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Hi Clemens,
Please here is the scripts:
import mne
import numpy as np
import os
import matplotlib
from mne.datasets import sample
from mne.time_frequency import csd_epochs, csd_array
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
raw = mne.io.read_raw_fif(raw_fname, preload=True, verbose=None )
eeg_channels=raw.pick_types(meg=False, eeg=True, stim=False, eog=False,
ecg=False, emg=False, ref_meg='auto', misc=False, resp=False, chpi=False,
exci=False, ias=False, syst=False, seeg=False, dipole=False, gof=False,
bio=False, ecog=False, fnirs=False, include=(), exclude='bads',
selection=None)
raw=raw.filter(l_freq=0.5, h_freq=35.0, picks=None, filter_length=10,
l_trans_bandwidth='auto', h_trans_bandwidth='auto', n_jobs=1, method='fir',
iir_params=None, phase='zero', fir_window='hamming', fir_design=None,
pad='edge', verbose=None)
mne.compute_proj_raw(raw, start=0, stop=None, duration=1, n_grad=0,
n_mag=0, n_eeg=5, reject=None, flat=None, n_jobs=1, verbose='INFO')
events = mne.find_events(eeg_channels, stim_channel='STI 014')
event_id = dict(aud_l=1, aud_r=2, vis_l=3, vis_r=4, smiley=5, button=32)
epochs = mne.Epochs(eeg_channels, events=events, event_id=event_id,
tmin=-0.2, tmax=0.5, proj=True, baseline=(None, 0), preload=True)
mne.time_frequency.csd_epochs(epochs, mode='multitaper', fmin=0.0,
fmax=35.0, fsum=False, tmin=-0.2, tmax=0.5, n_fft=None, mt_bandwidth=None,
mt_adaptive=False, mt_low_bias=True, projs=None, verbose=None)
X=epochs['aud_l', 'aud_r', 'vis_l', 'vis_r', 'smiley', 'button'].get_data()
mne.time_frequency.csd_array(X, sfreq=600.614990234375,
mode='multitaper', fmin=0.0, fmax=35.0, fsum=False, n_fft=None,
mt_bandwidth=None, mt_adaptive=False, mt_low_bias=True, verbose=None)
I am just starting work with MNE Python and practicing with online
available MNE data-set.
Please refer attached.
* Thanks With Warm Regards, MD. KHORSHED ALAM (Shishir) Graduate Research
Assistant (GRA) Center of Intelligent Signal and Imaging Research (CISIR)
Department of Electrical and Electronic Engineering Universiti Teknologi
PETRONAS Bandar Seri Iskandar 32610 Tronoh Perak Darul Ridzuan Malaysia
Mobile no: +60176459080 <+60%2017-645%209080> Email
ID: khorshed.alam at live.iium.edu.my <khorshed.alam at live.iium.edu.my>
Alternative :shishir_lmu at yahoo.com
<shishir_lmu at yahoo.com>, alam.0213 at gmail.com <alam.0213 at gmail.com>*
------------------------------
*From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (
clemens.brunner at uni-graz.at) <clemens.brunner at uni-graz.at>
*Sent:* Monday, January 15, 2018 11:06:52 AM
*To:* Discussion and support forum for the users of MNE Software
*Subject:* Re: [Mne_analysis] Need Help to do Cross Spectral Density
Analysis
Hi!
Could you share the raw data file with me so that I can reproduce the
issue? I'd also need your script, at least the part in which you load the
data, i.e. eeg_channels, events, event_id.
Clemens
>
> Hi,
>
> Epochs Object:
> epochs = mne.Epochs(eeg_channels, events=events, event_id=event_id,
tmin=-0.2, tmax=0.5, proj=True, baseline=(None, 0), preload=True)
>
> The following epochs is used for the following function and work
perfectly I think.
>
> import mne
> from mne.time_frequency import csd_epochs
> mne.time_frequency.csd_epochs(epochs, mode='multitaper', fmin=fmin,
fmax=fmax, fsum=False, tmin=tmin, tmax=tmax, n_fft=n_fft,
mt_bandwidth=None, mt_adaptive=False, mt_low_bias=True, projs=None,
verbose=None)
>
> Problem arises once I applied 'X'=3D array of epochs data to:
>
> mne.time_frequency.csd_array(X, sfreq, mode='multitaper', fmin=fmin,
fmax=fmax, fsum=True, n_fft=None, mt_bandwidth=None, mt_adaptive=False,
mt_low_bias=True, verbose=None)
>
> I am using windows system and I run your given code.
> Output: ['C:\\Anaconda2\\envs\\mymayavi\\lib\\site-packages\\mne']
>
> Unfortunately, I don't understand about your later instruction (e.g.
Replace $MNE, download test data and copy into the given path)
>
> Thanks With Warm Regards,
> MD. KHORSHED ALAM (Shishir)
> Graduate Research Assistant (GRA)
> Center of Intelligent Signal and Imaging Research (CISIR)
> Department of Electrical and Electronic Engineering
> Universiti Teknologi PETRONAS
> Bandar Seri Iskandar
> 32610 Tronoh
> Perak Darul Ridzuan
> Malaysia
> Mobile no: +60176459080 <+60%2017-645%209080>
> Email ID: khorshed.alam at live.iium.edu.my
> Alternative :shishir_lmu at yahoo.com, alam.0213 at gmail.com
>
> From: mne_analysis-bounces at nmr.mgh.harvard.edu <
mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (
clemens.brunner at uni-graz.at) <clemens.brunner at uni-graz.at>
> Sent: Monday, January 15, 2018 9:13:14 AM
> To: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] Need Help to do Cross Spectral Density
Analysis
>
> Hi!
>
> Could you please send me your Epochs object? I want to test if it works
on my machine.
>
> In addition, can you please run the tests in $MNE/time_frequency/tests?
You can find out where MNE is installed with:
>
> import mne
> mne.__path__
>
> Then replace $MNE in the path above with the actual path.
>
> Note that you also need to download the test data separately (
https://github.com/mne-tools/mne-python/tree/master/mne/io/tests/data)
and copy everything into $MNE/io/tests/data.
>
> Does someone else have an idea/suggestion what's going on?
>
> Clemens
>
>
>
> >
> > Hi,
> >
> > Yes, I am using Anaconda 2 python distribution and I followed all the
instruction on the given link.
> >
> > Thanks With Warm Regards,
> > MD. KHORSHED ALAM (Shishir)
> > Graduate Research Assistant (GRA)
> > Center of Intelligent Signal and Imaging Research (CISIR)
> > Department of Electrical and Electronic Engineering
> > Universiti Teknologi PETRONAS
> > Bandar Seri Iskandar
> > 32610 Tronoh
> > Perak Darul Ridzuan
> > Malaysia
> > Mobile no: +60176459080 <+60%2017-645%209080>
> > Email ID: khorshed.alam at live.iium.edu.my
> > Alternative :shishir_lmu at yahoo.com, alam.0213 at gmail.com
> >
> > From: mne_analysis-bounces at nmr.mgh.harvard.edu <
mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (
clemens.brunner at uni-graz.at) <clemens.brunner at uni-graz.at>
> > Sent: Monday, January 15, 2018 8:34:51 AM
> > To: Discussion and support forum for the users of MNE Software
> > Subject: Re: [Mne_analysis] Need Help to do Cross Spectral Density
Analysis
> >
> > Hi!
> >
> > Are you using the recommended Anaconda Python distribution? There
might be something wrong with you Python setup. Did you follow the
installation instructions summarized on https://martinos.org/mne/
stable/install_mne_python.html?
> >
> > Clemens
> >
> >
> > >
> > > Hi,
> > >
> > > Thank you and unfortunately, still getting the same errors after
executing the recommended codes.
> > >
> > > I am using WIN 64-bits, Python 2.7.14.
> > >
> > > I have checked the following code:
> > > import sys
> > > sys.maxint
> > >
> > > Output: 2147483647 <(214)%20748-3647> (32-bits integer value )
> > >
> > >
> > > I think, because of this may get the errors. Please anyone helps me
to update my 'sys' to 64-bits integer value?
> > >
> > >
> > > Thanks With Warm Regards,
> > > MD. KHORSHED ALAM (Shishir)
> > > Graduate Research Assistant (GRA)
> > > Center of Intelligent Signal and Imaging Research (CISIR)
> > > Department of Electrical and Electronic Engineering
> > > Universiti Teknologi PETRONAS
> > > Bandar Seri Iskandar
> > > 32610 Tronoh
> > > Perak Darul Ridzuan
> > > Malaysia
> > > Mobile no: +60176459080 <+60%2017-645%209080>
> > > Email ID: khorshed.alam at live.iium.edu.my
> > > Alternative :shishir_lmu at yahoo.com, alam.0213 at gmail.com
> > >
> > > From: mne_analysis-bounces at nmr.mgh.harvard.edu <
mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (
clemens.brunner at uni-graz.at) <clemens.brunner at uni-graz.at>
> > > Sent: Sunday, January 14, 2018 4:46:36 PM
> > > To: Discussion and support forum for the users of MNE Software
> > > Subject: Re: [Mne_analysis] Need Help to do Cross Spectral Density
Analysis
> > >
> > > Hi!
> > >
> > > I don?t really understand why the array is of type int64 (and why
that matters - are you on Python 2)?
> > >
> > > Can you try if this minimal example works for you:
> > >
> > > import mne
> > > import numpy as np
> > >
> > > X = np.random.rand(320, 60, 421)
> > > csd = mne.time_frequency.csd_array(X, 128)
> > >
> > > Clemens
> > >
> > >
> > > >
> > > > Hi,
> > > > Thank you for your suggestion.
> > > > However,
> > > > Code: epochs = mne.Epochs(eeg_channels, events=events,
event_id=event_id, tmin=-0.2, tmax=0.5, proj=True, baseline=(None, 0),
preload=True)
> > > > X=epochs['aud_l', 'aud_r', 'vis_l', 'vis_r', 'smiley',
'button'].get_data()
> > > > print(X.shape)
> > > > Output:
> > > > 320 matching events found
> > > > 3 projection items activated
> > > > Loading data for 320 events and 421 original time points ...
> > > > 0 bad epochs dropped
> > > > (320L, 60L, 421L)
> > > >
> > > >
> > > > Then i have applied 3D array 'X' to: mne.time_frequency.csd_array(X,
sfreq, mode='multitaper', fmin=0, fmax=35.0, fsum=False, n_fft=None,
mt_bandwidth=None, mt_adaptive=False, mt_low_bias=True, verbose=None)
> > > >
> > > > But still getting the following errors:
> > > >
> > > > ValueError
> > > > Traceback (most recent call last)
> > > >
> > > > <ipython-input-177-d7b62b6f3fe7> in <module>()
> > > > ----> 1 mne.time_frequency.csd_array(X, sfreq, mode='multitaper',
fmin=0, fmax=35.0, fsum=False, n_fft=None, mt_bandwidth=None,
mt_adaptive=False, mt_low_bias=True, verbose=None)
> > > >
> > > > ValueError: when using select="i", select_range must contain
integers, got dtype int64
> > > >
> > > >
> > > > Thanks With Warm Regards,
> > > > MD. KHORSHED ALAM (Shishir)
> > > > Graduate Research Assistant (GRA)
> > > > Center of Intelligent Signal and Imaging Research (CISIR)
> > > > Department of Electrical and Electronic Engineering
> > > > Universiti Teknologi PETRONAS
> > > > Bandar Seri Iskandar
> > > > 32610 Tronoh
> > > > Perak Darul Ridzuan
> > > > Malaysia
> > > > Mobile no: +60176459080 <+60%2017-645%209080>
> > > > Email ID: khorshed.alam at live.iium.edu.my
> > > > Alternative :shishir_lmu at yahoo.com, alam.0213 at gmail.com
> > > >
> > > > From: mne_analysis-bounces at nmr.mgh.harvard.edu <
mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (
clemens.brunner at uni-graz.at) <clemens.brunner at uni-graz.at>
> > > > Sent: Tuesday, January 9, 2018 8:40:03 AM
> > > > To: Discussion and support forum for the users of MNE Software
> > > > Subject: Re: [Mne_analysis] Need Help to do Cross Spectral Density
Analysis
> > > >
> > > > Hi!
> > > >
> > > > You can use the get_data method on your Epochs object, e.g.
> > > >
> > > > X = epochs.get_data()
> > > >
> > > > will return a 3D array of the desired shape.
> > > >
> > > > HTH
> > > > Clemens
> > > >
> > > >
> > > > >
> > > > > Hi,
> > > > >
> > > > > I want to do CSD analysis on EEG data but facing problem with
the following function:
> > > > >
> > > > > csd_array(X, sfreq, mode='multitaper' fmin=0 fmax=np.inf,
fsum=True, n_fft=None, mt_bandwidth=None, mt_adaptive=False,
mt_low_bias=True, verbose=None):
> > > > >
> > > > > I am unable to extract the "X" parameter values. Can you let me
know the file where "X" (data matrix) structure is defined in order to have
a better idea about "X" parameter.
> > > > >
> > > > > Thank you.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Thanks With Warm Regards,
> > > > > MD. KHORSHED ALAM (Shishir)
> > > > > Graduate Research Assistant (GRA)
> > > > > Center of Intelligent Signal and Imaging Research (CISIR)
> > > > > Department of Electrical and Electronic Engineering
> > > > > Universiti Teknologi PETRONAS
> > > > > Bandar Seri Iskandar
> > > > > 32610 Tronoh
> > > > > Perak Darul Ridzuan
> > > > > Malaysia
> > > > > Mobile no: +60176459080 <+60%2017-645%209080>
> > > > > Email ID: khorshed.alam at live.iium.edu.my
> > > > > Alternative :shishir_lmu at yahoo.com, alam.0213 at gmail.com
> > > > >
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