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 that you can try to find:

• Corticospinal tract. Efferent projection fibers that connect motor cortex to the brain stem and spinal cord.
  • See DTI image here
• Cingulum. A tract that runs along the top of the corpus callsoum connecting frontal, temporal, and parietal regions
  • See DTI image here
• Corpus Callosum. This massive bundle of white matter carries over 90% of all interhemispheric communication.
  • See DTI image here
• Corona Radiata. Widely spreading (fan-like) projections that connect the basal ganglia and spine to the cortex.
  • See DTI image here
• Superior longitudinal fasciculus. Fibers tract connecting the frontal lobe with parietal, temporal, and occipital lobes.
  • See DTI image here
• Inferior longitudinal fasciculus. Connects the occipital and temporal lobes.
  • See DTI image here
• Forceps major (aka posterior forceps). Connects the occipital lobes across the splenium of the corpus callosum.
  • See DTI image here
• Forceps minor (aka anterior forceps). Connects the frontal lobes across the genu of the corpus callosum.
  • See DTI image here

We will use TrackVis program to visualize white matter tracts.

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

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.

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.

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.

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)

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.

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.

Find Some Tracts!!

Use these methods, or others you discover, to isolate some of the tracts described at the top of the page following tracts.