Intracranial SEEG montage and layout

✉️ Mailing List Archive (read-only)
1

Dear all,

I am trying to import intracranial SEEG data into MNE.

Can anyone point me to tutorials and examples on how to import
subject-specific SEEG electrode positions (3D) and to produce a 3D or 2D
layout for plotting?

For what I read, the function to be used is mne.channels.DigMontage

However, I cannot understand how to import channel position and names
(and in which format they have to be)

Thanks a lot

Andrea

2

Hi Andrea,

you can check http://martinos.org/mne/stable/auto_tutorials/plot_ecog.html

JR

3

Thanks JR, yes I had tried that link.

But it seems that the current misc data does not contain the ECoG
dataset anymore. For example, I cannot find the '/ecog/sample_ecog.mat'
file required for this line:

mat = loadmat
<scipy.io.loadmat — SciPy v1.11.4 Manual + '/ecog/sample_ecog.mat')

In fact, I cannot find it in the dataset page:
http://martinos.org/mne/stable/manual/datasets_index.html

Any ideas?

Thanks

Andrea

Le 18/09/2017 ? 21:20, JR KING a ?crit?:

Hi Andrea,

you can check http://martinos.org/mne/stable/auto_tutorials/plot_ecog.html

JR

    Dear all,

    I am trying to import intracranial SEEG data into MNE.

    Can anyone point me to tutorials and examples on how to import
    subject-specific SEEG electrode positions (3D) and to produce a 3D
    or 2D
    layout for plotting?

    For what I read, the function to be used is mne.channels.DigMontage

    However, I cannot understand how to import channel position and names
    (and in which format they have to be)

    Thanks a lot

    Andrea

    _______________________________________________
    Mne_analysis mailing list
    Mne_analysis at nmr.mgh.harvard.edu
    <mailto:Mne_analysis at nmr.mgh.harvard.edu>
    Mne_analysis Info Page
    <mail.nmr.mgh.harvard.edu Mailing Lists;

    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
    MyComplianceReport.com: Compliance and Ethics Reporting
    <http://www.partners.org/complianceline&gt; . 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
Mne_analysis Info Page

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
MyComplianceReport.com: Compliance and Ethics Reporting . 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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20170919/31082aa9/attachment.html

4

You may have deleted the file accidentally? Try to force redownloading the
file

mne.datasets.misc.data_path(force_update=True)

Hope that helps

JR

5

Indeed, I forced the update and I now see the file. Sorry for bothering
with this "minor issue"

Thanks again

Andrea

Le 19-Sep-17 ? 3:40 PM, JR KING a ?crit?:

You may have deleted the file accidentally? Try to force redownloading
the file

mne.datasets.misc.data_path(force_update=True)

Hope that helps

JR

    Thanks JR, yes I had tried that link.

    But it seems that the current misc data does not contain the ECoG
    dataset anymore. For example, I cannot find the
    '/ecog/sample_ecog.mat' file required for this line:

    mat = loadmat
    <scipy.io.loadmat — SciPy v1.11.4 Manual + '/ecog/sample_ecog.mat')

    In fact, I cannot find it in the dataset page:
    http://martinos.org/mne/stable/manual/datasets_index.html
    <http://martinos.org/mne/stable/manual/datasets_index.html&gt;

    Any ideas?

    Thanks

    Andrea

    Le 18/09/2017 ? 21:20, JR KING a ?crit?:

    Hi Andrea,

    you can check
    http://martinos.org/mne/stable/auto_tutorials/plot_ecog.html
    <http://martinos.org/mne/stable/auto_tutorials/plot_ecog.html&gt;

    JR

        Dear all,

        I am trying to import intracranial SEEG data into MNE.

        Can anyone point me to tutorials and examples on how to import
        subject-specific SEEG electrode positions (3D) and to produce
        a 3D or 2D
        layout for plotting?

        For what I read, the function to be used is
        mne.channels.DigMontage

        However, I cannot understand how to import channel position
        and names
        (and in which format they have to be)

        Thanks a lot

        Andrea

        _______________________________________________
        Mne_analysis mailing list
        Mne_analysis at nmr.mgh.harvard.edu
        <mailto:Mne_analysis at nmr.mgh.harvard.edu>
        Mne_analysis Info Page
        <mail.nmr.mgh.harvard.edu Mailing Lists;

        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
        MyComplianceReport.com: Compliance and Ethics Reporting
        <http://www.partners.org/complianceline&gt; . 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
    <mailto:Mne_analysis at nmr.mgh.harvard.edu>
    Mne_analysis Info Page
    <mail.nmr.mgh.harvard.edu Mailing Lists;

    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
    MyComplianceReport.com: Compliance and Ethics Reporting
    <http://www.partners.org/complianceline&gt; . 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
    <mailto:Mne_analysis at nmr.mgh.harvard.edu>
    Mne_analysis Info Page
    <mail.nmr.mgh.harvard.edu Mailing Lists;

    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
    MyComplianceReport.com: Compliance and Ethics Reporting
    <http://www.partners.org/complianceline&gt; . 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
Mne_analysis Info Page

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
MyComplianceReport.com: Compliance and Ethics Reporting . 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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20170919/a19ab18b/attachment.html