[Mne_analysis] 3. Trans file without digitized data (Florian Aspart)

Saiz Alía, Marina marina.saiz-alia15 at imperial.ac.uk
Fri Sep 16 04:23:28 EDT 2016
Search archives: 
Hello Florian,

I do source reconstruction with EEG 64 channels and using fsaverage average brain from FreeSurfer too. 

I had the same problem. I was trying to get the trans file using mne coreg but my EEG data did not have the dig points. So what I did is to use the standard 10-20 electrode positions that I read using montage function, when loading the data.

I copied the positions of the EEG channels and the fiducial points into the raw.info[‘dig’] structure, saved the new raw file as .fif and then when I loaded it in mne correg I would see the digitized points over the fsaverage brain I previously selected. 

Let me know if you don’t know how to do it and I will try to help you but basically you just need to copy the positions into this info structure. Make sure LPA, RPA and nazion are ordered as dig structure requieres, just in case. You can load mne sample data set and check how this raw.info[‘dig’] structure has to be. 

Hope it helps although if you need more help I can send you my code or try to be more specific. I am not in the office now and I don’t exactly remember how I did it. But it is basically what I am telling you now.

Marina.


El 16/09/2016, a las 09:04, mne_analysis-request at nmr.mgh.harvard.edu escribió:

> 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. Re: Fwd: From raw MEG to publication - BIOMAG16	satellite
>      workshop, Oct 2, 2016 (Marijn van Vliet)
>   2. Re: Fwd: From raw MEG to publication - BIOMAG16 satellite
>      workshop, Oct 2, 2016 (Alexandre Gramfort)
>   3. Trans file without digitized data (Florian Aspart)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 15 Sep 2016 19:59:11 +0300
> From: Marijn van Vliet <w.m.vanvliet at gmail.com>
> Subject: Re: [Mne_analysis] Fwd: From raw MEG to publication -
> 	BIOMAG16	satellite workshop, Oct 2, 2016
> To: Discussion and support forum for the users of MNE Software
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <420C0CED-AA23-4756-BDE1-8E616EDB3511 at domarijn.nl>
> Content-Type: text/plain; charset=utf-8
> 
> That sounds really cool!
> 
> Who?s going to be MNE?s research team?
> 
> --
> Marijn van Vliet
> w.m.vanvliet at gmail.com
> 
> 
> 
> 
> 
>> On 15 Sep 2016, at 18:06, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> wrote:
>> 
>> [message from Vladimir Litvak]
>> 
>> Dear colleagues,
>> 
>> Apologies in advance for cross-posting. We would like to attract your
>> attention to the BIOMAG2016 satellite symposium which will take place
>> on Oct 2nd 2016 and is dedicated to group analysis of MEG data with
>> free academic toolboxes. Please read the full description below.
>> 
>> With best wishes,
>> 
>> Arnaud Delorme
>> Alexandre Gramfort
>> Vladimir Litvak
>> Srikantan Nagarajan
>> Robert Oostenveld
>> Francois Tadel
>> 
>> 
>> 
>> -------------------------------------------------------------------------------
>> 
>> 
>> From raw MEG to publication: how to perform MEG group analysis with
>> free academic software.
>> 
>> 
>> Organisers: Arnaud Delorme, Alexandre Gramfort, Vladimir Litvak,
>> Srikantan Nagarajan, Robert Oostenveld, Francois Tadel
>> 
>> 
>> Free academic toolboxes have gained increasing prominence in MEG
>> analysis as a means to disseminate cutting edge methods, share best
>> practices between different research groups and pool resources for
>> developing essential tools for the MEG community. In the recent years
>> large and vibrant research communities have emerged around several of
>> these toolboxes. Teaching events are regularly held around the world
>> where the basics of each toolbox are explained by its respective
>> developers and experienced power users. There are, however, two
>> knowledge gaps that our BIOMAG satellite symposium aims to address.
>> Firstly, most teaching examples only show analysis of a single
>> ?typical best? subject whereas most real MEG studies involve analysis
>> of group data. It is then left to the researchers in the field to
>> figure out for themselves how to make the transition and obtain
>> significant group results. Secondly, we are not familiar with any
>> examples of fully analyzing the same group dataset with different
>> academic toolboxes to assess the degree of agreement in scientific
>> conclusions and compare strengths and weaknesses of various analysis
>> methods and their independent implementations. Our workshop is
>> organised by the lead developers of six most popular free academic MEG
>> toolboxes (in alphabetic order): Brainstorm, EEGLAB, FieldTrip, MNE,
>> NUTMEG, and SPM. Ahead of the workshop the research team for each
>> toolbox will analyze the same group MEG/EEG dataset. This dataset
>> containing evoked responses to face stimuli was acquired by Richard
>> Henson and Daniel Wakeman, who won a special award at BIOMAG2010 to
>> make it freely available to the community. All the raw data are
>> available at
>> 
>> 
>> ftp://ftp.mrc-cbu.cam.ac.uk/personal/rik.henson/wakemandg_hensonrn/
>> 
>> and
>> 
>> https://openfmri.org/dataset/ds000117/
>> 
>> 
>> Detailed instructions for each toolbox will be made available online
>> including analysis scripts and figures of results. All analyses will
>> show a full pipeline from the raw data to detailed publication quality
>> results. Researchers who are interested in using the respective
>> toolbox will then be able to reproduce the analysis in their lab and
>> port it to their own data.
>> 
>> At the workshop each group will briefly introduce their software and
>> present the key results from their analysis. This will be followed by
>> a panel discussion and questions from the audience.
>> 
>> Following the event we plan to integrate the suggestions and questions
>> from the workshop audience and to publish the analyses details as part
>> of a special research topic in Frontiers in Neuroscience, section
>> Brain Imaging Methods so that the proposed best practices will be
>> endorsed by peer review and become citable in future publications.
>> Other research groups will be invited to contribute to the research
>> topic as long as they present detailed descriptions of analyses of
>> group data that are freely available online and make it possible for
>> others to fully reproduce their analysis and results.
>> 
>> 
>> We hope that this proposal will lead to creation of invaluable
>> resource for the whole MEG community and the workshop will contribute
>> to establishment of good practice and promoting consistent and
>> reproducible analysis approaches. The event will also showcase all the
>> toolboxes and will be of interest to beginners in the field with basic
>> background in MEG who contemplate the most suitable analysis approach
>> and software for their study as well as to experienced researchers who
>> would like to get up to date with the latest methodological
>> developments.
>> 
>> _______________________________________________
>> 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.
> 
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 15 Sep 2016 21:22:04 +0200
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> Subject: Re: [Mne_analysis] Fwd: From raw MEG to publication -
> 	BIOMAG16 satellite workshop, Oct 2, 2016
> To: Discussion and support forum for the users of MNE Software
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> 	<CADeotZoroJzov03OKy1h7VqAo3qddkKDsYcAdQ4Nw+JNCdUa7Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> hi Marijn,
> 
> so far this is jaakko, mainak, denis and myself.
> 
> We put everything here:
> 
> https://github.com/mne-tools/mne-biomag-group-demo/
> 
> but it's not ready yet for massive public advertising.
> 
> any help is welcome. Can be comments on our code, our parameters
> settings, our way to present results etc.
> 
> Alex
> 
> On Thu, Sep 15, 2016 at 6:59 PM, Marijn van Vliet
> <w.m.vanvliet at gmail.com> wrote:
>> That sounds really cool!
>> 
>> Who?s going to be MNE?s research team?
>> 
>> --
>> Marijn van Vliet
>> w.m.vanvliet at gmail.com
>> 
>> 
>> 
>> 
>> 
>>> On 15 Sep 2016, at 18:06, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> wrote:
>>> 
>>> [message from Vladimir Litvak]
>>> 
>>> Dear colleagues,
>>> 
>>> Apologies in advance for cross-posting. We would like to attract your
>>> attention to the BIOMAG2016 satellite symposium which will take place
>>> on Oct 2nd 2016 and is dedicated to group analysis of MEG data with
>>> free academic toolboxes. Please read the full description below.
>>> 
>>> With best wishes,
>>> 
>>> Arnaud Delorme
>>> Alexandre Gramfort
>>> Vladimir Litvak
>>> Srikantan Nagarajan
>>> Robert Oostenveld
>>> Francois Tadel
>>> 
>>> 
>>> 
>>> -------------------------------------------------------------------------------
>>> 
>>> 
>>> From raw MEG to publication: how to perform MEG group analysis with
>>> free academic software.
>>> 
>>> 
>>> Organisers: Arnaud Delorme, Alexandre Gramfort, Vladimir Litvak,
>>> Srikantan Nagarajan, Robert Oostenveld, Francois Tadel
>>> 
>>> 
>>> Free academic toolboxes have gained increasing prominence in MEG
>>> analysis as a means to disseminate cutting edge methods, share best
>>> practices between different research groups and pool resources for
>>> developing essential tools for the MEG community. In the recent years
>>> large and vibrant research communities have emerged around several of
>>> these toolboxes. Teaching events are regularly held around the world
>>> where the basics of each toolbox are explained by its respective
>>> developers and experienced power users. There are, however, two
>>> knowledge gaps that our BIOMAG satellite symposium aims to address.
>>> Firstly, most teaching examples only show analysis of a single
>>> ?typical best? subject whereas most real MEG studies involve analysis
>>> of group data. It is then left to the researchers in the field to
>>> figure out for themselves how to make the transition and obtain
>>> significant group results. Secondly, we are not familiar with any
>>> examples of fully analyzing the same group dataset with different
>>> academic toolboxes to assess the degree of agreement in scientific
>>> conclusions and compare strengths and weaknesses of various analysis
>>> methods and their independent implementations. Our workshop is
>>> organised by the lead developers of six most popular free academic MEG
>>> toolboxes (in alphabetic order): Brainstorm, EEGLAB, FieldTrip, MNE,
>>> NUTMEG, and SPM. Ahead of the workshop the research team for each
>>> toolbox will analyze the same group MEG/EEG dataset. This dataset
>>> containing evoked responses to face stimuli was acquired by Richard
>>> Henson and Daniel Wakeman, who won a special award at BIOMAG2010 to
>>> make it freely available to the community. All the raw data are
>>> available at
>>> 
>>> 
>>> ftp://ftp.mrc-cbu.cam.ac.uk/personal/rik.henson/wakemandg_hensonrn/
>>> 
>>> and
>>> 
>>> https://openfmri.org/dataset/ds000117/
>>> 
>>> 
>>> Detailed instructions for each toolbox will be made available online
>>> including analysis scripts and figures of results. All analyses will
>>> show a full pipeline from the raw data to detailed publication quality
>>> results. Researchers who are interested in using the respective
>>> toolbox will then be able to reproduce the analysis in their lab and
>>> port it to their own data.
>>> 
>>> At the workshop each group will briefly introduce their software and
>>> present the key results from their analysis. This will be followed by
>>> a panel discussion and questions from the audience.
>>> 
>>> Following the event we plan to integrate the suggestions and questions
>>> from the workshop audience and to publish the analyses details as part
>>> of a special research topic in Frontiers in Neuroscience, section
>>> Brain Imaging Methods so that the proposed best practices will be
>>> endorsed by peer review and become citable in future publications.
>>> Other research groups will be invited to contribute to the research
>>> topic as long as they present detailed descriptions of analyses of
>>> group data that are freely available online and make it possible for
>>> others to fully reproduce their analysis and results.
>>> 
>>> 
>>> We hope that this proposal will lead to creation of invaluable
>>> resource for the whole MEG community and the workshop will contribute
>>> to establishment of good practice and promoting consistent and
>>> reproducible analysis approaches. The event will also showcase all the
>>> toolboxes and will be of interest to beginners in the field with basic
>>> background in MEG who contemplate the most suitable analysis approach
>>> and software for their study as well as to experienced researchers who
>>> would like to get up to date with the latest methodological
>>> developments.
>>> 
>>> _______________________________________________
>>> 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
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 16 Sep 2016 10:03:54 +0200
> From: Florian Aspart <florian.aspart at gmail.com>
> Subject: [Mne_analysis] Trans file without digitized data
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID:
> 	<CAGA3+++ZQ8Gd_PdT6Y3uObEvZvt5ZfJSJhke0MUGMoxpbB+BoQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> first of all, thank you for developing MNE-python. I really like using it!
> 
> I am trying to apply source reconstruction on EEG data but I have neither
> subject specific MRI nor digitized point for the EEG montage.
> 
> I'm aware that without these data the source reconstruction will have
> little value but I would like to go for a rough guess using the provided
> fsaverage template for the MRI and standard 1020 montage with 64 electrodes.
> 
> The problem is I don't know how to get the Trans file since I have no
> digitized montage.
> How should I get the digitized points? Is there a way to create standard
> digitized montage? In this case, which value should I use?
> Or do you know of any "template" of digitized point for a standard 1020
> montage with 64 electrodes I could use?
> 
> I did not perform the experiment by myself, so digitizing a new participant
> with that montage would not be an option, or at least not in the near
> future.
> 
> This question was already asked on this mailing list a couple of month ago,
> but no clear solution was provided.
> https://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/2016-June/003414.html
> 
> Thanks,
> Florian
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160916/078e4b8f/attachment.html 
> 
> ------------------------------
> 
> _______________________________________________
> 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 104, Issue 18
> *********************************************

More information about the Mne_analysis mailing list