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<p style="margin-top:0;margin-bottom:0">Hi <span style="color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 14.6667px;">Clemens</span>,</p>
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<p style="margin-top:0;margin-bottom:0">Please here is the scripts:</p>
<p style="margin-top:0;margin-bottom:0"></p>
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<div>import mne</div>
<div>import numpy as np</div>
<div>import os</div>
<div>import matplotlib</div>
<div>from mne.datasets import sample</div>
<div>from mne.time_frequency import csd_epochs, csd_array</div>
<div>data_path = sample.data_path()</div>
<div>raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'</div>
<div>raw = mne.io.read_raw_fif(raw_fname, preload=True, verbose=None )</div>
<div>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)</div>
<div>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)</div>
<div>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')</div>
<div>events = mne.find_events(eeg_channels, stim_channel='STI 014')</div>
<div>event_id = dict(aud_l=1, aud_r=2, vis_l=3, vis_r=4, smiley=5, button=32)</div>
<div>epochs = mne.Epochs(eeg_channels, events=events, event_id=event_id, tmin=-0.2, tmax=0.5, proj=True, baseline=(None, 0), preload=True)</div>
<div>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)</div>
<div>X=epochs['aud_l', 'aud_r', 'vis_l', 'vis_r', 'smiley', 'button'].get_data()</div>
<div>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)</div>
<div><br>
</div>
I am just starting work with MNE Python and practicing with online available MNE data-set.
<p></p>
<p style="margin-top:0;margin-bottom:0">Please refer attached.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
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<p style=""><b><span style="font-size:10pt; font-family:Georgia,serif; color:black">Thanks With Warm Regards,</span></b></p>
<p style=""><b><span style="font-size:14pt; font-family:Georgia,serif; color:rgb(0,32,96)">MD. KHORSHED ALAM (Shishir)</span></b></p>
<p style=""><b><span style="font-size:14pt; font-family:Georgia,serif; color:rgb(0,32,96)"><b style="color:rgb(34,34,34); font-family:arial,sans-serif; font-size:16px"><span style="font-size:12pt"><span style="font-size:12pt"><span style="font-size:12pt"><span style="font-size:12pt"></span></span></span></span></b></span></b></p>
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<p><b><span style="font-size:14pt; font-family:Georgia,serif; color:rgb(0,32,96)">Graduate Research Assistant (GRA)</span></b></p>
</b></b></span>
<p></p>
<p style=""><font face="georgia, serif" color="#000000"><b><span style="font-size:12.8px">Center of Intelligent Signal and Imaging Research (CISIR)</span><br style="font-size:12.8px">
<span style="font-size:12.8px">Department of Electrical and Electronic Engineering</span><br style="font-size:12.8px">
<span style="font-size:12.8px">Universiti Teknologi PETRONAS</span><br style="font-size:12.8px">
<span style="font-size:12.8px">Bandar Seri Iskandar</span><br style="font-size:12.8px">
<span style="font-size:12.8px">32610 Tronoh</span><br style="font-size:12.8px">
<span style="font-size:12.8px">Perak Darul Ridzuan</span><br style="font-size:12.8px">
<span style="font-size:12.8px">Malaysia</span></b></font></p>
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<span style="font-family:'Franklin Gothic Medium',sans-serif; font-size:11pt">Email ID: </span><a href="mailto:khorshed.alam@live.iium.edu.my" title="mailto:khorshed.alam@live.iium.edu.my Ctrl+Click or tap to follow the link" target="_blank" style="color:rgb(17,85,204)" id="LPNoLP"><span style="font-family:'Franklin Gothic Medium',sans-serif; font-size:11pt">khorshed.alam@live.iium.edu.my</span></a><br style="font-family:'Franklin Gothic Medium',sans-serif; font-size:11pt">
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<span style="font-family:'Franklin Gothic Medium',sans-serif; font-size:11pt"></span><span style="color:rgb(34,34,34); font-family:'Franklin Gothic Medium',sans-serif; font-size:11pt">Alternative :<a href="mailto:shishir_lmu@yahoo.com" target="_blank" id="LPNoLP">shishir_lmu@yahoo.com</a>, <a href="mailto:alam.0213@gmail.com" target="_blank" id="LPNoLP">alam.0213@gmail.com</a></span></b>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (clemens.brunner@uni-graz.at)
<clemens.brunner@uni-graz.at><br>
<b>Sent:</b> Monday, January 15, 2018 11:06:52 AM<br>
<b>To:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] Need Help to do Cross Spectral Density Analysis</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hi!<br>
<br>
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.<br>
<br>
Clemens<br>
<br>
<br>
> On Jan 15, 2018, at 10:59, MD KHORSHED ALAM <khorshed.alam@live.iium.edu.my> wrote:<br>
> <br>
> Hi,<br>
> <br>
> Epochs Object: <br>
> epochs = mne.Epochs(eeg_channels, events=events, event_id=event_id, tmin=-0.2, tmax=0.5, proj=True, baseline=(None, 0), preload=True)<br>
> <br>
> The following epochs is used for the following function and work perfectly I think.<br>
> <br>
> import mne<br>
> from mne.time_frequency import csd_epochs<br>
> 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)<br>
> <br>
> Problem arises once I applied 'X'=3D array of epochs data to: <br>
> <br>
> 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)<br>
> <br>
> I am using windows system and I run your given code.<br>
> Output: ['C:\\Anaconda2\\envs\\mymayavi\\lib\\site-packages\\mne']<br>
> <br>
> Unfortunately, I don't understand about your later instruction (e.g. Replace $MNE, download test data and copy into the given path)<br>
> <br>
> Thanks With Warm Regards,<br>
> MD. KHORSHED ALAM (Shishir)<br>
> Graduate Research Assistant (GRA)<br>
> Center of Intelligent Signal and Imaging Research (CISIR)<br>
> Department of Electrical and Electronic Engineering<br>
> Universiti Teknologi PETRONAS<br>
> Bandar Seri Iskandar<br>
> 32610 Tronoh<br>
> Perak Darul Ridzuan<br>
> Malaysia<br>
> Mobile no: +60176459080<br>
> Email ID: khorshed.alam@live.iium.edu.my<br>
> Alternative :shishir_lmu@yahoo.com, alam.0213@gmail.com<br>
> <br>
> From: mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (clemens.brunner@uni-graz.at) <clemens.brunner@uni-graz.at><br>
> Sent: Monday, January 15, 2018 9:13:14 AM<br>
> To: Discussion and support forum for the users of MNE Software<br>
> Subject: Re: [Mne_analysis] Need Help to do Cross Spectral Density Analysis<br>
> <br>
> Hi!<br>
> <br>
> Could you please send me your Epochs object? I want to test if it works on my machine.<br>
> <br>
> In addition, can you please run the tests in $MNE/time_frequency/tests? You can find out where MNE is installed with:<br>
> <br>
> import mne<br>
> mne.__path__<br>
> <br>
> Then replace $MNE in the path above with the actual path.<br>
> <br>
> Note that you also need to download the test data separately (<a href="https://github.com/mne-tools/mne-python/tree/master/mne/io/tests/data">https://github.com/mne-tools/mne-python/tree/master/mne/io/tests/data</a>) and copy everything into $MNE/io/tests/data.<br>
> <br>
> Does someone else have an idea/suggestion what's going on?<br>
> <br>
> Clemens<br>
> <br>
> <br>
> <br>
> > On Jan 15, 2018, at 09:51, MD KHORSHED ALAM <khorshed.alam@live.iium.edu.my> wrote:<br>
> > <br>
> > Hi,<br>
> > <br>
> > Yes, I am using Anaconda 2 python distribution and I followed all the instruction on the given link.<br>
> > <br>
> > Thanks With Warm Regards,<br>
> > MD. KHORSHED ALAM (Shishir)<br>
> > Graduate Research Assistant (GRA)<br>
> > Center of Intelligent Signal and Imaging Research (CISIR)<br>
> > Department of Electrical and Electronic Engineering<br>
> > Universiti Teknologi PETRONAS<br>
> > Bandar Seri Iskandar<br>
> > 32610 Tronoh<br>
> > Perak Darul Ridzuan<br>
> > Malaysia<br>
> > Mobile no: +60176459080<br>
> > Email ID: khorshed.alam@live.iium.edu.my<br>
> > Alternative :shishir_lmu@yahoo.com, alam.0213@gmail.com<br>
> > <br>
> > From: mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (clemens.brunner@uni-graz.at) <clemens.brunner@uni-graz.at><br>
> > Sent: Monday, January 15, 2018 8:34:51 AM<br>
> > To: Discussion and support forum for the users of MNE Software<br>
> > Subject: Re: [Mne_analysis] Need Help to do Cross Spectral Density Analysis<br>
> > <br>
> > Hi!<br>
> > <br>
> > 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
<a href="https://martinos.org/mne/stable/install_mne_python.html?">https://martinos.org/mne/stable/install_mne_python.html?</a><br>
> > <br>
> > Clemens<br>
> > <br>
> > <br>
> > > On Jan 15, 2018, at 09:18, MD KHORSHED ALAM <khorshed.alam@live.iium.edu.my> wrote:<br>
> > > <br>
> > > Hi,<br>
> > > <br>
> > > Thank you and unfortunately, still getting the same errors after executing the recommended codes.<br>
> > > <br>
> > > I am using WIN 64-bits, Python 2.7.14.<br>
> > > <br>
> > > I have checked the following code: <br>
> > > import sys<br>
> > > sys.maxint<br>
> > > <br>
> > > Output: 2147483647 (32-bits integer value )<br>
> > > <br>
> > > <br>
> > > I think, because of this may get the errors. Please anyone helps me to update my 'sys' to 64-bits integer value?<br>
> > > <br>
> > > <br>
> > > Thanks With Warm Regards,<br>
> > > MD. KHORSHED ALAM (Shishir)<br>
> > > Graduate Research Assistant (GRA)<br>
> > > Center of Intelligent Signal and Imaging Research (CISIR)<br>
> > > Department of Electrical and Electronic Engineering<br>
> > > Universiti Teknologi PETRONAS<br>
> > > Bandar Seri Iskandar<br>
> > > 32610 Tronoh<br>
> > > Perak Darul Ridzuan<br>
> > > Malaysia<br>
> > > Mobile no: +60176459080<br>
> > > Email ID: khorshed.alam@live.iium.edu.my<br>
> > > Alternative :shishir_lmu@yahoo.com, alam.0213@gmail.com<br>
> > > <br>
> > > From: mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (clemens.brunner@uni-graz.at) <clemens.brunner@uni-graz.at><br>
> > > Sent: Sunday, January 14, 2018 4:46:36 PM<br>
> > > To: Discussion and support forum for the users of MNE Software<br>
> > > Subject: Re: [Mne_analysis] Need Help to do Cross Spectral Density Analysis<br>
> > > <br>
> > > Hi!<br>
> > > <br>
> > > I don’t really understand why the array is of type int64 (and why that matters - are you on Python 2)?<br>
> > > <br>
> > > Can you try if this minimal example works for you:<br>
> > > <br>
> > > import mne<br>
> > > import numpy as np<br>
> > > <br>
> > > X = np.random.rand(320, 60, 421)<br>
> > > csd = mne.time_frequency.csd_array(X, 128)<br>
> > > <br>
> > > Clemens<br>
> > > <br>
> > > <br>
> > > > On Jan 14, 2018, at 11:15, MD KHORSHED ALAM <khorshed.alam@live.iium.edu.my> wrote:<br>
> > > > <br>
> > > > Hi,<br>
> > > > Thank you for your suggestion. <br>
> > > > However, <br>
> > > > 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)<br>
> > > > X=epochs['aud_l', 'aud_r', 'vis_l', 'vis_r', 'smiley', 'button'].get_data()<br>
> > > > print(X.shape)<br>
> > > > Output: <br>
> > > > 320 matching events found<br>
> > > > 3 projection items activated<br>
> > > > Loading data for 320 events and 421 original time points ...<br>
> > > > 0 bad epochs dropped<br>
> > > > (320L, 60L, 421L)<br>
> > > > <br>
> > > > <br>
> > > > 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)<br>
> > > > <br>
> > > > But still getting the following errors: <br>
> > > > <br>
> > > > ValueError<br>
> > > > Traceback (most recent call last)<br>
> > > > <br>
> > > > <ipython-input-177-d7b62b6f3fe7> in <module>()<br>
> > > > ----> 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)<br>
> > > > <br>
> > > > ValueError: when using select="i", select_range must contain integers, got dtype int64<br>
> > > > <br>
> > > > <br>
> > > > Thanks With Warm Regards,<br>
> > > > MD. KHORSHED ALAM (Shishir)<br>
> > > > Graduate Research Assistant (GRA)<br>
> > > > Center of Intelligent Signal and Imaging Research (CISIR)<br>
> > > > Department of Electrical and Electronic Engineering<br>
> > > > Universiti Teknologi PETRONAS<br>
> > > > Bandar Seri Iskandar<br>
> > > > 32610 Tronoh<br>
> > > > Perak Darul Ridzuan<br>
> > > > Malaysia<br>
> > > > Mobile no: +60176459080<br>
> > > > Email ID: khorshed.alam@live.iium.edu.my<br>
> > > > Alternative :shishir_lmu@yahoo.com, alam.0213@gmail.com<br>
> > > > <br>
> > > > From: mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Brunner, Clemens (clemens.brunner@uni-graz.at) <clemens.brunner@uni-graz.at><br>
> > > > Sent: Tuesday, January 9, 2018 8:40:03 AM<br>
> > > > To: Discussion and support forum for the users of MNE Software<br>
> > > > Subject: Re: [Mne_analysis] Need Help to do Cross Spectral Density Analysis<br>
> > > > <br>
> > > > Hi!<br>
> > > > <br>
> > > > You can use the get_data method on your Epochs object, e.g.<br>
> > > > <br>
> > > > X = epochs.get_data()<br>
> > > > <br>
> > > > will return a 3D array of the desired shape.<br>
> > > > <br>
> > > > HTH<br>
> > > > Clemens<br>
> > > > <br>
> > > > <br>
> > > > > On Jan 9, 2018, at 07:25, MD KHORSHED ALAM <khorshed.alam@live.iium.edu.my> wrote:<br>
> > > > > <br>
> > > > > Hi,<br>
> > > > > <br>
> > > > > I want to do CSD analysis on EEG data but facing problem with the following function:
<br>
> > > > > <br>
> > > > > 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):<br>
> > > > > <br>
> > > > > 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.<br>
> > > > > <br>
> > > > > Thank you.<br>
> > > > > <br>
> > > > > <br>
> > > > > <br>
> > > > > <br>
> > > > > <br>
> > > > > Thanks With Warm Regards,<br>
> > > > > MD. KHORSHED ALAM (Shishir)<br>
> > > > > Graduate Research Assistant (GRA)<br>
> > > > > Center of Intelligent Signal and Imaging Research (CISIR)<br>
> > > > > Department of Electrical and Electronic Engineering<br>
> > > > > Universiti Teknologi PETRONAS<br>
> > > > > Bandar Seri Iskandar<br>
> > > > > 32610 Tronoh<br>
> > > > > Perak Darul Ridzuan<br>
> > > > > Malaysia<br>
> > > > > Mobile no: +60176459080<br>
> > > > > Email ID: khorshed.alam@live.iium.edu.my<br>
> > > > > Alternative :shishir_lmu@yahoo.com, alam.0213@gmail.com<br>
> > > > > <br>
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