[Mne_analysis] preprocessing/ICA: movement artifacts vs blinks

[Daniel McCloy]

Thanks all, for the suggestions.  Annotations seemed like the right way to go, since I know the block start/end times already.  [Jaakko, I can report that annotations are working for me (both adding programmatically via `raw.annotations = mne.Annotations(...)` and also interactively.]  After annotating the between-block times as "bad-between-blocks", `ica.plot_components` looks good: 3 components that make sense for my experiment, and one on the forehead/face (the blinks).  Unfortunately neither `find_eog_events` nor `create_eog_epochs` seems to respect annotations (yet?).  So although I can ignore the between-blocks times when fitting the ICA, it doesn't seem to help with the next step of `ica.find_bads_eog`.  Please let me know if I'm misunderstanding something about this process; otherwise I'll report back after I've had a chance to try some of the other suggestions.

On March 15, 2017 12:58:40 AM PDT, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> wrote:
>one more thing. If the movement artifacts can get mapped to strong
>peak-to-peak
>amplitudes the reject param in ICA can certainly help automatically
>excluding these
>segments from the ICA fit.
>
>Alex
>
>On Tue, Mar 14, 2017 at 3:18 PM, Eric Larson <larson.eric.d at gmail.com>
>wrote:
>>> My approach is to fit ICA on the epochs as I want to analyze them,
>and use
>>> ica.plot_properties to inspect every component and manually identify
>the
>>> EOG-related components. This is usually very easy to do based on
>scalp
>>> distribution, variance, and the epochs raster plots (and easy to
>teach
>>> undergrads to reliably identify as well).
>>
>>
>> Assuming the movement artifacts are much bigger than the blinks, I
>wonder if
>> this suggestion be adapted to this use case with something like:
>>
>> 1. Use `make_fixed_length_events` to make regularly-spaced events of
>some
>> duration (not sure if e.g., 1 sec or 10 sec would work better)
>> 2. Create Epochs using a rejection threshold that throws away epochs
>based
>> on movement artifacts, but not the blink artifacts.
>> 3. Run ICA on the Epochs.
>>
>> Eric
>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to
>whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>you in
>> error
>> but does not contain patient information, please contact the sender
>and
>> properly
>> dispose of the e-mail.
>>
>_______________________________________________
>Mne_analysis mailing list
>Mne_analysis at nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis