~~ODT~~

====== 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 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 [[http://www.ajnr.org/content/25/3/356/F10.large.jpg| here]]
  * Cingulum. A tract that runs along the top of the corpus callsoum connecting frontal, temporal, and parietal regions
    * See DTI image [[http://www.ajnr.org/content/25/3/356/F4.large.jpg| here]]
  * Corpus Callosum. This massive bundle of white matter carries over 90% of all interhemispheric communication.
    * See DTI image [[http://www.ajnr.org/content/25/3/356/F15.large.jpg| here]]
  * Corona Radiata. Widely spreading (fan-like) projections that connect the basal ganglia and spine to the cortex.
    * See DTI image [[http://www.ajnr.org/content/25/3/356/F11.large.jpg| here]]
  * Superior longitudinal fasciculus. Fibers tract connecting the frontal lobe with parietal, temporal, and occipital lobes.
    * See DTI image [[http://www.ajnr.org/content/25/3/356/F8.large.jpg| here]]
  * Inferior longitudinal fasciculus. Connects the occipital and temporal lobes.
    * See DTI image [[http://www.ajnr.org/content/25/3/356/F9.large.jpg| here]]
  * Forceps major (aka posterior forceps). Connects the occipital lobes across the splenium of the corpus callosum.
    * See DTI image [[http://file.scirp.org/Html/4-2060044%5Caddf30c2-9fa3-4f9e-a38f-2d171bc28592.jpg| here]]
  * Forceps minor (aka anterior forceps). Connects the frontal lobes across the genu of the corpus callosum.
    * See DTI image [[http://images.radiopaedia.org/images/12586/a70f7df1f6cf2f43ea0725a9f38b0d.jpg| here]]

===== Tractography =====


==== Visualizing Tracts with TrackVis ====

<WRAP center round info 90%>
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.
</WRAP>

We will use [[http://trackvis.org/|TrackVis]] program to visualize white matter tracts.

**1.** Open ''TrackVis'' by clicking on the icon in your dock. {{:psyc410_s15:images:trackvis_icon.png?50|}}

<WRAP center round tip 90%>
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.
</WRAP>

**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''.

{{ :course:lab03:screenshot_2015-01-28_13.06.03.png?direct&800 |}}

''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 [[http://www.trackvis.org/demo|here.]]

<WRAP center round alert 90%>
Before proceeding, watch the [[http://www.trackvis.org/demo/|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). 
</WRAP>

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.

{{ :undefined:trackvis_propertypane.jpg?300 |}}

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.

<WRAP center round tip 90%>
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. //
</WRAP>

=== 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)

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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''
</WRAP>

**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''

{{ :undefined:trackvis_roi.jpg?300 |}}


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.

<WRAP center round tip 90%>
You can similarly create a TrackGroup based upon a hand-traced ROI like in the [[http://www.trackvis.org/demo/?3|linked video]].
</WRAP>


**Find Some Tracts!!**

Use these methods, or others you discover, to isolate some of the tracts described at the [[http://www.andrewengell.com/wiki/doku.php?id=kpnl:reu_dti_demo&#diffusion_weighted_imaging|top of the page]] following tracts.