Kenyon Psychological Neuroscience Lab

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====== PSYC 410 EEG/ERP Project ======

Today we will conclude our three-part lab exercise concerned with EEG and ERP recording and analysis. You will analyze the EEG/ERP data collected during various EEG sessions.

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<WRAP centeralign><wrap em> This EEG/ERP report is due on __Wednesday May 13<sup>rd</sup> @ 11:55 pm__</wrap></WRAP>

See [[#Turning in your assignment|below]] for specific instructions on how to submit.
</WRAP>

This assignment will be very similar to the lab reports you've done throughout the semester. The primary difference is that I will not furnish you with a step-by-step guide for carrying out the analyses.

As was the case for the fMRI project, you are allowed to use any resource you'd like, including our lab wikis, to assist you in your analyses. This also means you are permitted to ask each other for assistance. However, you are <wrap em>not permitted to work together</wrap>. That is, asking for a little help here and there when you get really stuck with something is fine, but I expect you to primarily work independently. 

<WRAP center round tip 100%>
**What do I mean when I say you can each other for a "little help", but that you are not permitted to work together?**

Pretend your classmates are professional colleagues with whom you have a friendly relationship. You would definitely not hesitate to reach out to such a colleague if you hit a brick wall and needed some advice. But you certainly would //not// fill up their inbox and expect them to hold your hand through your analysis. 
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<WRAP center round tip 100%>
<WRAP centeralign> <wrap em> Go Slow. Be Methodical. Redux</wrap> </WRAP>
<wrap em> Go Slow. Be Methodical.</wrap> The same warning I gave you for your fMRI project equally applies here.<wrap em> Go Slow. Be Methodical.</wrap> 

<wrap em> Go Slow. Be Methodical.</wrap> Setting up analyses can be repetitive and tedious, so it's only natural to want to breeze through it. But you must fight the temptation to just click-click-click-Go. I can't begin to count the many dozens of hours I've spent //re-doing// analyses because I was hasty and careless the first time. Think about each setting as you set it. Make sure you understand **why** you're using it, and that you're setting it correctly. <wrap em> Go Slow. Be Methodical.</wrap> 
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===== Readings to be completed prior to this lab: =====
    *   {{psyc410:documents:engell_2010_jneuro.pdf|Engell, A.D. & McCarthy, G. (2010). Selective Attention Modulates Face-Specific Induced Gamma Oscillations Recorded from Ventral Occipitotemporal Cortex.}}
    *   {{psyc410:documents:rossion_2015.pdf|Rossion, Torfs, Jacques, & Liu-Shuang (2015). Fast periodic presentation of natural images reveals a robust face-selective electrophysiological response in the human brain.}}

===== Readings to be completed prior to next week's lab: =====
  * There is no next week!

===== Housekeeping =====
<WRAP center round todo 80%>

**1. ** Rename the old EEG directories. In Terminal:

<code bash>
mv ~/Desktop/input/eeg/N170 ~/Desktop/input/eeg/N170_old1

</code>

**2.** Download the [[https://www.dropbox.com/s/l42d8cvy7uui6ag/N170.zip?dl=0|data]] for lab EEG Project.
  * Make sure the downloaded file ''N170.zip'' is on your Desktop. If not, move it there.
  * Double click the file to unzip it.

**3.** Move the data directory. In Terminal:
<code bash>
mv ~/Desktop/N170 ~/Desktop/input/eeg/

</code> 
</WRAP>

===== Turning in your assignment =====

  * //EEG Report//: Turn in your report via Moodle.
  * //EEG Analysis//: Turn in your data analysis on your by following the instructions below.


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**1.** Save all output into the '~/Desktop/input/eeg/N170'' directory''

**2.**. Once you have **completed the project**, create a zipped copy of the ''N170'' directory and move it to your Desktop.
  * Highlight the ''N170'' directory in the Finder window.
  * Select ''File'' --> ''Compress "N170"''.
    * This will create ''N170.zip''
  * Upload ''N170.zip'' to the Google folder that you shared with me for your fMRI project
    * You do not need to change the name of the folder. You can leave it named ''yourlastname_410_fMRI'', and I will just look for ''N170.zip'' folder inside.

//Remember: this is only to be done once you are entirely done with the analysis portion of your project.//
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/*
SHOULDN'T BE NECESSARY
==== USB Drive error ====
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<WRAP centeralign><wrap em>ISSUES WITH USB DRIVE</wrap></WRAP>

If you are having issues with your USB drive such that it has appended a '' 1'' to the drive name (e.g., ''lil_andrew 1'', then try the following fixes.

**FIX 1**
  * Unmount the drive by dragging it to the recycle bin
  * Physically remove the drive
  * Restart computer
    * If you're unable to restart without an admin password, then just log out and log back in
  * Re-insert the drive

Hopefully this will fix the problem and remove the '' 1''. It's possible that your drive name will appear in a ll uppercase (e.g., ''LIL_ANDREW''), but this should be okay. //When you are specifying your output directory, still specify using all lower case!//

**FIX 2**

Fix 1 should work. If for some reason it does not ...

  * Create a temporary directory on your desktop and move the entire contents of your USB drive to that directory
  * In your terminal, enter ''open /Applications/Utilities/Disk\ Utility.app''
  * In the left column highlight your drive (see image below).
  * Click the ''Erase'' button
  * Change **Format** to ''Mac OS Extended (Case-sensitive, Journaled''
  * Put in the correct drive name (e.g., ''lil_andrew'')
  * Click ''Erase''
  * That should do it. However, sometimes it might fail and say that it was unable to erase the drive or some sucvh thing. If os, just repeat these same steps a second time. Now it will magically work. Computers, amiright!?
  * **Move the files you put into the temporary directory on your desktop back onto the USB drive**

Of course, if you are still having an issue you should email me ASAP.

{{ :psyc410_s18:fix1.jpeg?400 |}}
{{ :psyc410_s18:fix2.jpeg?400 |}}

</WRAP>
*/

===== N170 Paradigm =====

==== The Gist ====

The N170 is a large negative deflection that is maximal over right occipitotemporal scalp (for example, electrodes P10 and P08). The deflection is observed in response to most visual stimuli, but the amplitude of the response is significantly larger to faces than to all other stimuli. Because of this amplitude difference, it is thought that the N170 reflects the activation of "face selective" neurons. That is, neural populations that are tuned to prefer faces to all other visual stimuli.

<WRAP center round info 60%>
You can learn more about the N170 [[https://en.wikipedia.org/wiki/N170|here]],{{:psyc410:documents:the_n170_understanding_the_time_course_of_face_perception_in_the_human_brain.pdf|here}}, and {{:psyc410:documents:eimer_2011_2.pdf|here}}.
</WRAP>

===== Data Used for This Project =====

=== Participants ===
  * 3 participants
  * All right-handed
  * Mean age 20.6

/*
I don't really know the participant demographics, so I just made them up
*/

=== Task Description ===

In this experiment, participants viewed images from one of four possible categories: //faces//, //[[https://en.wikipedia.org/wiki/Greeble_(psychology)|greebles]]//, //tools//, and //targets// (see examples below). The participant was asked to press a button as quickly as possible whenever they saw a target (a large colored circle). The images appeared every 1800-2200 ms in random order. The study was designed so that there were 60 trials each for the faces, greebles, and tools categories, and 20 trials for targets (200 trials in total).

<WRAP center round tip 80%>
Because there were so few ''target'' trials (and thus low SNR) and because they are not an important control stimulus, you probably don't want to plot them in your figures. 
</WRAP>

{{  :psyc410:images:greeble_exampe.png?300  |  }}

=== Task Parameters ===
The data for this section of the lab were acquired at Kenyon using the BioSemi ActiveTwo system. EEG was acquired at a sampling rate of 2048 Hz from 64 scalp electrodes arranged in the 10/20 system. Data was digitized with 24-bit resolution. After acquisition, the data were downsampled from 2048 to 256 Hz.

=== Event Marker Codes ===
^Code^Condition^
|1|Faces|
|2|Greebles|
|4|Tools|
|8|Targetrs|

<WRAP center round tip 80%>
Notice that the event codes are ''1'',''2'',''4'',''8'', rather than 1 to 4. Keep this in mind when you create your eventlists, and remember that event codes are not the same as bin codes.
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===== Analysis =====

  * Preprocess the EEG data (you can skip doing artifact rejection for the purposes of this small analysis/report)
    * Rereference to the average reference
    * Apply a 4th order IIR Butterworth bandpass filter of .01 - 30 Hz
  * Create ERPs and scalp topographies for the three participants
  * Create a grand-average ERP and scalp topography

<WRAP center round tip 60%>
Think carefully about how you want to create your topography. Remember, you want to set your parameters to best highlight any observed effect.
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====== EEG/ERP Report ======
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**Your lab report should be written in the format of a brief journal article, which includes the following sections.**

**//Introduction//**
  * Brief description of the N170 phenomenon. This can be just a paragraph or so.

Here are a couple of papers describing the ERP:
  * {{:psyc410:documents:the_n170_understanding_the_time_course_of_face_perception_in_the_human_brain.pdf|Rossion and Jacques.pdf}}
  * {{:psyc410:documents:eimer_2011_2.pdf|Eimer.pdf}}

**//Methods//**
  * A description of the task paradigm.
  * The number of participants (i.e., sample size)
  * A description of the EEG parameters (e.g. sampling rate, ADC conversion, bandpass parameters, number of electrodes, etc.)
  * As with [[:psyc410_s19:eeg3|lab 09]], you are not expected to know all of the info you'd find in a published paper, but be sure to report all the info you have.
  * Include **plain language descriptions** of what you did and why you did it.
    * Of course, this is not something that would would be found in a "real" paper

<WRAP center round info 90%>
Things to keep in mind when you do your analysis...

Do not blindly use the same values that you used for the CNV study. For instance, the N170 is a fast ERP that is complete after a few hundred milliseconds. So do you think you'd want to create epochs that go all the way out to 3000 ms?

/*
These data are kind of noisy and we don't have many trials to begin with. So you can try different artifact rejection methods/thresholds until you find one that gives you at least 20-25 trials of faces, greebles, and tools. For targets, you just need at least one trial. But you'll need to use the same method/thresholds for all three subjects. And, of course, report whatever you do.
*/
</WRAP>


**//Results//**
  * A summary of your main findings with figures (see list of considerations below)
  * At minimum, include the following figures to demonstrate your results
    * Time-voltage plots (i.e., ERPs) illustrating the major experimental comparisons for your experiment
      * Include at least one difference wave
    * Topographic maps illustrative of the major experimental effects.
    * Your primary figures should be of the group average, but it is often useful to include an example from a single subject as well.

<WRAP center round info 80%>
I do not expect any statistical analysis of your data (i.e., if the difference //looks// real, then we will accept it to //be// real. Sadly, this approach does not work in real life).

I **do** expect to see <wrap em>polished and attractive figures</wrap> with legends.
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<WRAP center round tip 80%>
When you create your topgographic maps, you'll want to make sure ''outside'' is selected in the **Map type** section (if you're creating a 2D plot). This will ensure that relevant electrodes like P10 are displayed.
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**//Discussion//**
  * Briefly discuss your results with regard to the task (this can be a simple paragraph or two)
  * If you were the first person to run a face perception ERP study, what would you conclude? What did you learn about visual processing of faces compared to other objects? The time frame of face processing? Etc.

**//References//**
If you cite any work in your paper, be sure to include an APA style reference section.

<WRAP center round info 100%>
Your report should consider the following:
  * Identify the experimental effects in your ERP waveforms.
    * Do you have a a face effect?
      * What conditions should be compared to evaluate these effects? 
    * Is the effect consistent across subjects?
      * Look at one or more individual subjects, and also at the across-subject (group) summary data
    * When does this effect occur in time?
      * What is the latency in ms of your main effect?
    * What is the scalp distribution of this effect?
      * Map the scalp topography.

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<WRAP center round tip 90%>
Even though you are //not// writing a full intro and discussion, I would still like you to use the {{:psyc410:psyc410_fmriproject_formatting_template.doc|template manuscript}}I suppled for the fMRI project (but ignore the minimum word counts in that document). 
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<WRAP em><WRAP centeralign>This is the "Mini-Empirical Paper EEG/ERP" assignment on Moodle.</WRAP></WRAP>
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