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kpnl:reu_dti_demo [2016/06/27 15:50] – [Part 1: Introduction to Diffusion and White Matter Tracts] adminkpnl:reu_dti_demo [2016/06/27 17:06] (current) – [Visualizing Tracts with TrackVis] admin
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 ====== Diffusion Weighted Imaging ====== ====== 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:+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. A good review is linked [[http://en.wikipedia.org/wiki/Pyramidal_tracts|here.]] +  * Corticospinal tract. Efferent projection fibers that connect motor cortex to the brain stem and spinal cord. 
-  * Corpus callosum. Its divisions are discussed [[http://www.jneurosci.org/content/28/7/1535.full|here]] and [[http://en.wikipedia.org/wiki/Corpus_callosum|here.]] +    * See DTI image [[http://www.ajnr.org/content/25/3/356/F10.large.jpg| here]] 
-  * Superior longitudinal fasciculus.It is discussed  [[http://cercor.oxfordjournals.org/content/15/6/854.full|here]] [[http://en.wikipedia.org/wiki/Superior_longitudinal_fasciculus|here.]] +  * Cingulum. A tract that runs along the top of the corpus callsoum connecting frontal, temporal, and parietal regions 
-  * Inferior longitudinal fasciculus. +    * 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. 
-A review of tracts using DTI can be found [[http://www.ajnr.org/cgi/content/figsonly/25/3/356|here.]] +    * 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. 
-In this lab we will investigate relatively new methods in MRI to visualize the integrity and direction of white matter tracts. +    * 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]] 
-<WRAP center round todo 60%> +  * Forceps minor (aka anterior forceps). Connects the frontal lobes across the genu of the corpus callosum. 
-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. +    * See DTI image [[http://images.radiopaedia.org/images/12586/a70f7df1f6cf2f43ea0725a9f38b0d.jpg| here]]
- +
-  * **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)! +
- +
- +
-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 +
-</WRAP>+
  
 ===== Tractography ===== ===== Tractography =====
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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|}}
  
-<WRAP center round tip 80%>+<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. 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.]]
  
-<WRAP center round alert 80%>+<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).  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> </WRAP>
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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.
  
-<WRAP center round tip 80%>+<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 ... 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)
  
-<WRAP center round tip 80%>+<WRAP center round tip 90%>
 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''
 </WRAP> </WRAP>
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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.
  
-<WRAP center round tip 80%>+<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]]. 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.1467060655.txt.gz · Last modified: 2016/06/27 15:50 by admin
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