[Mne_analysis] maxfilter for head movement compensation only

Evgenii Kalenkovich e.kalenkovich at gmail.com
Tue May 7 09:29:32 EDT 2019
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Hi, dear Mainak.

Let me make sure I understand correctly what you are proposing:

   1. Run `maxwell_filter` without setting bad channels.
   2. Run `autoreject` on the results of step 1 and identify bad channels.
   3. Run `maxwell_filter` again supplying the list of channels identified
   in step 2.

Does that make sense?

I've just realized I have two further questions:

   1. In this <https://github.com/autoreject/autoreject/issues/123>
   issue, @dengemann mentioned that `autoreject` does not identify flat
   channels. Do you think adding the following step would be appropriate?
      - 0. Run `mne.preprocessing.mark_flat` to identify flat channels.
   2. Would you add temporal filtering before `autoreject`?


On Tue, May 7, 2019 at 3:06 PM Mainak Jas <mainakjas at gmail.com> wrote:

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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.
> Mainak
>> 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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