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kpnl:reu_dti_demo [2016/06/27 15:29] – [Compensate for eddy currents] 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. 
 +    * 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]]
  
-A review of tracts using DTI can be found [[http://www.ajnr.org/cgi/content/figsonly/25/3/356|here.]] +===== Tractography =====
- +
-In this lab we will investigate relatively new methods in MRI to visualize the integrity and direction of white matter tracts. +
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-===== Part 1: Introduction to Diffusion and White Matter Tracts ===== +
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-**6.** 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. +
- +
-  * **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)! +
- +
-Feel free to explore some of the other fiber tracts on your own. Do you notice any other tracts that might either cross or come very close to each other? +
- +
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-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 +
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-==== Strip your skulls! ==== +
- +
-<WRAP center round tip 80%> +
-Need a refresher on using BET? **[[psyc410_s15:brain_extraction_segmentation#part_2skull_stripping_your_test_brain_using_fsl_bet_est_20_min|Click here]]** to go back to the the walkthrough from Lab 03 +
-</WRAP> +
- +
-You will need a brain mask for this exercise. A brain mask is a binary image that contains ones wherever there is brain and zeros everywhere else (e.g., skull, scalp, outside of brain). Such a mask can then be used to remove from computation any region that is not brain. Brain masks can be created with FSL's Brain Extraction Tool (BET). Be sure to **specify your eddy corrected images as input**. +
- +
-The ''33470_LAS_eddy.nii.gz'' is a T2-weighted image (with no diffusion gradients applied). T2 images provide some challenges to skull stripping, because the skull and scalp are not well defined in T2 contrast.  +
- +
-<WRAP center round tip 80%> +
-You might find using the option for lowering the ''Fractional intensity threshold'' improves skull stripping in this image. Try using the ''Robust brain centre estimation'' option and lower the threshold to ''.35'' to get good separation of skull and brain. However, you can try different values and view the results in ''FSLview'' until you are satisfied. +
-</WRAP> +
- +
-Also, because we need a brain mask, you need to check the option (under ''Advanced Options'') to ''output a binary brain mask image'', and a brain-extracted image. Skull stripping should only take a few seconds. +
- +
-{{ :psyc410_s15:images:bet_dti.png?400 |}} +
- +
-Before proceeding, make sure you have a good brain mask and a good skull stripped brain. Quality is important. Make a note of their names, as this will need to be provided in the next step. +
-==== Compute DTI and FA ==== +
- +
-Choose the ''FDT diffusion'' program from the FSL menu, and the ''**DTIFIT reconstruction**'' from the FDT menu. +
- +
-{{ :psyc410_s15:images:fdt1.png?400 |}} +
- +
-Now //(note the numbered list below corresponds to the numbers in the image below)//: +
- +
-  - Check the ''**Specify input files manually**'' box. This program will run automatically if certain naming conventions are used. However, as we named our image volumes unconventionally, we need to check that box. +
-  - Be sure to specify the eddy-current corrected diffusion data ''33470_LAS_edd.nii.gz'' (<wrap em>not </wrap>the skull-stripped data you just computed) as input.  +
-  - Specify your brain mask from the skull stripping step +
-  - FSL will automatically set the output file +
-  - The gradient directions are provided in the ''bvecs'' file +
-  - The b vals are the ''bvals'' files +
- +
-{{ :psyc410_s15:images:fdt2.png?500 |}} +
- +
-Press ''Go'' - this runs within a couple of minutes - so be patient and **don't hit ''Go'' repeatedly**. +
- +
-==== Examine the DTI and FA results ==== +
- +
-You will need ''FSLView'' for this step. You will need to open a new ''FSLView'' window because these data are in a different space than the standard brain used to visualize the white-matter atlas tracts.  +
- +
-**1.** Examine your FA (fractional anisotropy) image.  +
- +
-  * Click **File** => **Open** +
-  * Open the ''**dti_FA.nii.gz**'' file +
- +
-<WRAP center round help 80%> +
-Can you see what tissue types have high FA, and what tissue types have low FA? If the answers are not obvious - make sure to check with me.  +
-</WRAP> +
- +
-**2.** Examine the DTI images for the 3 orthogonal axes that describe the tensor at each voxel. +
- +
-  * Click **File** => **Add** +
-  * Add the ''**dti_V1.nii.gz**'' file followed by the ''**dti_V2.nii.gz**'' and ''**dti_V3.nii.gz**'' files. +
- +
-<WRAP center round info 80%> +
-Note that the V1 image (''**dti_V1.nii.gz**'') represents the principal diffusion axis at each voxel (//axial diffusivity//), whereas V2 and V3 represent the two axes that are perpendicular to the principal axis (//radial diffusivity//). We will explore this idea further below. +
-</WRAP> +
- +
-You can appreciate this by plotting the color coded principal diffusion axes. +
- +
-  - First, let's hide ''dti_V2'' and ''dti_V3'' by unchecking the checkbox next to eye icon next to their names. (you can also double-click on the filename to achieve the same thing) +
-  - Highlight ''dti_V1'' and click on the on the information button (i character on the blue circle) at the bottom of the overlay settings in the ''FSLView'' window. +
- +
-{{ :psyc410_s15:images:fsl_fdt1.png?0x200 |}} +
- +
-This brings up a box of options. Choose DTI display options and then select ''Lines (RGB)''.  +
- +
-{{ :psyc410_s15:images:fsl_fdt2.png?400 |}} +
- +
-<WRAP center round info 80%> +
-The lines point in the direction of the principal direction of diffusion. +
-  * RED = Left/Right +
-  * BLUE = Superior/Inferior +
-  * GREEN = Anterior/Posterior +
-</WRAP> +
- +
-<WRAP center round tip 60%> +
-To get larger images of a particular orthogonal slice of the brain (axial, sagittal, or coronal) you can switch to single view. +
-  * Select ''Tools'' => ''Single View'' +
-  * Close the window with the three views +
-  * To cycle through the three cardinal axes, press the ''Switch view'' button +
-{{ :course:lab03:fslview_toolbar_view.png?nolink |}} +
-</WRAP> +
- +
- +
-<WRAP center round important 100%> +
-<WRAP centeralign> +
-<wrap em>LAB REPORT Part 2 - #1</wrap> +
-</WRAP> +
-  * Use your new found knowledge of major white matter tracts to identify the structures below in your V1 image. Include labeled screenshots in your report. +
-    * corpus callosum +
-    * corticospinal tract +
- +
-//Hint: you can refer back to the JHU white matter atlas in your previous instance of ''FSLView'' to find particular white matter tracts.// +
-</WRAP> +
-===== Part 3: Tractography =====+
  
  
 ==== 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" 
-</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.1467059399.txt.gz · Last modified: 2016/06/27 15:29 by admin
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