Example 3b: Modifying the Script to Work for Different Subjects - ucdavis/erplab GitHub Wiki

Note: A complete version of this script is available in Test_Data > Script_Examples > Script3b.m.

The script you made in the previous step is nice for processing the data from subject S1, but it would be a hassle to make it work for subject S2, because you'd have to change every instance of S1 to S2 in the script. In this example, you'll learn how to make the script more flexible so that it can easily work for other subjects.

First, you need to know about a little Matlab trick for combining different strings together. In our script, we'd like to be able to construct strings like 'S1_EEG.set' and 'S2_EEG.set'. That is, we want to combine 'S1' or 'S2' with '_EEG.set'. To see how this can be done in Matlab, type the following into the command line:

x = 'S1';

y = 'S2';

z = '_EEG.set';  

You have now created 3 variables—x, y, and z. To see the value of a variable, you can just type the name of the variable at the command line (without a semicolon), like this:

>> x

x =

S1  

Now we will create a new variable named filename that combines the x and z variables. To do this, type the following into the command line:

filename = [x z]  

Make sure you do it without the semicolon at the end. When you do this, you've created the filename variable and given it a value that concatenates the values of the x and y variables. Because you did not put a semicolon at the end of the command, Matlab will print the value of the command in the command window, which should look something like this:

filename =

S1_EEG.set  

You've now created a variable that contains the string 'S1_EEG.set'. It would be easy to change the variable to be 'S2_EEG.set' by typing filename = [y z]. Try this and verify that it gives you 'S2_EEG.set'. You can also do this by combining a string and a variable. For example, try typing filename = ['S3' z]. This should give you 'S3_EEG.set'.

Now that you've learned this little trick, let's apply it to the script you created in the previous step. Start by creating a new script file that is exactly like the previous one. Put the following two lines at the very top to define a variable named subject that will initially contain 'S1' and a variable named subjectfolder that contains the path to the subject's folder:

subject = 'S1';

subjectfolder = ['/Users/luck/Documents/Software_Development/ERPLAB_Toolbox/Test_Data/' subject '/']; [_Note that you must replace this path with the appropriate path for your computer_]  

Note that there are spaces before and after subject in the second of these two lines — without these spaces, Matlab will not know that subject is separate from the strings that precede and follow it. If you are missing one or more of these spaces, you will get a (very unhelpful) message from Matlab saying "Error: Unexpected MATLAB expression".

In addition, you should keep in mind that there is nothing special about the variable names subject and subjectfolder—you could use qwerty or bobsyouruncle or anything else that is a legal Matlab variable name. But it's a very good idea to use meaningful variable names rather than things like x or qzzaz. Also, note that the first part of the subjectfolder definition should reflect the appropriate path for your computer (which you can see by typing pwd in the command window).

The next step is to go through the script and use our new Matlab trick to replace every occurrence of S1 with a set of square brackets containing subject or subjectfolder along with the rest of the string. For example, you should replace 'S1_EEG.set' with [subject '_EEG.set'] in the pop_loadset command, and you should replace 'S1_Chan' with [subject '_Chan'] in the pop_editset command. You should also follow each occurrence of 'filepath' with subjectfolder. The result will look like this (notice that the lines beginning with a percent sign are comments that I've inserted to explain the changes on the following line):

subject = 'S1';

subjectfolder = ['/Users/luck/Documents/Software_Development/ERPLAB_Toolbox/Test_Data/' subject '/'];



% 'S1_EEG.set' was replaced with [subject '_EEG.set'], and

% '/Users/luck/Documents/Software_Development/ERPLAB_Toolbox/Test_Data/S1/' was replaced with subjectfolder

EEG = pop_loadset('filename', [subject '_EEG.set'],'filepath', subjectfolder);



EEG=pop_chanedit(EEG, 'lookup','/Users/luck/Documents/Software_Development/eeglab9_0_2_3b/plugins/dipfit2.2/standard_BESA/standard-10-5-cap385.elp');



% 'S1_Chan'was replaced with [subject '_Chan']

EEG = pop_editset(EEG, 'setname', [subject '_Chan']);



% 'S1_Chan.set'was replaced with [subject '_Chan.set'], and

% '/Users/luck/Documents/Software_Development/ERPLAB_Toolbox/Test_Data/S1/' was replaced with subjectfolder

EEG = pop_saveset( EEG, 'filename', [subject '_Chan.set'],'filepath', subjectfolder);



EEG = pop_creabasiceventlist( EEG , 'AlphanumericCleaning', 'on', 'BoundaryNumeric', { -99 }, 'BoundaryString', { 'boundary' }, 'Warning', 'on' );

EEG = pop_binlister( EEG , 'BDF', '/Users/luck/Documents/Software_Development/ERPLAB_Toolbox/Test_Data/binlister_demo_1.txt', 'IndexEL', '1', 'SendEL2', 'EEG', 'Voutput', 'EEG', 'Warning', 'on' );

EEG = pop_epochbin( EEG , [-200.0 800.0], 'pre');

EEG = pop_artmwppth( EEG , 'Channel', 1:16, 'Flag', 1, 'Threshold', 100, 'Twindow', [ -200 798], 'Windowsize', 200, 'Windowstep', 50 );

ERP = pop_averager( EEG , 'Criterion', 'good', 'DSindex', 6, 'ExcludeBoundary', 'on', 'SEM', 'on');



% 'S1_ERP'was replaced with [subject '_ERP'], and

% '/Users/luck/Documents/Software_Development/ERPLAB_Toolbox/Test_Data/S1/S1_ERP.erp'

% was replaced with [subjectfolder subject '_ERP.erp']

ERP = pop_savemyerp(ERP, 'erpname', [subject '_ERP'], 'filename', [subject '_ERP.erp'], 'filepath', subjectfolder, 'warning', 'off');



[ALLEEG, EEG, CURRENTSET] = eeg_store( ALLEEG, EEG, 0 );
ALLERP = ERP;

eeglab redraw;

erplab redraw;  

Once you've made all of these changes, try running the script.

Unless you were incredibly careful, you probably made at least one error when making all of these changes. For example, if you didn't leave a space between subject and '_Chan' in the pop_editset command, you would get an error message like this:

??? Error: File: Script3b.m Line: 17 Column: 44

The input character is not valid in MATLAB statements or expressions.  

Similarly, if you did not put the correct path for the Test_Data folder in the subjectfolder variable, you will get a message like this:

??? Error using ==> load Unable to read file /Users/luck/Documents/Software_Development/ERPLAB_Toolbox2/Test_Data/S1/S1_EEG.set: No such file or directory.  Error in ==> pop_loadset at 107 TMPVAR = load(filename, '-mat'); Error in ==> Script3b at 10 EEG = pop_loadset('filename', [subject '_EEG.set'],'filepath', subject folder);  

You will doubtless find this aggravating and frustrating. I'm not sure if you will find this comforting, but for most scripts you will probably spend more time tracking down and fixing problems than you will spend actually writing the initial script. That has always been my experience, and it's also true for professional programmers. Click here for some tips on debugging.

The next thing you need to fix is the location of the bin descriptor file, 'binlister_demo_1.txt'. In our script so far, we've assumed that this file is in the S1 folder. You will use the same bin descriptor file for every subject, so it doesn't make sense to have a separate copy in every subject's folder. Instead, you should put it in the parent folder (the folder that contains the S1 folder and the folders for all the other subjects). After you've done this, you will need to make some changes to your script so that it looks in the right place for this file. First, you will define a variable named parentfolder in your script (and use it when defining the subjectfolder variable), as follows:

subject = 'S1';

parentfolder = '/Users/luck/Documents/Software_Development/ERPLAB_Toolbox/Test_Data/';

subjectfolder = [parentfolder subject '/'];  

As usual, the exact path should reflect your computer's organization. The final step is to update the pop_binlister command so that it looks for the bin descriptor file in the parent folder:

EEG = pop_binlister( EEG , 'BDF', [parentfolder 'binlister_demo_1.txt'], 'IndexEL', 1, 'SendEL2', 'EEG', 'Voutput', 'EEG' );  

The last little thing you need to fix is the location of the file used to add the electrode locations, standard-10-5-cap385.elp. In our script so far, we've used the full path to the file, which we've gotten from the EEGLAB history. This file is probably located in the EEGLAB folder, and if you upgrade to a new version of EEGLAB, this folder will have a different name, and the script will stop working properly. To avoid this, we can just rid of the path information that precedes the standard-10-5-cap385.elp filename. As long as the folder that contains this file is in your Matlab path, EEGLAB will be able to find the file. To make this change, just edit the line with the pop_chanedit() command so that it looks like this:

EEG=pop_chanedit(EEG, 'lookup','standard-10-5-cap385.elp');  

The whole script should now look something like this:

subject = 'S1';
parentfolder = '/Users/luck/Documents/Software_Development/ERPLAB_Toolbox/Test_Data/';
subjectfolder = [parentfolder subject '/'];
EEG = pop_loadset('filename',[subject '_EEG.set'],'filepath',subjectfolder);
EEG=pop_chanedit(EEG, 'lookup','standard-10-5-cap385.elp');
EEG = pop_editset(EEG, 'setname', [subject '_Chan']);
EEG = pop_saveset( EEG, 'filename', [subject '_Chan.set'],'filepath', subjectfolder);
EEG = pop_creabasiceventlist( EEG , 'AlphanumericCleaning', 'on', 'BoundaryNumeric', { -99 }, 'BoundaryString', { 'boundary' }, 'Warning', 'on' );
EEG = pop_binlister( EEG , 'BDF', [parentfolder 'binlister_demo_1.txt'], 'IndexEL', 1, 'SendEL2', 'EEG', 'Voutput', 'EEG' );
EEG = pop_epochbin( EEG , [-200.0 800.0], 'pre');
EEG = pop_artmwppth( EEG , 'Channel', 1:16, 'Flag', 1, 'Threshold', 100, 'Twindow', [ -200 798], 'Windowsize', 200, 'Windowstep', 50 );
ERP = pop_averager( EEG , 'Criterion', 'good', 'DSindex', 6, 'ExcludeBoundary', 'on', 'SEM', 'on');
ERP = pop_savemyerp(ERP, 'erpname', [subject '_ERP'], 'filename', [subject '_ERP.erp'], 'filepath', subjectfolder, 'warning', 'off');
[ALLEEG, EEG, CURRENTSET] = eeg_store( ALLEEG, EEG, 0 );
ALLERP = ERP;
eeglab redraw
erplab redraw;  

You can now go ahead and run this script. You don't need to quit and relaunch EEGLAB before running the script (although it's often a good idea).

Notice that the datasets created by this script are appended onto the EEGsets panel or Datasets menu, so you will probably now have 2 datasets instead of 1. However, you just have the most recent ERPset, because you copied the current ERP structure into the ALLERP variable. However, you saved each ERP structure as a file on your hard drive, so you can always reload later. In addition, I will explain how to maintain multiple ERP structures in the ERPsets panel/menu in the next example.

Now you are ready to run this script on subject S2. To do this, simply change the assignment of the subject variable in the first line to this:

subject = 'S2';  

Now you can run the script for S2. And then you can change this one line to 'S3' to run the script on subject #3. It has taken a while to get to this point, but now you can (I hope!) see how scripting can make your life easier once you get the hang of it.