Continue to hold your cursor down on the now black line, and drag your cursor outside of the center image box. This will erase that sulci line.
To save your sulci lines, hit the "SAVE sulci" button at the bottom of the screen. Make sure you are in base mode when you hit the "SAVE sulci" button, or your sulci lines will not save. If you want to save more lines, hit "SAVE sulci" again after drawing them. A window will pop up asking if you want to overwrite your existing file. Click on the "Overwrite" button to save your new sulci.
SEG mode is used to segment. To enter SEG mode, click on the "SEG" button under "Quit." If you look at the top box under the three boxes for NAV, SEG, and REV mode, you will see the word SEG on the second line. Next to it is the word base, indicating that you are in base mode. There are many different drawing methods available for use in SEG mode. The method you are using will always appear next to the word SEG.
Underneath the center image block you should see a line that reads OVERLAY. This is similar to the SULCI FILE in NAV mode in that it tells you what brain you are working on. Below that is the prefix line. In SEG mode, your prefix is just your initials (no "s."). For example, if your name is John Frank Brown, your prefix is jfb. Click on the line next to the word "prefix." Enter your initials, and hit return. You should see your initials become part of the line next to OVERLAY.
There are a few differences between NAV mode and SEG mode. One of the most apparent differences is the way projection lines work. Up to this point you've been playing with the projection lines in NAV mode. In SEG mode, they are not as automatic. Click on the projection box to bring up the crosshairs. In NAV mode, you could double click anywhere on the image in the center box to Cortical Parcellation - Method and Utilization 6 Center for Morphometric Analysis Version 2 ; May 2004
reveal the same place in the sag and axial views. This doesn't work in SEG mode. To move the crosshairs to a specific point, use scroll bars next to the small coronal image in the right side of the screen. Using the knobs on these scroll bars, position the crosshairs to the area you want to investigate. Then hit the "Transform" button next to the SAG and AXI words. This will move the crosshairs to that position in these 2 views. Click the "Projection" button to turn off the projection lines.
The point of SEG mode is to create outlines (also referred to as "otls") that can be used in volumetric analysis. For example, you will create an outline of the amygdala on every slice that has amygdala. This enables statisticians to estimate the amygdala volume for the brain. There are four drawing methods we use to help in creating outlines: the intensity contour, the histogram, drawing, and the optional auto-seg. These are all explained in greater detail in the "General Methods and Tools of Segmentation" section. Anytime you enter into one of these drawing methods, the word "ok" in the upper left box will change, to indicate which method you are in. When you exit that method, that word will return to "base."
The four methods of drawing enable you to trace brain structures. When you are done tracing a particular structure, you extract it. Extracted outlines can be saved, labeled, and are what we use in analysis.
Now we'll try and create a simple outline. We'll do this by drawing. Drawing in seg mode works slightly differently than it does in NAV mode. Place your cursor in the center image box. Click the right mouse button. You'll notice you've switched from "base" to "draw_mode." Hold down the first mouse button and drag it across the screen. You've just drawn a line. Now click the right mouse button again to exit draw mode. Now try to draw a circle. Click the right mouse button again to enter draw mode. Hold down the left mouse button and draw a closed circle; this can be a sloppy circle, just make sure you create some sort of closed shape. Click the right mouse button again to exit draw mode. Now place your cursor inside the circle. Press "e" to extract the outline. You'll notice part of
your red circle is now green. Hit the "SAVE" button. Now hit the
clear button. How hit the load button. If all went well, your green
outline was saved, and loaded, and the red contour disappeared
when you hit the clear button; this is because only extracted
outlines can be saved.
Notice that there are eight colored boxes in the upper left white
box. We'll focus on the first five. These boxes are your contour
boxes. There is a small black box in the red box. This means that
any contours you create or erase will be red. Using the method
described above, draw a red line (make sure to exit draw mode
when you are done). Now click on the yellow box. The little black
box has moved from the red box to the yellow box. Draw a line. It
should be yellow. Now hit "x." The "x" function is used to get rid
of all contours of a given color. Your yellow line should be gone, but the red one still remains. Click on the red box. Now hit "x." The red contour should be gone. Play around with the 5 different colored contours. Draw different shapes in different colors, and extract them. You'll notice that no matter what color you draw a shape in, it will always turn green when you extract it. You can even create shapes out of two different colored contours. Being able to create outlines using many different colored contours makes segmenting easier and faster.
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The concept of extracting is a bit tricky to understand. Here is an exercise to try to make it clearer. First hit the clear button to clear the screen. Next draw a house: First draw a square (make sure that there are no gaps between the four sides). Now draw a triangle roof on top of the square; making sure the ends of the roof touch the top of the box, and that the two slanted sides of the roof intersect.
Place your cursor inside the triangle (roof) and press "e" to extract it. Only the triangle should turn green. Now hit "w," this un-extracts the last thing you extracted (in this case the triangle). Place your cursor inside the box and extract it. Only the box is green. Hit "w" to unextract it. Now place your cursor underneath the box. Hit x. You'll notice that your "house" is green: the shape comprised of 3 sides of the box and 2 sides of the triangle was extracted.
The way the extract command works is as follows: The program detects the first contour you drew that is immediately ABOVE your mouse cursor. Then it follows that contour all the way around until the contour ends. So if you are INSIDE an enclosed shape like your box, the program detects the upper part of the box, and then follows the contour all the way around along the inside of the box. When you extract the house from the OUTSIDE, the cursor hits the bottom of the box, and then follows around the outside of the house. In order to create outlines that can be used in analysis, all structures must be extracted from the inside. We often extract things from the outside as a useful tool during segmentation (this will be described in the methods section). However, remember that structures must be extracted from the inside in order to be used in morphometric analysis.
While you are segmenting, the easiest way to move around is to use the "-" and "+" buttons underneath your prefix. This will automatically change your saved outlines as you change slices.
After you have extracted structures on a slice, you must click the “Save” button before moving to the next slice using the “+” and “-“ buttons. Otherwise, you will lose your outlines.
Click on the REV button. You'll notice the "review panel" pop up in the left corner of the screen. Review mode is used to check and label the brain. There isn't much to play with until you actually have some saved "otls."
Tile Display Mode
Click on the tile display button. A large screen will appear. Click on the "GO" button that is about one quarter down from the top of the screen. You should see a whole bunch of brain images. Tile display enables you to see many slices at one time and is used to check the brain, examine tricky areas, and draw sulci lines. Notice the numbers and scroll bars at the top of the screen. These indicate which slices you are on, and allow you to move to different slices. Just a warning... these scroll bars are tricky to use. Click on the TOP scroll bar and drag it all the way to your left. As you did that, the bottom scroll bar also moved left. You should see the number 3 on the top line, and 32 on the bottom line. Click the "GO" button again. You are now looking at slices 3-32. Click on the BOTTOM scroll bar and drag it to your right. When you do this, make sure you do not drag the mouse cursor outside of that left panel (that is, not past the white line that separates the buttons from the brain images). The program will not cooperate with you if you drag your cursor too far. The top line should read 30, and the bottom should read 59. Click GO again. You are looking at slices 30-59.
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Click on the box next to the word "zoom" that is located to the left of the GO button. You'll notice the slice numbers next to the scroll bar have changed. Now click on GO. You are looking at six zoomed images. Play around with the scroll bars to move to different slices. Always click GO to transform the images. If you want to look at the smaller images again, just click the box next to zoom to turn off this feature. And then click GO.
You can look at multiple sagittal or axial images by clicking the sag or axi box underneath the scroll bars. Then click on GO.
As with review mode, there isn't a lot more you can do in tile display without segmenting first.
To return to the main page of CardViews, click on the CARDVWS button.
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Cortical Parcellation – Getting Started
Cortical parcellation is our MRI-based methodology used to subdivide the human cortex into discrete, volumetrically identifiable "closed" regions of interest. This method is applied on any particular brain under investigation and utilizes topographical descriptors, i.e. fissures and nodes/planes of the individual brain.
Naming Your Files
Parcellation requires the assignment of fissures, nodes, and parcellation units. Upon opening CardViews, the first step is to give a name to these new files. When you enter CardViews you will be in NAV mode. The general format for entering the information on how to name your files is:
":ce 'your segmentation prefix' 'your sulci prefix' 'your parcellation prefix'"
Note where there are spaces in this format. Now click on the central image in NAV mode and type:
This will tell CardViews that you are about to enter the prefixes it will use to name the various files you will create while drawing sulci, defining nodes, and defining parcellation units. Next, type:
"your segmentation prefix" (usually your initials followed by an "I"
(upper-case "i" not to be confused with a lower-case "L")
"your sulci prefix" (your segmentation prefix followed by an "s" without any spaces) "your parcellation prefix" (your sulci prefix followed by a "J" without any spaces)
For example, if your name was Amy Leigh Sonricker you would type:
:ce alsI alss alssJ
By setting these parameters the program knows how to overlay the sulci and nodes onto the segmentation, and what to call the resultant outline file.
What the Prefixes Mean
Segmentation files are generally saved with your initials as the file name, followed by an "I" which tells CardViews to load the "I-files" which have a cortical ribbon for you to parcellate. Sulci files are saved with an "s" at the end of your initials as the file name. The "s" stands for sulci. Parcellation files are saved with both the "s" as well as a capital "J" at the end of your initials as the file name. The "J" stands for Jim Meyer, the original programmer of CardViews (he wanted to go down in history as a part of CardViews, thanks Jim!).
Left and Right
It is also important to be sure that you understand where the "left" and "right" side of the brain are located in the different views. In coronal views, "left" and "right" are as if you were looking at a persons face; therefore "your right" is the coronal sections "left." In sagittal views the lower numbered sections are the right side, whereas the higher numbered sections are the left side. In axial views, you are looking from underneath upon the section; therefore "your right" is the axial sections "left." Cortical Parcellation - Method and Utilization 10 Center for Morphometric Analysis Version 2 ; May 2004