[Mne_analysis] Mne_analysis Digest, Vol 122, Issue 15

Sun Mar 11 16:11:04 EDT 2018

Alex,

That is exactly what I was searching, thank you !

Kind Regards,
Gertjan De Mulder

On 11 mrt. 2018 20:41 +0100, mne_analysis-request at nmr.mgh.harvard.edu, wrote:
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> Today's Topics:
>
> 1. Re: Approach for creating epochs (Gertjan De Mulder)
> 2. Re: Approach for creating epochs (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 11 Mar 2018 18:23:12 +0100
> From: Gertjan De Mulder <gertjan.demulder at ugent.be
> Subject: Re: [Mne_analysis] Approach for creating epochs
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID: <dfc6827a-824b-4ae8-990c-f574c4106dba at Spark
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> Assuming trials (e.g. with a duration of 25min), 14 eeg-only channels, no marker/event data, and only interested in the change of frequencyband-power over time, using fixed time windows.
> I would like to ask whether it is a good approach to create equally spread events (ignoring the details concerning interval size between events), in order to create an epoch for each artificial event?
>
> Kind Regards,
> Gertjan
>
> On 11 mrt. 2018 17:03 +0100, mne_analysis-request at nmr.mgh.harvard.edu, wrote:
> > Send Mne_analysis mailing list submissions to
> > mne_analysis at nmr.mgh.harvard.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > or, via email, send a message with subject or body 'help' to
> > mne_analysis-request at nmr.mgh.harvard.edu
> >
> > You can reach the person managing the list at
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Mne_analysis digest..."
> >
> >
> > Today's Topics:
> >
> > 1. [MNE_analysis] converting EEGlab ICAed .set file to MNE ICA
> > object (Taehwan Kim)
> > 2. Re: [MNE_analysis] converting EEGlab ICAed .set file to MNE
> > ICA object (Brunner, Clemens (clemens.brunner at uni-graz.at))
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sat, 10 Mar 2018 15:46:03 -0500
> > From: Taehwan Kim <iankim at nyu.edu
> > Subject: [Mne_analysis] [MNE_analysis] converting EEGlab ICAed .set
> > file to MNE ICA object
> > To: mne_analysis at nmr.mgh.harvard.edu
> > Message-ID:
> > <CAKWgqchEbmxKvyfMRz+9UfApeKK9QOCA=Hn-M67-q=Gr8UHKYg at mail.gmail.com
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> >
> > I fitted ICA on EEGlab with EEG data, and generated some .set files. I want
> > to try the MNE Python ICA functions, and want to try converting those .set
> > files into MNE Python ICA objects. Is there a way to do that?
> >
> > Thanks in advance!
> > Ian
> > -------------- next part --------------
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> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 11 Mar 2018 07:44:33 +0000
> > From: "Brunner, Clemens (clemens.brunner at uni-graz.at)"
> > <clemens.brunner at uni-graz.at
> > Subject: Re: [Mne_analysis] [MNE_analysis] converting EEGlab ICAed
> > .set file to MNE ICA object
> > To: Discussion and support forum for the users of MNE Software
> > <mne_analysis at nmr.mgh.harvard.edu
> > Message-ID: <508389A3-2C07-499F-9502-C6B92F11379A at uni-graz.at
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi!
> >
> > In principle this should be possible. You can load the .set file with scipy.io.loadmat (because it is a valid .mat file). The important ICA-related parts are stored in EEG.weights and EEG.sphering - these roughly correspond to MNE?s ICA.unmixing_matrix_ and ICA.pca_components_. You could create a new ICA object with ica = mne.preprocessing.ICA() and then set these two fields. However, you might need to set other attributes in order for this to work (https://martinos.org/mne/stable/generated/mne.preprocessing.ICA.html#attributes). Furthermore, EEGLAB and MNE handle these matrices slightly differently in terms of performed transformations. MNE performs a pre-whitening transform (which is usually a scaling to unit variance), and this is not included in the two matrices. I?m currently trying to simplify this process, so if it doesn?t work please feel free to contact me again.
> >
> > Clemens
> >
> >
> >
> > > On Mar 10, 2018, at 21:46, Taehwan Kim <iankim at nyu.edu> wrote:
> > >
> > > Hi,
> > >
> > > I fitted ICA on EEGlab with EEG data, and generated some .set files. I want to try the MNE Python ICA functions, and want to try converting those .set files into MNE Python ICA objects. Is there a way to do that?
> > >
> > > Thanks in advance!
> > > Ian
> > > _______________________________________________
> > > 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
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> > > contains patient information, please contact the Partners Compliance HelpLine at
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> > > but does not contain patient information, please contact the sender and properly
> > > dispose of the e-mail.
> >
> >
> >
> >
> > ------------------------------
> >
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> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
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> > End of Mne_analysis Digest, Vol 122, Issue 14
> > *********************************************
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> ------------------------------
>
> Message: 2
> Date: Sun, 11 Mar 2018 20:39:51 +0100
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr
> Subject: Re: [Mne_analysis] Approach for creating epochs
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu
> Message-ID:
> <CADeotZr1q3iy9iHJLUdwnxy8qtddbthEn4rJRPAtrR-L9ZJ35A at mail.gmail.com
> Content-Type: text/plain; charset="utf-8"
>
> hi,
>
> not sure to understand what you're asking but maybe this can help:
>
> https://martinos.org/mne/stable/generated/mne.make_fixed_length_events.html
>
> Best,
> Alex
>
>
> On Sun, Mar 11, 2018 at 6:23 PM, Gertjan De Mulder <
> gertjan.demulder at ugent.be> wrote:
>
> > Hi,
> >
> > Assuming trials (e.g. with a duration of 25min), 14 eeg-only channels, no
> > marker/event data, and only interested in the change of frequencyband-power
> > over time, using fixed time windows.
> > I would like to ask whether it is a good approach to create equally spread
> > events (ignoring the details concerning interval size between events), in
> > order to create an epoch for each artificial event?
> >
> > Kind Regards,
> > Gertjan
> >
> > On 11 mrt. 2018 17:03 +0100, mne_analysis-request at nmr.mgh.harvard.edu,
> > wrote:
> >
> > Send Mne_analysis mailing list submissions to
> > mne_analysis at nmr.mgh.harvard.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > or, via email, send a message with subject or body 'help' to
> > mne_analysis-request at nmr.mgh.harvard.edu
> >
> > You can reach the person managing the list at
> > mne_analysis-owner at nmr.mgh.harvard.edu
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Mne_analysis digest..."
> >
> >
> > Today's Topics:
> >
> > 1. [MNE_analysis] converting EEGlab ICAed .set file to MNE ICA
> > object (Taehwan Kim)
> > 2. Re: [MNE_analysis] converting EEGlab ICAed .set file to MNE
> > ICA object (Brunner, Clemens (clemens.brunner at uni-graz.at))
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sat, 10 Mar 2018 15:46:03 -0500
> > From: Taehwan Kim <iankim at nyu.edu
> > Subject: [Mne_analysis] [MNE_analysis] converting EEGlab ICAed .set
> > file to MNE ICA object
> > To: mne_analysis at nmr.mgh.harvard.edu
> > Message-ID:
> > <CAKWgqchEbmxKvyfMRz+9UfApeKK9QOCA=Hn-M67-q=Gr8UHKYg at mail.gmail.com
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> >
> > I fitted ICA on EEGlab with EEG data, and generated some .set files. I want
> > to try the MNE Python ICA functions, and want to try converting those .set
> > files into MNE Python ICA objects. Is there a way to do that?
> >
> > Thanks in advance!
> > Ian
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/
> > attachments/20180310/cc969a3e/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 11 Mar 2018 07:44:33 +0000
> > From: "Brunner, Clemens (clemens.brunner at uni-graz.at)"
> > <clemens.brunner at uni-graz.at
> > Subject: Re: [Mne_analysis] [MNE_analysis] converting EEGlab ICAed
> > .set file to MNE ICA object
> > To: Discussion and support forum for the users of MNE Software
> > <mne_analysis at nmr.mgh.harvard.edu
> > Message-ID: <508389A3-2C07-499F-9502-C6B92F11379A at uni-graz.at
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi!
> >
> > In principle this should be possible. You can load the .set file with
> > scipy.io.loadmat (because it is a valid .mat file). The important
> > ICA-related parts are stored in EEG.weights and EEG.sphering - these
> > roughly correspond to MNE?s ICA.unmixing_matrix_ and ICA.pca_components_.
> > You could create a new ICA object with ica = mne.preprocessing.ICA() and
> > then set these two fields. However, you might need to set other attributes
> > in order for this to work (https://martinos.org/mne/stable/generated/mne.
> > preprocessing.ICA.html#attributes). Furthermore, EEGLAB and MNE handle
> > these matrices slightly differently in terms of performed transformations.
> > MNE performs a pre-whitening transform (which is usually a scaling to unit
> > variance), and this is not included in the two matrices. I?m currently
> > trying to simplify this process, so if it doesn?t work please feel free to
> > contact me again.
> >
> > Clemens
> >
> >
> >
> > On Mar 10, 2018, at 21:46, Taehwan Kim <iankim at nyu.edu> wrote:
> >
> > Hi,
> >
> > I fitted ICA on EEGlab with EEG data, and generated some .set files. I
> > want to try the MNE Python ICA functions, and want to try converting those
> > .set files into MNE Python ICA objects. Is there a way to do that?
> >
> > Thanks in advance!
> > Ian
> > _______________________________________________
> > 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
> >
> > End of Mne_analysis Digest, Vol 122, Issue 14
> > *********************************************
> >
> >
> > _______________________________________________
> > 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.
> >
> >
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