Thank you so much for this wonderful PCA tool! I am trying to run a PCA on .erp files that were prepared in ERPLAB/EEGLAB. However, I have not found documentation about how the ERP PCA Toolkit reads particular parts of the .erp files. Particularly, I am wondering about three things:
1) Should I remove all data epochs (i.e., trials) that have been marked as including an artifact prior to the PCA (since I don't want to include trials with artifacts)? Or does the PCA Toolkit can read these epochs as marked with artifacts and not include them in the PCA?
2) Similarly, do I need to remove all non-EEG channels (e.g., EOG) from the .erp files prior to the PCA?
3) I have a large number of bins that are not part of the data I am interested in running a PCA on; would it be beneficial to remove these extra bins from the .erp file prior to running the PCA?
I have included a sample .erp file. If this has been addressed elsewhere, please let me know. Thank you for your guidance!
The EP Toolkit should be reading in all artifact marking information. I didn't follow all of that, but the best thing is always to check yourself as you know your own data best. Use the Edit function to see what is going on with the channels and so forth. Use the View>Scan function to see how bad channels and trials have been marked. PCA will only include channels that are EEG and it will automatically exclude channels and trials that are marked bad. If you have EEG data in there that you don't want to include in the PCA then yes you should edit it out using one tool or the other.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Oh, one other thing is that EOG channels are just EEG channels that are positioned around the eyes so normally they are treated just like any other EEG channel and should be retained in the PCA. The artifact correction routines take care of the eye artifacts (or at least the EP Toolkit one does). If you have some reason to drop them (like the hardware of some systems reference EOG channels differently than the other channels) then yes drop them by all means.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello Dr. Dien,
Thank you so much for this wonderful PCA tool! I am trying to run a PCA on .erp files that were prepared in ERPLAB/EEGLAB. However, I have not found documentation about how the ERP PCA Toolkit reads particular parts of the .erp files. Particularly, I am wondering about three things:
1) Should I remove all data epochs (i.e., trials) that have been marked as including an artifact prior to the PCA (since I don't want to include trials with artifacts)? Or does the PCA Toolkit can read these epochs as marked with artifacts and not include them in the PCA?
2) Similarly, do I need to remove all non-EEG channels (e.g., EOG) from the .erp files prior to the PCA?
3) I have a large number of bins that are not part of the data I am interested in running a PCA on; would it be beneficial to remove these extra bins from the .erp file prior to running the PCA?
I have included a sample .erp file. If this has been addressed elsewhere, please let me know. Thank you for your guidance!
Best,
Nathan
The EP Toolkit should be reading in all artifact marking information. I didn't follow all of that, but the best thing is always to check yourself as you know your own data best. Use the Edit function to see what is going on with the channels and so forth. Use the View>Scan function to see how bad channels and trials have been marked. PCA will only include channels that are EEG and it will automatically exclude channels and trials that are marked bad. If you have EEG data in there that you don't want to include in the PCA then yes you should edit it out using one tool or the other.
If you see any problems with how the EP Toolkit read in your data, let me know and I'll fix it.
Cheers!
Joe
Oh, one other thing is that EOG channels are just EEG channels that are positioned around the eyes so normally they are treated just like any other EEG channel and should be retained in the PCA. The artifact correction routines take care of the eye artifacts (or at least the EP Toolkit one does). If you have some reason to drop them (like the hardware of some systems reference EOG channels differently than the other channels) then yes drop them by all means.