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kpnl:reu_dti_demo [2016/06/27 16:53] – [Diffusion Weighted Imaging] adminkpnl:reu_dti_demo [2016/06/27 17:06] (current) – [Visualizing Tracts with TrackVis] admin
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 ==== Visualizing Tracts with TrackVis ==== ==== Visualizing Tracts with TrackVis ====
  
-<WRAP center round info 80%> +<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 and particularly for resolving crossing fibers+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> </WRAP>
  
-In this section we will use [[http://trackvis.org/|TrackVis]] program to visualize white matter tracts.+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|}} **1.** Open ''TrackVis'' by clicking on the icon in your dock. {{:psyc410_s15:images:trackvis_icon.png?50|}}
  
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 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. 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> </WRAP>
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 ''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.]] ''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.]]
  
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 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).  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). 
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   * 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.   * 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.
  
-<WRAP center round todo 60%> +{{ :undefined:trackvis_propertypane.jpg?300 |}}
-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. +
-</WRAP> +
  
 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. 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.
  
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 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 ... 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   * Only view the long tracks and then only view the short tracks
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 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) 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'' 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''
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   * Double-click on the ''2'' next to ''Radius'' and set this value to ''3''   * 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.+{{ :undefined:trackvis_roi.jpg?300 |}}
  
-<WRAP center round todo 60%> 
-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 
-</WRAP> 
  
 +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) **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)
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 **4** You can add a second ROI sphere by simply repeating steps 1-3. **4** You can add a second ROI sphere by simply repeating steps 1-3.
  
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 You can similarly create a TrackGroup based upon a hand-traced ROI like in the [[http://www.trackvis.org/demo/?3|linked video]]. You can similarly create a TrackGroup based upon a hand-traced ROI like in the [[http://www.trackvis.org/demo/?3|linked video]].
 </WRAP> </WRAP>
  
  
-**Find Some Tracts** +**Find Some Tracts!!**
- +
-Use these methods, or others you discover, to isolate the following tracts. +
- +
-<WRAP center round todo 60%> +
-Include links and pictures to help them identify these images +
-</WRAP> +
  
-  * minor forceps +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.
-  * major forceps +
-  * corticospinal tract +
-  * cingulum+
  
kpnl/reu_dti_demo.1467064423.txt.gz · Last modified: 2016/06/27 16:53 by admin
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