Dear MNE-Python community,
Thank you for having built this great Python package!
I am a student with little experience in the area of EEG analysis. I am currently working on my master thesis. I conducted an EEG experiment with three different conditions (A, B and C). Every participant was exposed to all three conditions (sequentially). I would like to find out whether the different conditions involved different scalp topographical distributions of theta oscillations. I hypothesise (among other things) that participants’ theta activity in condition C was dispersed over a wider brain area than their theta activity in conditions A and B. I am trying to test this hypothesis, but I am experiencing some difficulties. I hope you can help me. My apologies if any of my questions seem silly.
I am currently taking the following steps:
- For each participant, I identify all bad channels and I apply independent components analysis (ICA). I have one data file per participant.
- For each participant, I extract epochs from that participant’s data file.
- For each participant, I ‘average the epochs for each condition’. Example:
conditionAverage_A = epochs[‘A’].average(). - For each condition, I create a list that contains all participant ‘averages’ for that condition. Example:
participantAverages_A = [conditionAverage_A_P1, conditionAverage_A_P2, …]. - For each condition, I average all participant ‘averages’ for that condition. I call the resulting averages (evoked data) ‘sample averages’. For example:
sampleAverage_A = mne.combine_evoked(participantAverages_A, weights= 'equal').
I now have three ‘sample averages’, one for each condition. I would like to do two more things.
[1/2] First of all, for each ‘sample average’, I would like to produce a topomap that ‘displays theta activity’. (I currently define theta activity as activity in the 4 to 7Hz range.) For sampleAverage_A, for instance, I would like to produce a map similar to the one that epochs[‘A’].plot_psd_topomap(ch_type='eeg', bands=[(4,7,'Theta’)]) would produce for a single participants’ epochs for condition A (please see figure 1 below; code adapted from the tutorial ‘Visualizing epoched data’). Unfortunately, the plot_psd_topomap function does not work for evoked data. I tried to work my way around this by using the following code (adapted from the tutorial ‘Frequency and time-frequency sensor analysis’; I do not understand every aspect of this code yet).
freqs = [4, 7]
power = tfr_morlet(sampleAverages[condition], freqs=freqs, n_cycles = 1, use_fft=True, return_itc=False)
power.plot_topomap(ch_type= 'eeg' , tmin = 0, tmax = 1, fmin=4, fmax=7, mode= 'mean' , show_names=True,
baseline=(None, None), title= ‘Condition A (Theta)’ , show=True)
The result can be found in figure 2 below . Is there perhaps a way to get an image that is even more similar to the one produced by the plot_psd_topomap function?
[2/2] Secondly, I would also like to statistically examine whether participants’ theta activity was more widely distributed in condition C than it was in conditions A and B. I currently think the ‘Permutation t-test on source data with spatio-temporal clustering’ tutorial would be most relevant tutorial for me to look at, but I lack the experience required to assess whether that is indeed correct. Could you perhaps tell me whether or not I am on the right track, and if not, could you perhaps point me to the tutorial that you think would be most relevant for me?
Thank you very much in advance for your help!
Best regards,
Alexander.
Figure 1:
Figure 2:
