Hi everyone, I am trying to display raw data using mne.viz.plot_epochs(…) (as channels and epochs) after I programmatically remove bad channels and epochs. Only the good channels and epochs are displayed after removing the bad ones. I want all channels and epoch to be displayed, including the bad ones (highlighted in a different color). I’ve had a look through the MNE code and it appears that perhaps the behavior that I am after can’t be done in MNE - bad data is just deleted before it can be displayed.
So, can someone confirm that I am correct and there is no way to do this (without a substantial rewrite of the code)? Or, I would be very happy if you prove me wrong and can explain how to achieve this.
By default, picks=None in epochs.plot() shows only good channels. If you want to show all channels, set it to picks="all" (mne.Epochs — MNE 1.8.0 documentation).
Regarding bad epochs, if you don’t see them anymore, you might have dropped them. You should therefore visualize epochs before dropping (i.e., set preload=False, which is the default anyway, and/or defer epochs.load_data()).
Thanks for your response Clemens. I understand what you are saying about including bad channels in the epoch plot. I don’t however fully understand what you are saying about including bad epochs in the plot. I am calling drop_bad() before plotting. So, I have dropped epochs by using that. What I want to know is if there is a way to mark the bad epochs as bad without dropping them - so that I can see them in the plot, highlighted in some way. I want to visually inspect what the epoch rejection criteria I am using is doing with the data. I want to be able to see the characteristics of the rejected epoch data along with the good data. So, do you think that this can be done?
