[Mne_analysis] help

Alberto G Vilanova5 at hotmail.com
Wed Aug 1 05:53:32 EDT 2018
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help


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De: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> en nombre de mne_analysis-request at nmr.mgh.harvard.edu <mne_analysis-request at nmr.mgh.harvard.edu>
Enviado: miércoles, 1 de agosto de 2018 2:37
Para: mne_analysis at nmr.mgh.harvard.edu
Asunto: Mne_analysis Digest, Vol 126, Issue 24

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Today's Topics:

   1. Manipulating Channels on Raw Preloaded to Workfile
      (Rockhill, Alexander P.)
   2. Re: Manipulating Channels on Raw Preloaded to     Workfile
      (Eric Larson)
   3. mne.SourceEstimate.data array (Corey Scheideman)
   4. Re: mne.SourceEstimate.data array (Eric Larson)


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Message: 1
Date: Tue, 31 Jul 2018 16:34:12 +0000
From: "Rockhill, Alexander P." <AROCKHILL at mgh.harvard.edu>
Subject: [Mne_analysis] Manipulating Channels on Raw Preloaded to
        Workfile
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        <mne_analysis at nmr.mgh.harvard.edu>
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        <8116B7BF4F63514F93CDD2BB034BA0A613DE4C36 at PHSX10MB4.partners.org>
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Hi all,

    I have a very large Raw file (several hours sampled at 25 kHz) and the analysis depends on not decimating the data. I have been trying to use a memory-mapped file but when I add channels, I get the error:

>>> raw.add_channels([Cz], force_update_info=False)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/autofs/space/karima_001/users/alex/software/anaconda2/lib/python2.7/site-packages/mne/channels/channels.py", line 877, in add_channels
    data = np.concatenate(data, axis=con_axis)
MemoryError

    If anyone has helpful information about a way around this, I would appreciate it greatly.

Thanks,

Alex Rockhill

Translational NeuroEngineering Laboratory
Division of Neurotherapeutics, Department of Psychiatry
Massachusetts General Hospital, Martinos Center
149 13th St Charlestown #2301, Boston, MA 02129
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Message: 2
Date: Tue, 31 Jul 2018 12:42:42 -0400
From: Eric Larson <larson.eric.d at gmail.com>
Subject: Re: [Mne_analysis] Manipulating Channels on Raw Preloaded to
        Workfile
To: Discussion and support forum for the users of MNE Software
        <mne_analysis at nmr.mgh.harvard.edu>
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        <CAGu2niXhHDiiZ_G+mU=Vy+LDch1VA5nL_cYjTi4xF7k_h_FSTw at mail.gmail.com>
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We probably do not handle preload-as-str properly. Can you open an MNE
issue about this on GitHub?

Eric


On Tue, Jul 31, 2018 at 12:34 PM Rockhill, Alexander P. <
AROCKHILL at mgh.harvard.edu> wrote:

> Hi all,
>
>     I have a very large Raw file (several hours sampled at 25 kHz) and the
> analysis depends on not decimating the data. I have been trying to use a
> memory-mapped file but when I add channels, I get the error:
>
> >>> raw.add_channels([Cz], force_update_info=False)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/autofs/space/karima_001/users/alex/software/anaconda2/lib/python2.7/site-packages/mne/channels/channels.py",
> line 877, in add_channels
>     data = np.concatenate(data, axis=con_axis)
> MemoryError
>
>     If anyone has helpful information about a way around this, I would
> appreciate it greatly.
>
> Thanks,
>
> Alex Rockhill
>
> Translational NeuroEngineering Laboratory
> Division of Neurotherapeutics, Department of Psychiatry
> Massachusetts General Hospital, Martinos Center
> 149 13th St Charlestown #2301, Boston, MA 02129
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Message: 3
Date: Tue, 31 Jul 2018 12:23:04 -0400
From: Corey Scheideman <coreys1 at umbc.edu>
Subject: [Mne_analysis] mne.SourceEstimate.data array
To: mne_analysis at nmr.mgh.harvard.edu
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Hi,

My current question is, what exactly is stc.data?

I know that it's a 2D array of vertices x time and that vertices could be voxels. But I'm not sure if the float values in that array are current density, and what are the XYZ coordinates for each of the 8000+ vertices if they really are voxels. If they are not voxels, then what are they? What units are the values found in stc.data?

We're working on processing EEG data using sLORETA method. We would like to move to MNE Python since using LORETA-KEY and EEGLAB is a pretty slow and manual process. What we?re interested in is getting the xyz coordinates and current density data as well as lobe location, just like the sLORETA Viewer shows, in an automated way. Is there any way we can do this in MNE?

Thanks,
Corey



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Message: 4
Date: Tue, 31 Jul 2018 20:37:09 -0400
From: Eric Larson <larson.eric.d at gmail.com>
Subject: Re: [Mne_analysis] mne.SourceEstimate.data array
To: Discussion and support forum for the users of MNE Software
        <mne_analysis at nmr.mgh.harvard.edu>
Message-ID:
        <CAGu2niWYxBjVj638On+n4K43LXNpehYQi+JMyM52LwBztXrzGQ at mail.gmail.com>
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>
> if the float values in that array are current density


They are currents (nAm) for method='MNE' and noise-normalized versions of
these for other methods.


> what are the XYZ coordinates for each of the 8000+ vertices


The `stc.vertices[0]` are the left-hemisphere vertex numbers of the
high-resolution Freesurfer surfaces for the subject.


> What we?re interested in is getting the xyz coordinates and current
> density data as well as lobe location, just like the sLORETA Viewer shows,
> in an automated way. Is there any way we can do this in MNE?
>

I have not used the sLORETA viewer so I can't comment on that, but yes it
should be possible to get these values. You can load the surfaces with
`rr_lh = mne.read_surface('subjects_dir/subject/surf/lh.white')[0]`, then
your locations are `rr_lh[stc.vertices[0]]`. For the right hemisphere, load
`rh.white` and use `rr_rh[stc.vertices[1]]`.

I see that you have opened an MNE-Python issue about this, too. Perhaps we
should discuss there how to add a tutorial for the Freesurfer surfaces /
source-space information to make it clear how to get these values.

Eric
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