[Mne_analysis] Need Help to do Cross Spectral Density Analysis

Mon Jan 15 08:41:41 EST 2018

Hi Khorsed,

can you run the attached script (do remember to change the code in line 15
accordingly so it matches with the path you have for the data).
I fixed a couple of the errors in your code (you were rejecting the stim
channel when picking types, but then trying to find events afterwards using
a stim channel). This has been run on a couple of different workstations
now, and should work. If it doesn't, then it's likely there is something
wrong with the installation you're using. Can you let us know which version
of mne-python you're running? It's also probably worth you updating your
scipy installation.

Sammi

On 15 January 2018 at 12:12, MD KHORSHED ALAM <
khorshed.alam at live.iium.edu.my> wrote:

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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
>
>
> > On Jan 15, 2018, at 10:59, MD KHORSHED ALAM <
> khorshed.alam at live.iium.edu.my> wrote:
> >
> > 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
> >
> >
> >
> > > On Jan 15, 2018, at 09:51, MD KHORSHED ALAM <
> khorshed.alam at live.iium.edu.my> wrote:
> > >
> > > 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
> > >
> > >
> > > > On Jan 15, 2018, at 09:18, MD KHORSHED ALAM <
> khorshed.alam at live.iium.edu.my> wrote:
> > > >
> > > > 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
> > > >
> > > >
> > > > > On Jan 14, 2018, at 11:15, MD KHORSHED ALAM <
> khorshed.alam at live.iium.edu.my> wrote:
> > > > >
> > > > > 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
> > > > >
> > > > >
> > > > > > On Jan 9, 2018, at 07:25, MD KHORSHED ALAM <
> khorshed.alam at live.iium.edu.my> wrote:
> > > > > >
> > > > > > 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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