I am trying to figure out what would be better to go towards source modeling activity with the hcp data. Should I use the hcp-mne toolbox and start from the raw instance or load in only what I need from the tmegpreproc files (preprocessed meg files) and raw files into mne? My hold back on using the hcp-mne toolbox is there is a whole 'Gotchas' sections that seems to say something about it not producing accurate source models, and it is not very clear to me what the workarounds are if there are any. I am assuming the tmegpreproc files cannot be brought over with the hcp-mne toolbox, so if I am wrong please let me know.
So I do still need to ask then, is there anything special I need to do to the raw data, I notice that when I plot the psd, the meg sensors on the head model are all crunched together on the left side. Should I just ignore that? I did a correction with hcp.preprocessing.map_ch_coords_to_mne() but that the part that says source localization will be wrong. So should I not do that is the big question.
I have tried read_epochs() but I keep getting an epochs.times error I can't seem to fix. I can do read_evokeds() just fine, but I do want the epochs so I can take coherence measures. That's why I was trying to use the tmegpreproc files, because I have had better luck recreating them into mne readable structures. I didn't realize the read_epochs pulls in preprocesed data, is that pulled from the tmegpreproc file then? I do want to use preprocessed stuff if possible so I can run all the participants on a more automated pipeline.