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Diffusion Weighted Imaging

A white matter fiber connects the output of one neuron to one or more target neurons. There are well known bundles or tracts of fibers that run through the brain and spinal cord and connect distant brain regions. Here are a few examples of major tracts:

Corticospinal tract. A good review is linked here.
Corpus callosum. Its divisions are discussed here and here.
Superior longitudinal fasciculus.It is discussed here here.
Inferior longitudinal fasciculus.

A review of tracts using DTI can be found here.

In this lab we will investigate relatively new methods in MRI to visualize the integrity and direction of white matter tracts.

Part 1: Introduction to Diffusion and White Matter Tracts

6. Identify each of the following structures one by one. Note we are only going through the left hemisphere tracts here to conserve time. For the following four, make sure to take a screenshot.

Corticospinal tract L: nerves within the corticospinal tract are involved in movement of muscles of the body.
Cingulum (cingulate gyrus) L: white matter fibers that project from the cingulate gyrus to the entorhinal cortex.
Forceps minor: connects the lateral and medial surfaces of the frontal lobes and crosses the midline via the genu of the corpus callosum.
Inferior fronto-occipital fasciculus L: passes backward from the frontal lobe to the occipital and temporal lobes. Also note the proximity of this tract to the forceps minor and to the corticospinal tract (this might be important later when discussing crossing fibers)!

Feel free to explore some of the other fiber tracts on your own. Do you notice any other tracts that might either cross or come very close to each other?

We have just opened four tracts primarily in the left hemisphere:

Corticospinal tract in blue indicating it mainly goes between superior and inferior
Cingulum in green indicating it mainly goes between anterior and posterior
Forceps minor in red indicating it mainly goes between lateral and medial
Inferior fronto-occipital fasciculus in green like the cingulum

Tractography

Visualizing Tracts with TrackVis

The sample data for this exercise are located in ~/Desktop/class/input/dti/dipy. We will be using a very high quality dataset in this section (It is the demo dataset given by the `dipy` software package). It is data from one subject with 150 directions and 10 B0 scans. The higher number of directions is critical for accurate tractography and particularly for resolving crossing fibers

In this section we will use TrackVis program to visualize white matter tracts.

1. Open TrackVis by clicking on the icon in your dock.

If you don't see the icon in your dock, you can open it from your Applications directory. If you're not a Mac user, just ask me for help.

2. Select File ⇒ Open Track or Scene … and open the tensor_streamlines.trk file in the ~/Desktop/class/input/dti/dipy/dipy directory.

3. You will also want to have an anatomical image to help guide your track selection. Select File ⇒ Load Image and open tensor_fa.nii.gz.

TrackVis has tons of options. We will explicitly cover a few below. For a fuller description of the options you can refer to the TrackVis website here http://www.trackvis.org/. The website offers some brief tutorial movies that can be viewed in your browser that illustrate the use of the program. These are very helpful in quickly learning the interface. You can find a list of these movies here.

Before proceeding, watch the TrackVis movies. At minimum, watch the first and second movies to quickly get familiar with the interface. Each movie runs for about 90 sec (although you must click at certain points to move the movie forward).

The main value of TrackVis is to isolate particular fiber tracks by use of TrackGroups, Slices, Regions of Interests, Balls/Spheres, etc. You can toggle different TrackGroups on and off, for example

if you right click on Track 1 in the upper-right Objects panel, you can hide this track view, or delete it.
- NOTE: On a Mac you can “right click” by holding down the control key when while you click
In the lower-right Property pane, you can double-click on most properties of the selected TrackGroup and change them. For example, you can change the way the current slice looks, which axis it is drawn along, how dense the fibers are drawn, etc.

Add some screenshots of the track and peroperty windows and options.

Show an example of how changing the length affects which fiber tracts are shown.

Play with the controls to get a sense of how you can navigate through space, rotate the brain, adjust which fiber tracts are displayed, etc.

It'll take a little bit of time playing around before you get the hang of it. Your goal isn't to become an expert user, but you should get a feel for the basic image/track manipulation options. And if things go totally off the rails, you can always close and reopen the program to start fresh. Try to …

Only view the long tracks and then only view the short tracks
- Click on Track in the Property Window
- Adjust the Length Threshold settings
Play around with the Slice Filters, which will only show fibers that travel through the selected slice.
- Activate the check box next to the X, Y, or Z Sliced Filter
- Click on the slice number to the right of the checkbox and move the slider
- Adjust the Thickness
  - Hint: If you turn on the X slice filter, and change the Operator to Not then you will only see fiber tracks that do not pass through your slice. Change the Operator to And and you'll only see fibers that do pass through your slice. You can add additional slice filters and set the operators such that you'll only see fibers that pass through both your slices, none of your slices, one of your slices, etc.

Creating an ROI Sphere

Let's create a ball-shaped region of interest (ROI) to select some tracts. This will help us identify only the tracks that run through areas we're interested in (our ROI)

To clear your workspace, you might consider turning off, or hiding, the current slice-based view. To do so, right-click on Track1 in the Objects box and select Hide

1. Select TrackGroup ⇒ New Track Group from Sphere

A small ball will show up at the cross-hairs of your 3 orthogonal views. You can make this ball bigger or small by manipulating its properties.

2. Let's make the ball a little bigger.

Click on the ROI tab in the lower-right Property window.
Double-click on the 2 next to Radius and set this value to 3

You can drag the ball around within your three orthogonal slice windows along the bottom of the screen.

Include a sceenshot of what I mean by “orthogonal slices”

you have to click on x ad check the checkbox to select the slice filters

3. If your three orthogonal slices are not moving as you move your sphere around, click on the Sync Slice to ROI center button. (this button is in the Image window. It is the button that looks like a window-pane with a ball in the middle of it)

4 You can add a second ROI sphere by simply repeating steps 1-3.

You can similarly create a TrackGroup based upon a hand-traced ROI like in the linked video.

Find Some Tracts

Use these methods, or others you discover, to isolate the following tracts.

Include links and pictures to help them identify these images

minor forceps
major forceps
corticospinal tract
cingulum

Kenyon Psychological Neuroscience Lab

Table of Contents

Diffusion Weighted Imaging

Part 1: Introduction to Diffusion and White Matter Tracts

Tractography

Visualizing Tracts with TrackVis

Creating an ROI Sphere