[Mne_analysis] maxfilter for head movement compensation only

Mainak Jas mainakjas at gmail.com
Tue May 7 08:05:00 EDT 2019
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Hi Evgenii,

I remove bad channels/epochs at a later stage using the autoreject package.
>> One reproducible option would be to use autoreject or some other
>> automated routine to determine bad channels. MaxFilter even has an
>> `autobad` option you could try running before the head position estimation
>> step to get a list of bad channels. In principle you should be able to
>> combine head position estimation -headpos and automatic bad channel
>> detection -autobad, but in practice you can encounter bugs this way, so
>> it's safer to separate it into two steps.
> I did try running `autoreject` on the raw data cut into constant-width
> segments. Unfortunately, it results in half-to-all the channels being
> flagged as bad in most of the epochs. Also, the worst dozen or so channels
> were different both from the manually selected bad channels and the
> `autoreject`'s results with different settings (I've varied
> pre-`autoreject` linear filtering cutoffs, decimation factor, and segment
> length).

Just a note, the data before MaxFilter _does_ look bad, so it's not
surprising that these are all flagged as bad. Thus, I would say it's a
little hard to decouple SSS from the bad channel selection that SSS
requires. One option that might work for you is to apply first an SSP on a
copy of the data so you mimic the situation when you  select bad channels.
And then apply autoreject on the SSP-ed data.


> I haven't tried MaxFilter's `-autobad` yet. Every person telling me how to
> use MaxFilter made sure to mention its unreliability so I've never
> considered it an option :-) I'll try and see whether the results are far
> from what manual inspection yields.
> Again, really appreciated your answer.
> Evgenii
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