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:
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.
We will use TrackVis program to visualize white matter tracts.
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
3. You will also want to have an anatomical image to help guide your track selection. Select File ⇒ Load Image and open
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
Objectspanel, you can hide this track view, or delete it.
controlkey when while you click
Propertypane, 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.
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 …
Slice Filters, which will only show fibers that travel through the selected slice.
Notthen you will only see fiber tracks that do not pass through your slice. Change the
Andand 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.
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
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.
ROItab in the lower-right
Radiusand set this value to
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.
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 some of the tracts described at the top of the page following tracts.