[Mne_analysis] Mne_analysis Digest, Vol 131, Issue 40

SPAGNA Alfredo alfredo.spagna at icm-institute.org
Wed Dec 26 09:39:43 EST 2018
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        External Email - Use Caution        

Hello JR,
Thanks!

you can use scipy.io.load_mat to read a mat file, and then put the
corresponding information into an mne object:

This looks pretty clear;

e.g.
import mne
from scipy.io<http://scipy.io> import load_mat
info = mne.create_info(32, sfreq=256., ch_types='eeg')  # 32 EEG channels
sampled at 256Hz
mat = load_mat('data.mat')  # matrix of32 channels x n time samples
raw = mne.RawArray(mat, info=info)
or
mat = load_mat('data.mat')
epochs = mne.EpochsArray(mat, info=info, tmin=-.500)  # first time sample @
-500ms


Here I have one questions;
Right now, I was working with math files that were carrying information about each trial and sensory (i.e., 102 mag sensors x 84 correct trials in a specific condition)
Therefore, my .mat file right now is 102 (sensors) x 84 (in that specific condition) x 1150 time points (2ms bins).

If what I have to give MNE is ONE “ mat = load_mat('data.mat')  # matrix of 32 channels x n time samples “, then I guess that I’’ll need to work on weighted average files for each task condiiton
This way, my matrix will be 102 x 84 (one per each of the four conditions).

Am I correct?

Please, let me know if any additional clarification is needed;
Best,

For the anova you can check
https://martinos.org/mne/stable/auto_tutorials/plot_background_statistics.html?highlight=anova

best regards,

JR


Alfredo Spagna, Ph. D.
alfredo.spagna at icm-institute.org<mailto:alfredo.spagna at icm-institute.org>
PICNIC Lab @ Institut du Cerveau
et de la Moelle épinière
Inserm U 1127, Paris, France

On 24 Dec 2018, at 11:00, mne_analysis-request at nmr.mgh.harvard.edu<mailto:mne_analysis-request at nmr.mgh.harvard.edu> wrote:

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Today's Topics:

  1. Repeated measures ANOVA on source data with spatio-temporal
     clustering on epochs from Mat files (SPAGNA Alfredo)
  2. Re: Repeated measures ANOVA on source data with
     spatio-temporal clustering on epochs from Mat files (JR KING)


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

Message: 1
Date: Mon, 24 Dec 2018 14:08:15 +0000
From: SPAGNA Alfredo <alfredo.spagna at icm-institute.org>
Subject: [Mne_analysis] Repeated measures ANOVA on source data with
spatio-temporal clustering on epochs from Mat files
To: "mne_analysis at nmr.mgh.harvard.edu"
<mne_analysis at nmr.mgh.harvard.edu>
Message-ID: <6FC0ED9A-FCDA-4A51-BD16-888B0C688627 at icm-institute.org>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution

Hello everyone;
I am quite new to MNE, since I have used field trip + brainstorm to conduct most of the analysis I?ld done before.

Now, I?d like to use the repeated measures ANOVA tutorial but starting from .mat files instead of the raw fit file;
This is because I already conducted all the pre-processing using field trip and brainstorm, and have already have epochs files per each condition and subject.

Has anybody already done that? Any advice?
I am slowly finding my way through the code, but I am not sure whether there is already some material out there that could shortcut the process or, even worse, some advice like ?no, that?s not possible to do it?.

Thanks, and happy holidays y?all!
Alfredo Spagna, Ph. D.
alfredo.spagna at icm-institute.org<mailto:alfredo.spagna at icm-institute.org>
PICNIC Lab @ Institut du Cerveau
et de la Moelle e?pinie?re
Inserm U 1127, Paris, France

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Message: 2
Date: Mon, 24 Dec 2018 16:06:21 +0100
From: JR KING <jeanremi.king at gmail.com>
Subject: Re: [Mne_analysis] Repeated measures ANOVA on source data
with spatio-temporal clustering on epochs from Mat files
To: Discussion and support forum for the users of MNE Software
<mne_analysis at nmr.mgh.harvard.edu>
Message-ID:
<CAOcgdcjqnE0t3ev=L2b2jVJZXMpnvU4-1BWZQ68pS9tdNQT4BQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution

Hi Alfredo,

you can use scipy.io.load_mat to read a mat file, and then put the
corresponding information into an mne object:

e.g.
import mne
from scipy.io import load_mat
info = mne.create_info(32, sfreq=256., ch_types='eeg')  # 32 EEG channels
sampled at 256Hz
mat = load_mat('data.mat')  # matrix of32 channels x n time samples
raw = mne.RawArray(mat, info=info)
or
mat = load_mat('data.mat')
epochs = mne.EpochsArray(mat, info=info, tmin=-.500)  # first time sample @
-500ms

For the anova you can check
https://martinos.org/mne/stable/auto_tutorials/plot_background_statistics.html?highlight=anova

best regards,

JR

On Mon, 24 Dec 2018 at 15:09, SPAGNA Alfredo <
alfredo.spagna at icm-institute.org> wrote:

       External Email - Use Caution

Hello everyone;
I am quite new to MNE, since I have used field trip + brainstorm to
conduct most of the analysis I?ld done before.

Now, I?d like to use the repeated measures ANOVA tutorial but starting
from .mat files instead of the raw fit file;
This is because I already conducted all the pre-processing using field
trip and brainstorm, and have already have epochs files per each condition
and subject.

Has anybody already done that? Any advice?
I am slowly finding my way through the code, but I am not sure whether
there is already some material out there that could shortcut the process
or, even worse, some advice like ?no, that?s not possible to do it?.

Thanks, and happy holidays y?all!
Alfredo Spagna, Ph. D.
alfredo.spagna at icm-institute.org
PICNIC Lab @ Institut du Cerveau
et de la Moelle e?pinie?re
Inserm U 1127, Paris, France

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