I used raw.plot() to look at the raw MEG data. Here is what I have (screenshot attached). This looks completely different from the example data from the MNE website. I see large areas of blue in my data. Is this normal? I am new to this so would appreciate any help/advice on what I am looking at.
If you hit the minus key a bunch of times, it will bring your sensors into range.
You may have already done this, but notch_filtering (raw.notch_filter([60,120,180])) the raw data and possibly t/SSS-ing your data (again you may have already done this) will clean up the signal a little bit.
Thank you so much for your reply.
I was under the impression that you pick out the bad channels first before running the maxwell_filter/tsss-ing raw data.
Which method is better?
(1) tsss raw MEG data → manually pick out bad channels → run tsss again on data with the bad channels omitted
(2) low pass filter (55Hz) → manually pickout bad channels → run tsss
Or do both methods accomplish the same thing?
I understand that it is important to pick out the bad channels early or else I will have to redo everything.
I forgot about the picking bad channels first before doing t/SSS - but you are correct, you should pick the bad channels first and then do the t/SSS process - or else it will corrupt your SSS-ed data. (I haven’t worked in an Elekta/MEGIN site in several years).
And regarding choice 1 or 2 – I wouldn’t even filter your data - just look at the raw in the correct amplitude and you will see popping channels / jumps or very high freq noise.
Also - just an FYI I think that the plot command has a filtering option, so that you can just filter for visualization but not actually filter your data. Just look at the options in the raw.plot? . I think there you can also set a standard amplitude different from the default so that you dont need to reduce it after loading.
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