Visual Cognitive Neuroscience

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teaching:writing_assignment_part_2

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teaching:writing_assignment_part_2 [2017/11/07 01:23] – Page name changed from teaching:test_page to teaching:writing_assignment_part_2 adminteaching:writing_assignment_part_2 [2020/03/26 13:06] (current) – [2.3 Find brain regions activated by both cognitive skills] anthony
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 ~~NOCACHE~~ ~~NOCACHE~~
 +~~NOTOC~~
  
 {{INLINETOC:width24 1-3}} {{INLINETOC:width24 1-3}}
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 https://canvas.vt.edu/courses/57758/files/folder/writing_assignment/brain https://canvas.vt.edu/courses/57758/files/folder/writing_assignment/brain
  
-File name: mni<sub>icbm152t1talnlinasym09aacMasked.nii.gz+File name: ''mni_icbm152_t1_tal_nlin_asym_09a_acMasked.nii.gz''
  
 (**NOTE:** If your computer asks you to unzip this (or do anything else) with this file, respond "No." The only reason this file is zipped (compressed to reduce the size of the file) is to make it easier to download and save. Mango will read this file without you having to unzip it first.) (**NOTE:** If your computer asks you to unzip this (or do anything else) with this file, respond "No." The only reason this file is zipped (compressed to reduce the size of the file) is to make it easier to download and save. Mango will read this file without you having to unzip it first.)
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 ==== - Download the brain map image for your topic ==== ==== - Download the brain map image for your topic ====
  
-[{{:teaching:neurosynth_download_icon.png| Click on the "download arrow" icon at the end of the "reverse inference" line.}}]+[{{:teaching:neurosynth_download_icon.png| Click on the "download arrow" icon at the end of the "association test" line.}}]
 \\ \\
 ---- ----
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 If you don't see any orange/red activation blobs after loading your first overlay, try clicking and dragging the mouse all around the brain, moving the blue crosshairs, until you've looked all over the entire brain. There is almost certainly a blob there somewhere. If you don't see any orange/red activation blobs after loading your first overlay, try clicking and dragging the mouse all around the brain, moving the blue crosshairs, until you've looked all over the entire brain. There is almost certainly a blob there somewhere.
  
-it is possible that your particular Neurosynth map might not have any activation blobs that happen to be visible at the+it is possible that your particular Neurosynth map might not have any activation blobs that happen to be visible at the current view of the brain.
  
 [{{:teaching:mango_overlay_added.png| The display should look like this after adding the first functional activation map overlay.}}] [{{:teaching:mango_overlay_added.png| The display should look like this after adding the first functional activation map overlay.}}]
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 Refer to your answer to Part 1, question 2.B.iii.b ("Pick what you think is the most important of these brain regions, and briefly state why you think it's the most important."). Refer to your answer to Part 1, question 2.B.iii.b ("Pick what you think is the most important of these brain regions, and briefly state why you think it's the most important.").
 +
 +//
 +[If, and only if, your answer to question 2.B.iii.b was "my article didn't mention any brain regions," then skip ahead to the section entilted I HAD NO BRAIN REGION]//
  
 Does any of the Neurosynth brain map activation fall in this region? Does any of the Neurosynth brain map activation fall in this region?
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 **Answer**: Try Googling the name of the brain region you're looking for. Try searching for images, if necessary. Then use the results as a guide of where to look in Mango. **Answer**: Try Googling the name of the brain region you're looking for. Try searching for images, if necessary. Then use the results as a guide of where to look in Mango.
 +
 +=== I HAD NO BRAIN REGION ===
 +
 +Choose a blob of activation in your brain overlay, and figure out its name by hovering your mouse over it (with the Mango atlas enabled).  Then provide this name as your answer to Item 1, and use this region to answer Items 2, 3, and 4.
 +
  
 === Is the key brain region from your article part of the Neurosynth brain map? === === Is the key brain region from your article part of the Neurosynth brain map? ===
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 Is the brain region that you named in your answer to Is the brain region that you named in your answer to
 Part 1, question 2.B.iii.b part of the Neurosynth brain map? Part 1, question 2.B.iii.b part of the Neurosynth brain map?
 +(This is a one-word answer: yes or no.)
 +
 +[Or, if you had no brain region for question 2.B.iii.b:
 +Type the name of the brain region that you choose from your activation overlay]
 </code> </code>
  
-(This is a one-word answer: yes or no.)+
  
 === Take a screenshot of the region === === Take a screenshot of the region ===
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 </code> </code>
  
-Regardless of whether your answer is yes or no, take a screenshot of Mango when you have placed the **crosshairs** on the region in question.+Regardless of what your answer was for Item 1, take a screenshot of Mango when you have placed the **crosshairs** on the region in question.
  
 **NOTE** that the crosshairs are not the same thing as the mouse pointer; to place the crosshairs (the two thin blue lines) you need to click the mouse. **NOTE** that the crosshairs are not the same thing as the mouse pointer; to place the crosshairs (the two thin blue lines) you need to click the mouse.
  
-PLEASE USE THE MANGO SCREENSHOT TOOL and not some other method for taking screenshots. Clicking on the "camera" icon in the main (smaller) Mango window will save an image file to the same folder that holds the **average structural brain image** file (i.e. mni<sub>icbm152t1talnlinasym09aacMasked.nii).+PLEASE USE THE MANGO SCREENSHOT TOOL and not some other method for taking screenshots. Clicking on the "camera" icon in the main (smaller) Mango window will save an image file to the same folder that holds the **average structural brain image** file (i.e. ''mni_icbm152_t1_tal_nlin_asym_09a_acMasked.nii'').
  
 Rename the file "[name of the key brain region].png" and upload it to Canvas. Examples of a good file name: "SupTempGyr.png" or "Superior Temporal Gyrus.png". Rename the file "[name of the key brain region].png" and upload it to Canvas. Examples of a good file name: "SupTempGyr.png" or "Superior Temporal Gyrus.png".
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 ==== - Find brain regions activated by both cognitive skills ==== ==== - Find brain regions activated by both cognitive skills ====
  
-Scroll/click/hover around the brain to get a sense of how the Neurosynth activation map for your "other" skill differs from the map for your primary cognitive skill. In most cases, the two maps will overlap in many places, but not always. Think about the similarities and differences between the two cognitive skills, and whether these are reflected by the degree to which their functional maps overlap.+Scroll/click/hover around the brain to get a sense of how the Neurosynth activation map for your "other" skill differs from the map for your primary cognitive skill. Think about the similarities and differences between the two cognitive skills, and whether these are reflected by the degree to which their functional maps overlap. 
 + 
 +In most cases, the two maps will overlap in many places, but not always.  
 + 
 +=== [WHAT IF MY TWO MAPS DON'T OVERLAP?] ===  
 + 
 +[If your two maps //really// don't overlap, you will get messages saying things like "Zero components found" for the following activities.  This happens rarely, but there are some pairs of Neurosynth maps for this assignment that do not overlap.  If, and only if, this happens to you, **you may type "my maps didn't overlap" as your answers** for Items 6, 7, 8, and 9.  You won't be penalized.] 
 + 
 +\\
  
 Now, let's do a more precise investigation of the locations where the two maps overlap. We can use Mango to define a "region of interest" (ROI) that marks all of the overlapping locations. Now, let's do a more precise investigation of the locations where the two maps overlap. We can use Mango to define a "region of interest" (ROI) that marks all of the overlapping locations.
teaching/writing_assignment_part_2.1510035800.txt.gz · Last modified: (external edit)