[Mne_analysis] some questions regarding the source modelling of evoked potentials/fields (Irina Anurova)

[Geller, Jason]

        External Email - Use Caution        

  Irina,

   Here is what I use to get grand average sources:

   all_stcs=3Dnp.average([x.data for x in all_stcs2], axis=3D0) # you should have list with all stcs
   
   morphed_stcs=mne.SourceEstimate(data1, all_stcs[0].vertices, all_stcs[0].=
   tmin, all_stcs[0].tstep, all_stcs[0].subject) 
# this will save the grand av=
   erage stc

> On Nov 5, 2019, at 12:58 PM, mne_analysis-request at nmr.mgh.harvard.edu wrote:
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> Today's Topics:
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>   1. Re: some questions regarding the source modelling of evoked
>      potentials/fields (Irina Anurova)
>   2. Goldman montage subtracting channel from average (Zuhaib Asad)
>   3. Re: some questions regarding the source modelling of evoked
>      potentials/fields (Irina Anurova)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 5 Nov 2019 20:19:08 +0200
> From: Irina Anurova <anurova.irina at gmail.com>
> Subject: Re: [Mne_analysis] some questions regarding the source
> 	modelling of evoked potentials/fields
> To: Discussion and support forum for the users of MNE Software
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> 	<CAMwUYNzptWsbB=2z6zgXYs=-KOHUSAh6MUkBNKGNkd-jGX-A6g at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
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> 
> Hi Alexandre,
> Thank you very much for your help!
> I prepared morphed (to fsaverage) stcs for all subjects. Which function
> should I use to get the grand average?
> Thank you!
> 
> On Mon, Oct 21, 2019 at 4:32 PM Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
> 
>>        External Email - Use Caution
>> 
>> get the stc for the full window and then use:
>> 
>> 
>> https://mne.tools/stable/generated/mne.SourceEstimate.html#mne.SourceEstimate.mean
>> 
>> HTH
>> Alex
>> 
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> Message: 2
> Date: Tue, 5 Nov 2019 18:55:27 +0000
> From: Zuhaib Asad <19100201 at lums.edu.pk>
> Subject: [Mne_analysis] Goldman montage subtracting channel from
> 	average
> To: "mne_analysis at nmr.mgh.harvard.edu"
> 	<mne_analysis at nmr.mgh.harvard.edu>
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> Hi all,
> 
> I have data of eeg in .edf files. I want different montages like Goldman, Round etc. But the problem is in Goldman montage we need to subtract average from all channels. So how do I subtract it? Should I use
> raw.set_eeg_reference('average')
> but after using it how do I subtract Average from channel Fp1 and some other channel?
> In round montage, we need to subtract standard deviation from channel, how to do it?
> 
> Thank you!
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> Message: 3
> Date: Tue, 5 Nov 2019 20:58:27 +0200
> From: Irina Anurova <anurova.irina at gmail.com>
> Subject: Re: [Mne_analysis] some questions regarding the source
> 	modelling of evoked potentials/fields
> To: Discussion and support forum for the users of MNE Software
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> 	<CAMwUYNyGTSRokvLi+nKuDak-7Pi4R5NW6_haMSRLEND5h5vecA at mail.gmail.com>
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> 
> Sorry,
> I did not understand "get the stc for the full window".
> I tried this:
> morph_group = [morphS1, morphS2, morphS3, morphS4]
> grand_average = mne.SourceEstimate.mean(morph_group)
> 
> returns error: "AttributeError: 'list' object has no attribute 'sum'"
> 
> 
> 
> On Mon, Oct 21, 2019 at 4:32 PM Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
> 
>>        External Email - Use Caution
>> 
>> get the stc for the full window and then use:
>> 
>> 
>> https://mne.tools/stable/generated/mne.SourceEstimate.html#mne.SourceEstimate.mean
>> 
>> HTH
>> Alex
>> 
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