Hi this is for a psychology lab called neuropsychology which you’ll be using MATLAB with the attached file called (CD2010) to answer the questions under the instruction by the instructor below which contains all the instruction for the MATLAB software and the short answer question which doesn’t need to be long as long as it answers the question. I will also attach the document that contain this same instruction if that makes it easier to see the whole thing here better since it doesn’t show some of the picture here. It also doesn’t let me attach the CD2010 file and MATLAB file here but I can send through any convinient means.
Instruction by the Instructor
Lab 3 – EEG
We will be replicating analyses from Curran_Doyle_2011.pdf.(file attached)
1. Use the file attached for CD2010.zip and MATLAB.zip
Matlab Setup Instructions
a. Download and unzip “MATLAB.zip� on your computer. Place this folder in your Documents folder.
b. Download and unzip “CD2010.zip� on your computer. Keep the components of the zip file together in the same folder, DO NOT move the folder out of the “Downloads� folder or move any files within or out of the CD2010 folder.
c. Open MATLAB from Applications folder.
d.Click on the “Home� tab in MATLAB,and then click “Set Path�.Select “Add Folder…� (NOT subfolders), and navigate to Documents/MATLAB/eeglab/eeglab2022.1. Once eeglab2022.1 is highlighted, click “Open�, and then hit “Save� in the “Set Path� window.
e. Drag the “CD2010� folder into Matlab command window (whole unzipped folder, not the cd2010.m file or the CD2010.zip file).
f. Within Matlab, double-click on the cd2010.m file in the left panel.
If Matlab asks if you want to open the cd2010.m file as a “live scriptâ€�. Ignore that prompt
or x it out in the upper right corner.
g. Code sections are separate in Matlab with double percent symbols (%%).The first section is “%% 0 – Setup� which contains a lot of setup code that you don’t need to worry about, but you do need to execute.Place your cursor anywhere in that section, and it should all become highlighted. Execute that section by hitting the “Run Section� (NOT the “Run�) button in the top EDITOR panel.If you accidently ever hit “Run� then all sections in the file will be run.If you do that, it is probably best to quit Matlab and start over. If you start over, trash the CD2010 folder, and unzip a fresh version.
(After you have run the “%% 0 – Setup� section:)
Skip the two un-numbered code sections and go to the Q1 section.
h.Run the “%% Q1 – Load and view raw EEGâ€� section. You should now see a window like this:
Once you see this, wait for the rest of the class to catch up. If you don’t see this, ask for help.
Intro To ERPs online course (we will go through parts of this course below):
https://erpinfo.org/intro-to-erps-course-materials
Recording and Analysis 2- Recording
https://www.youtube.com/watch?v=sdesLHEgohU&feature=youtu.be
Assignment Instructions
Answer the following questions in a separate file that contains only your numbered/lettered answers; DO NOT include the questions in your answer file. Name the file “EEG_YOURLASTNAME.doc� (or .docx). Working with other students is not acceptable, complete the assignment on your own.
1 -Load and view raw EEG
After you run the section, you should see a Scroll Channels window (Channels are Electrodes) that displays the data from a single subject from Curran & Doyle’s (2010) Experiment 1. Increase its size by dragging the lower right corner and repositioning. From the “Settings” menu at the top of the Scroll Channels window, change the number of channels displayed to “10â€�.Change the amplitude scale in the lower right box to “200â€�. Make sure you are seeing the first 10 electrodes (E1 – E10) by moving the leftward vertical scroll bar to the top.You can scroll left (earlier) and right (later) through time by pressing the << (5 sec left), < (1 sec left), > (1 sec right), and >> (5 sec right) buttons. If you hover your cursor on any EEG trace, notice the Chan, Time, and Values are displayed at the bottom of the window.
a.Which electrode seems most different from all the others?
b.Scroll to the right, until seconds 15 to 19 appear along the x-axis.Now you can see the first event markers for this subject. Use your cursor to identify the time at which the first fixation cross (fix+) and first stimulus (stm+) were presented. Report those time values. Some event markers are too small to read, so if you select the lower left “Event types� menu, it will show you a list in larger font, with color coding to help you find thing as follows (see next page):
c. Scroll 5 seconds to the right (>> button) to display seconds 20 to 24. You’ll see the next stimulus around 22.5 seconds, where superimposed blue and black lines make the event labels hard to read.From the “Settings” menu at the top of the Scroll Channels window, change the time range to display to “1â€�, and scroll right to display second 22. Now, what are the labels for the black and blue lines?
d. Since analyses depend on knowing whether each stimulus is either new (New1), a studied picture (Pic2), or a studied word (Wrd3); these labels are provided next to each stimulus. Because we only want to include stimuli to which subjects responded correctly, whenever you see a “stm+� event without a condition label, it means that the subject responded incorrectly to that stimulus, so that trial will not be included in the analysis.At what times do the first New1 and Pic2 events occur?
Later parts of the code will sometimes refer to conditions with numbers rather than words, so remember the condition numbers, 1 = New, 2 = Picture, 3 = Word (alphabetic order). These are sometimes called “bin numbers�.
Note, if you are having trouble returning to the cd2010.m code file, go to the far upper left “Window� menu, and select “MATLAB R2020a�. This menu is also helpful for finding data figures. Lower figures are newer than upper figures, so you can use these to select the results of different analysis steps even when the figure names are the same.
DO NOT close the Scroll Channels window before running the next section.
(If you do close it, re-run section 1 before running section 2.)
ERP Basics 5- Sources of Noise
https://www.youtube.com/watch?v=vlv8JEqZuSI&feature=youtu.be
2 – Interpolate bad channels
a. Summarize what is interpolation of bad channels.
b. Look back at the matlab code.Which channel is being interpolated?
c. Verify that the channel looks normal now. For your new “Scroll channel…� window, make all setting the same as the original “Scroll channel…� window.Paste before and after interpolation screen shots into your answer file.
DO NOT close the Scroll Channels window before running the next section.
(If you do close it, re-run section 2 before running section 3.)
3 – Filtering
This takes a couple of minutes to run.While it is running, note the values for “passband edges� (Hz) in the command window. These will help you answer a later question.
a. Summarize what is filtering.
b. What is the main source of high frequency noise, and what is its frequency?
c. Between what two values (in Hz) were the data filtered?
d. Visually compare the filtered vs. unfiltered data.Again, set all parameters for the new window to be the same as for the previous windows, except for the amplitude scale in the lower right box, which should now be set to “40� for both the unfiltered and filtered data. Also, go to timepoint zero in each window, when the data was noisier.How do they compare visually?
e. Paste before and after filtering screen shots into your answer file.
f.For the filtered EEG, scroll vertically to display channels 70-80, and scroll horizontally to display the 6th second. Now count the major bumps in channel 72 to verify the presence of 8-12 Hz alpha during this pre-experimental EEG while the subject was resting. What is your estimate of this subject’s alpha rate (in Hz), based on your counting these bumps by hand?
g. Paste a screen shot of the alpha activity.
h. Within the “plot� menu of the EEGLAB window, select Plot > Channel Locations by number.What is the approximate location of channels 70-80 on the scalp. You just need one general location that roughly applies to all channels.
4 – Epoching (or Segmenting)
a. Summarize what is epoching.
b. How much pre-stimulus and post-stimulus EEG was included in each epoch?
c. What are the condition labels associated with each of our 3 conditions?
Recording and Analysis 5- Common Artifacts
https://www.youtube.com/watch?v=QZyjrHTrTwc&feature=youtu.be
Recording and Analysis 6- Artifact Rejection and Correction
https://www.youtube.com/watch?v=GD7kr-Ts-fI&feature=youtu.be
5 – Automatic artifact detection
a. Summarize what is auto artifact detection.
b. After running, go to the MATLAB 2020a command window, scroll up and look for a table formatted like the table below (see next page). Copy and paste the complete table into your answer sheet. Several tables like this will be generated, so be sure to get the last table that includes non-zero values in column #F6. Use 8 point courier forbetter formatting in answer sheet.
Bin#(%) accepted#(%) rejected# F2# F3# F4# F5# F6# F7# F8
1
2
3
____________________________________________________________________________________________________
Total
c.Which condition had the most trials rejected? Give full condition label, as in 4c above.
6 – Manual artifact detection
After your run this section, there is no need to change settings in this window like before.
Epochs with artifacts are colored yellow, and you can manually mark other trials as artifacts by clicking on any waveforms within an epoch, so be careful clicking around so you do not inadvertently mark a good trial as having an artifact. If you do, click it again to remove the yellow.
a. Summarize what is manual artifact detection.
b. What is the first epoch number that was automatically rejected?
c. Does the epoch identified in part “b� look much worse than the nearby epochs?We can manually unmark it as an artifact by clicking once anywhere within that epoch.Clicking should turn it white like other trials.Similarly, if you think an epoch that is automatically marked as good has artifacts, you can manually click on that to turn it yellow.
d. Enter in epoch 154 in the box between the horizontal scrolling arrows.Change the far lower right box to “40� (amplitude scale), This is a blink epoch.Notice how the upper channels (above the eyes) are going positive, while lower channels (below) the eyes are going negative.Paste a screenshot of the entire window, including blink epoch, into your answer sheet.
Now select “UPDATE MARKS� in the lower right corner of the Scroll Channel window.Next select, “OK� for the “Warning� window.
ERP Basics 2- Averaged ERPs
https://www.youtube.com/watch?v=XX4yr5tEv8I&feature=youtu.be
7 – Compute and plot ERPs
Respond “Yes� if you get a warning about overwriting files.
If the new figure takes up your entire screen, hover your cursor in the upper left corner, below the red/yellow/green circles on the blue bar. Hovering there will prompt the appearance of reed/green circles below that location (at the top of the figure widow). Select the lower green button and the window should become smaller. Grab the lower right corner to resize etc.
a. Summarize how ERPs are computed from EEG.
b. Copy and paste the two lines of code that compute and save the ERPs.
c. The new figure displays all channels topographically.Click anywhere on the E90 ERPs (lower right quandrant) to display a bigger figure of that channel alone. It is slow and inconsistent, so single click pause for 5 seconds, reposition and repeat until a new figure appears that only shows E90.Is positive up or down?
d. Copy and paste a screenshot of the entire Channel E90 window into your answer sheet.
e. Locate the P100 and N170 components.What are the approximate latencies (peak times) for each component in the Picture condition?
f.For which two conditions is the N170 most negative?
Skip the two un-numbered code sections and go to the Q8 section.
ERP Basics 6- Conventions
https://www.youtube.com/watch?v=fm7xGPWDfCI&feature=youtu.be
8.Grand Averages
Everything above was a single subject. Each of the other 26 subjects was processed in the same manner, and now will we start looking at results for the entire sample.The new figure shows the “grand average� across all 27 subjects. Let’s repeat the above questions (#7) for the grand average.
a. Summarize how the Grand Average is computed.
b. The figure displays all channels topographically.Click anywhere on the E90 ERPs to display a bigger figure of that channel alone. Its slow and inconsistent, so single click pause for 5 seconds, reposition and repeat until a new figure appears that only shows E90.Is positive up or down?
c. Copy and paste a screenshot of the entire Channel E90 window into your answer sheet.
d. Locate the P100 and N170 components.What are the approximate latencies (peak times) for each component in the Picture condition?
e. For which one condition is the N170 most negative?
9.1.Topographic Maps
a. Copy and paste a screenshot of the entire topographic map window into your answer sheet. Might help to first grab the right edge of the window and drag it leftward to squeeze the figure horizontally.
Notice you can click and hold on any of the heads, to spin them around etc.
b. P100.For the Bin2(Picture) condition, what channel shows the highest amplitude P100, and what is that approximate amplitude it is showing?
c. N170.For the Bin2(Picture) condition, what channel shows the highest amplitude N170, and what is that approximate amplitude it is showing?
d. Do you see any differences between conditions that may be related to effects emphasized in the paper?
9.2Animation
a.Resize the figure so all three conditions are visible.Conditions are ordered New, Picture, Word, as before. Controls are in upper left of window. The play control is too fast, so use the step control, two buttons to the right of play. Find the time at which the parietal amplitude is most positive within the Picture condition. Copy and paste the figure into your answer sheet. Be sure time is displayed in your copy of the figure.
10.Analysis Clusters ERPs
a.Copy and Paste new figure into your answer sheet.
b. Which figure from the paper does it match?
11.Analysis Clusters Means
a.Which figure from the paper do the two new figures match?
b. Arrange the two new figures similarly to the figure in the paper, and copy and paste them into your answer sheet.
12.Topographic Maps of Old-New Differences
a.Which figure from the paper do the two new figures match?
b. Arrange the two new figures similarly to the figure in the paper, and copy and paste them into your answer sheet.
c. Explain what is being plotted in each of the four heads.What conditions and what times? Use meaningful conditions labels rather than just bin numbers.If labels above heads are obscured, it might help to take a look at the code.
d.Although our eyes gravitate to where effects look largest on these heads, the actual analysis clusters are not exactly aligned with the largest differences.Referring back to Figure 2 in the paper. For each of the heads, capture a screen shot that starts at the most anterior LAS/RAS electrodes and ends with the most posterior LPS/RPS electrodes. You should be able to capture the two upper heads in one shot and the two lower heads in another.Now you should be able to verify that these topographic differences correspond to the effects shown in Figures 3 and 4.
13.Get Subject Means for ANOVAs
a. After running, type “FN400_data� into command window, without quotes.Notice this shows the mean amplitude for each subject , in each condition, in both the LAS and RAS regions. If we want to do an ANOVA on these results, what is the dependent variable and independent variables, along with the levels of each independent variable.
b. To just show the first column, Type “FN400_data(:,1)� into command window, without quotes.Copy and paste the first column output into your answer sheet.
c.Type “Parietal_data� into command window, without quotes.Notice this shows the mean amplitude for each subject , in each condition, in both the LPS and RPS regions. If we want to do an ANOVA on these results, what is the dependent variable and independent variables, along with the levels of each independent variable.
d. To just show the first column, Type “Parietal_data(:,1)� into command window, without quotes.Copy and paste the first column output into your answer sheet.
14.FN400 ANOVA
The ANOVA input format is a bit odd, so the data files from step 13 were reformatted by hand to conform.You should be able to see that the beginning of the first column of the “N4 =� variable in the code is the same as the first column of FN400_data(:,1) above.
a.After running this section, scroll up to the ANOVA output table in your command window. Copy and paste the ANOVA table, starting with the “The number of IV1 levels…� line. If you use ~ 8 point courier font, it should be readable in your answer sheet.
b.Based on the levels indicated above the ANOVA table, indicate which of the independent variables (IV1, IV2) are the independent variables you named above in 13a.
ANOVA output will not be identical to the values in the paper, because of processing differences between 2010 and now, but they should be close.
c. Copy and paste the ANOVA output line that is consistent with the conclusion that mean amplitude significantly differed between conditions.
d. Copy and paste the ANOVA output line that is consistent with the conclusion that condition differences significantly varied across hemispheres.
15.Parietal ANOVA
a.After running this section, scroll up to the ANOVA output table in your command window. Copy and paste the ANOVA table, starting with the “The number of IV1 levels…� line. If you use ~ 8 point courier font, it should be readable in your answer sheet.
b. Copy and paste the ANOVA output line that is consistent with the conclusion that mean amplitude significantly differed between conditions.
c. Copy and paste the ANOVA output line that is consistent with the conclusion that condition differences significantly varied across hemispheres.
Thank you!!!