[Mne_analysis] simulated EEG to simulated MEG

Saeed Zahran saeedzahran at hotmail.com
Wed Feb 8 21:04:18 EST 2017
Search archives: 
Goodmorning,


How do you convert the simulated EEG to simulated MEG,

Its possible to convert the electrical potential generated at each cells to

magnetic potential? without modelling the MEG


Best regards

 Saeed Zahran


________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of mne_analysis-request at nmr.mgh.harvard.edu <mne_analysis-request at nmr.mgh.harvard.edu>
Sent: Thursday, February 9, 2017 1:18 AM
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Subject: Mne_analysis Digest, Vol 109, Issue 12

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Today's Topics:

   1. plot_label_from_stc (Elisabeth Fonteneau)
   2. Re: plot_label_from_stc (Sheraz Khan, PhD)
   3. Re: plot_label_from_stc (Elisabeth Fonteneau)
   4. Re: plot_label_from_stc (Sheraz Khan, PhD)


----------------------------------------------------------------------

Message: 1
Date: Wed, 8 Feb 2017 19:34:45 -0000
From: "Elisabeth Fonteneau" <ef309 at cam.ac.uk>
Subject: [Mne_analysis] plot_label_from_stc
To: <mne_analysis at nmr.mgh.harvard.edu>
Message-ID: <007e01d28242$67480030$35d80090$@cam.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Hello MNE experts,

I have a question for creating a Label from a functional STC file



I found the script plot_label_from_stc.py which is great!



However when I use the function mne.stc_to_label I am running into a problem




My STC file is an average and morph file and I read it via the command
mne_read_source_estimate.

I don't have the source space and I am forced to save the label as
unconnected vertices.



I try to reconnect the vertices in FreeSurfer but with no success so far..



Is there a way to overpass this problem in a way I can save my label as a
connected surface?



Thanks in advance

Elisabeth







__________________________________________________________



Dr Elisabeth Fonteneau

Department of Psychology

University of Cambridge

Downing Street, Cambridge CB2 3EB, UK

Email:  <mailto:ef309 at cam.ac.uk> ef309 at cam.ac.uk

Web:  <http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk<http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>









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Message: 2
Date: Wed, 8 Feb 2017 15:38:49 -0500 (EST)
From: "Sheraz Khan, PhD" <sheraz at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] plot_label_from_stc
To: "Discussion and support forum for the users of MNE Software"
        <mne_analysis at nmr.mgh.harvard.edu>
Cc: mne_analysis at nmr.mgh.harvard.edu
Message-ID:
        <51824.209.95.50.113.1486586329.squirrel at mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1

if its fsaverage, you are morphed to for averaging

# select morph grade
src_fsaverage_fname = subjects_dir + '/fsaverage/bem/fsaverage-ico-5-src.fif'

src_fsaverage = mne.read_source_spaces(src_fsaverage_fname)

func_labels= mne.stc_to_label(stc_mean_label, src_fsaverage, smooth=True,
connected=True)[0]



> Hello MNE experts,
>
> I have a question for creating a Label from a functional STC file
>
>
>
> I found the script plot_label_from_stc.py which is great!
>
>
>
> However when I use the function mne.stc_to_label I am running into a
> problem
>
>
>
>
> My STC file is an average and morph file and I read it via the command
> mne_read_source_estimate.
>
> I don't have the source space and I am forced to save the label as
> unconnected vertices.
>
>
>
> I try to reconnect the vertices in FreeSurfer but with no success so far..
>
>
>
> Is there a way to overpass this problem in a way I can save my label as a
> connected surface?
>
>
>
> Thanks in advance
>
> Elisabeth
>
>
>
>
>
>
>
> __________________________________________________________
>
>
>
> Dr Elisabeth Fonteneau
>
> Department of Psychology
>
> University of Cambridge
>
> Downing Street, Cambridge CB2 3EB, UK
>
> Email:  <mailto:ef309 at cam.ac.uk> ef309 at cam.ac.uk
>
> Web:  <http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
> www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk<http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis


-------------------------
Sheraz Khan, M.Eng, Ph.D.
Instructor in Neurology

Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School

McGovern Institute for Brain Research
Massachusetts Institute of Technology

Tel:   +1 617-643-5634
Fax:   +1 617-948-5966
Email: sheraz at nmr.mgh.harvard.edu
       sheraz at mit.edu
Web:   http://sheraz.mit.edu


------------------------------

Message: 3
Date: Wed, 8 Feb 2017 21:02:29 -0000
From: "Elisabeth Fonteneau" <ef309 at cam.ac.uk>
Subject: Re: [Mne_analysis] plot_label_from_stc
To: <sheraz at nmr.mgh.harvard.edu>,       "'Discussion and support forum for
        the users of MNE Software'"     <mne_analysis at nmr.mgh.harvard.edu>
Message-ID: <009a01d2824e$a8a792a0$f9f6b7e0$@cam.ac.uk>
Content-Type: text/plain;       charset="us-ascii"

Hi Sheraz,
Thanks for your quick answer
I already checked for this directory and file (+
'/fsaverage/bem/fsaverage-ico-5-src.fif')
unfortunately I do not have the directory "bem" in my Average directory
(only label/mri/surf/)
I am reanalysing some old data and I used older version of mne & FreeSurfer
(mne_ version 2.7.3 and freesurfer 4.3.0)
With the command make_average_subject --subjects <list of subjects>
Is there a way or command to create this bem directory and files?
Elisabeth


__________________________________________________________

Dr Elisabeth Fonteneau
Department of Psychology
University of Cambridge
Downing Street, Cambridge CB2 3EB, UK
Email: ef309 at cam.ac.uk
Web: www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk<http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>




-----Original Message-----
From: mne_analysis-bounces at nmr.mgh.harvard.edu
[mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Sheraz Khan,
PhD
Sent: 08 February 2017 20:39
To: Discussion and support forum for the users of MNE Software
Cc: mne_analysis at nmr.mgh.harvard.edu
Subject: Re: [Mne_analysis] plot_label_from_stc

if its fsaverage, you are morphed to for averaging

# select morph grade
src_fsaverage_fname = subjects_dir +
'/fsaverage/bem/fsaverage-ico-5-src.fif'

src_fsaverage = mne.read_source_spaces(src_fsaverage_fname)

func_labels= mne.stc_to_label(stc_mean_label, src_fsaverage, smooth=True,
connected=True)[0]



> Hello MNE experts,
>
> I have a question for creating a Label from a functional STC file
>
>
>
> I found the script plot_label_from_stc.py which is great!
>
>
>
> However when I use the function mne.stc_to_label I am running into a
> problem
>
>
>
>
> My STC file is an average and morph file and I read it via the command
> mne_read_source_estimate.
>
> I don't have the source space and I am forced to save the label as
> unconnected vertices.
>
>
>
> I try to reconnect the vertices in FreeSurfer but with no success so far..
>
>
>
> Is there a way to overpass this problem in a way I can save my label
> as a connected surface?
>
>
>
> Thanks in advance
>
> Elisabeth
>
>
>
>
>
>
>
> __________________________________________________________
>
>
>
> Dr Elisabeth Fonteneau
>
> Department of Psychology
>
> University of Cambridge
>
> Downing Street, Cambridge CB2 3EB, UK
>
> Email:  <mailto:ef309 at cam.ac.uk> ef309 at cam.ac.uk
>
> Web:
> <http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
> www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk<http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis


-------------------------
Sheraz Khan, M.Eng, Ph.D.
Instructor in Neurology

Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General
Hospital Harvard Medical School

McGovern Institute for Brain Research
Massachusetts Institute of Technology

Tel:   +1 617-643-5634
Fax:   +1 617-948-5966
Email: sheraz at nmr.mgh.harvard.edu
       sheraz at mit.edu
Web:   http://sheraz.mit.edu
_______________________________________________
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
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sender and properly dispose of the e-mail.




------------------------------

Message: 4
Date: Wed, 8 Feb 2017 18:18:56 -0500 (EST)
From: "Sheraz Khan, PhD" <sheraz at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] plot_label_from_stc
To: "Elisabeth Fonteneau" <ef309 at cam.ac.uk>
Cc: 'Discussion and support forum for the users of MNE Software'
        <mne_analysis at nmr.mgh.harvard.edu>
Message-ID:
        <50933.172.21.16.227.1486595936.squirrel at mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1

please use following commands, they are data independent, requires only
anatomical information. mne.setup_source_space is the one you need for the
src file.


conductivity = (0.3,) #MEG only
model = mne.make_bem_model(subject=subject, ico=4,
                           conductivity=conductivity,
                           subjects_dir=subjects_dir)
bem = mne.make_bem_solution(model)
src = mne.setup_source_space(subject, spacing='ico5',
                             subjects_dir=subjects_dir,
                             add_dist=False, overwrite=True)

Sheraz


> Hi Sheraz,
> Thanks for your quick answer
> I already checked for this directory and file (+
> '/fsaverage/bem/fsaverage-ico-5-src.fif')
> unfortunately I do not have the directory "bem" in my Average directory
> (only label/mri/surf/)
> I am reanalysing some old data and I used older version of mne &
> FreeSurfer
> (mne_ version 2.7.3 and freesurfer 4.3.0)
> With the command make_average_subject --subjects <list of subjects>
> Is there a way or command to create this bem directory and files?
> Elisabeth
>
>
> __________________________________________________________
>
> Dr Elisabeth Fonteneau
> Department of Psychology
> University of Cambridge
> Downing Street, Cambridge CB2 3EB, UK
> Email: ef309 at cam.ac.uk
> Web: www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk<http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
>
>
>
>
> -----Original Message-----
> From: mne_analysis-bounces at nmr.mgh.harvard.edu
> [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Sheraz
> Khan,
> PhD
> Sent: 08 February 2017 20:39
> To: Discussion and support forum for the users of MNE Software
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] plot_label_from_stc
>
> if its fsaverage, you are morphed to for averaging
>
> # select morph grade
> src_fsaverage_fname = subjects_dir +
> '/fsaverage/bem/fsaverage-ico-5-src.fif'
>
> src_fsaverage = mne.read_source_spaces(src_fsaverage_fname)
>
> func_labels= mne.stc_to_label(stc_mean_label, src_fsaverage, smooth=True,
> connected=True)[0]
>
>
>
>> Hello MNE experts,
>>
>> I have a question for creating a Label from a functional STC file
>>
>>
>>
>> I found the script plot_label_from_stc.py which is great!
>>
>>
>>
>> However when I use the function mne.stc_to_label I am running into a
>> problem
>>
>>
>>
>>
>> My STC file is an average and morph file and I read it via the command
>> mne_read_source_estimate.
>>
>> I don't have the source space and I am forced to save the label as
>> unconnected vertices.
>>
>>
>>
>> I try to reconnect the vertices in FreeSurfer but with no success so
>> far..
>>
>>
>>
>> Is there a way to overpass this problem in a way I can save my label
>> as a connected surface?
>>
>>
>>
>> Thanks in advance
>>
>> Elisabeth
>>
>>
>>
>>
>>
>>
>>
>> __________________________________________________________
>>
>>
>>
>> Dr Elisabeth Fonteneau
>>
>> Department of Psychology
>>
>> University of Cambridge
>>
>> Downing Street, Cambridge CB2 3EB, UK
>>
>> Email:  <mailto:ef309 at cam.ac.uk> ef309 at cam.ac.uk
>>
>> Web:
>> <http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
>> www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk<http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> -------------------------
> Sheraz Khan, M.Eng, Ph.D.
> Instructor in Neurology
>
> Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General
> Hospital Harvard Medical School
>
> McGovern Institute for Brain Research
> Massachusetts Institute of Technology
>
> Tel:   +1 617-643-5634
> Fax:   +1 617-948-5966
> Email: sheraz at nmr.mgh.harvard.edu
>        sheraz at mit.edu
> Web:   http://sheraz.mit.edu
> _______________________________________________
> 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.
>
>
>
>


-------------------------
Sheraz Khan, M.Eng, Ph.D.
Instructor in Neurology

Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School

McGovern Institute for Brain Research
Massachusetts Institute of Technology

Tel:   +1 617-643-5634
Fax:   +1 617-948-5966
Email: sheraz at nmr.mgh.harvard.edu
       sheraz at mit.edu
Web:   http://sheraz.mit.edu


------------------------------

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