[Mne_analysis] ICA Analysis

[Denis A. Engemann]

        External Email - Use Caution        

Hi, 

it does not look so bad to me.
I would not call that “all over the place”.
Perhaps there is a bit of noise but you seem to capture the main components. How many components it takes to describe your artefact not only depends on the number of channels but also on how long the recording is, if there were head movements and on your filter settings. You can for example lowpass filter your data at 2hz at fit-time or fit ICA run by run
to mitigate issues with non-stationarity that may drive up your component numbers.
Anyways, your plot does look rather encouraging to me, having 2-3 more components than expected is not a catastrophe if the results are ok.
Did you look at the overlay plots to see how the average EOG looks after rejection?

Hope that helps,
Denis

On Tue 13 Aug 2019 at 20:24, Bianca Islas, BS <biancaisla1 at gmail.com> wrote:
>         External Email - Use Caution        
> 
> MNE Team,
>  
> First and foremost we’d like to thank you for the responses and suggestions to our last email.  As we get closer to finalizing our Py script, you have all certainly given us some food for thought.
>  
> We now have a new concern relating to the ICA analysis.  We have been consulting the documentation and have followed the tutorial for ICA analysis: 
> https://mne.tools/stable/auto_tutorials/preprocessing/plot_artifacts_correction_ica.html
>  
> However, our component scores seem to be all over the place.  It’s also saying that there are three EOG channels in the latent sources plot, when there should only be HEO and VEO. Historically, we have used the Semlitsch algorithm [Semlitsch HV, Anderer P, Schuster P, Presslich O., (1986) A solution for reliable and valid reduction of ocular artifacts, applied to the P300 ERP, Psychophysiology,23(6):695-703] with no issues.  Is there a way to use this method in MNE-Python instead?  We realize that the Semlitsch algorithm may be outdated, is there a reason/reference ICA may stand apart from this algorithm?
>  
> As always thank you for your assistance,
>  
> UNLV PEPLab
> Bianca Islas
> Research Assistant
>  
>  
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis


> On 13 Aug 2019, at 20:23, Bianca Islas, BS <biancaisla1 at gmail.com> wrote:
> 
>         External Email - Use Caution        
> 
> MNE Team,
>  
> First and foremost we’d like to thank you for the responses and suggestions to our last email.  As we get closer to finalizing our Py script, you have all certainly given us some food for thought.
>  
> We now have a new concern relating to the ICA analysis.  We have been consulting the documentation and have followed the tutorial for ICA analysis:
> https://mne.tools/stable/auto_tutorials/preprocessing/plot_artifacts_correction_ica.html
>  
> However, our component scores seem to be all over the place.  It’s also saying that there are three EOG channels in the latent sources plot, when there should only be HEO and VEO. Historically, we have used the Semlitsch algorithm [Semlitsch HV, Anderer P, Schuster P, Presslich O., (1986) A solution for reliable and valid reduction of ocular artifacts, applied to the P300 ERP, Psychophysiology,23(6):695-703] with no issues.  Is there a way to use this method in MNE-Python instead?  We realize that the Semlitsch algorithm may be outdated, is there a reason/reference ICA may stand apart from this algorithm?
>  
> As always thank you for your assistance,
>  
> UNLV PEPLab
> Bianca Islas
> Research Assistant
>  
>  
> <Comp_scores.PNG>
> <Lat_Sources.PNG>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20190813/7bcd35c4/attachment.html