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<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p>
I can’t recall offhand if there is an explicit way to do this. One work around would be to loop through your epochs and send them one-by-one. In prior versions, you could need to put the epoch back into a list (of length 1) in order for the function to function.
So, for example: for epoch in epochs: spectral_connectivity([epoch], …)
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<div class="">On Nov 4, 2020, at 7:12 AM, <a href="mailto:balandongiv@gmail.com" class="">
balandongiv@gmail.com</a> wrote:</div>
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<p style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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Email - Use Caution </span></p>
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<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
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<span lang="EN-US" class="">Dear Group,<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">The objective is to compute frequency connectivity measures. Say we have 70 epochs of an event with the id 1, and I would like the connectivity measures each of the epoch.<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">However, I noticed the spectral_connectivity() return an average connectivity measures value of all the 70 epochs (please correct this if I'm wrong).<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">I have checked the documentation (<a href="https://secure-web.cisco.com/1JHYhvePBuZSfOcyruZnRTehIQyF7J9JjEGEij4dTwDwIzig9G_08JjrORapltjEh-y4IYa1s33w-ptI7jOo3n3_RHj7rLrtZrC90_5dtZDqqX_PsCW08u572k0XxLnqMinNJzvLhirSTO0_BZX-rmfuvAPv5Ex4zkP2qCA2jKsZw43bLALj7X7FWthZsRLYY-vN3d2o-WucVqmoUm1i5uA/https%3A%2F%2Fmne.tools%2Fstable%2Fgenerated%2Fmne.connectivity.spectral_connectivity.html%23mne.connectivity.spectral_connectivity" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><font color="red" class=""><b class="">MailScanner
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</b></font><span class="Apple-converted-space"> </span>https://mne.tools/stable/generated/mne.connectivity.spectral_connectivity.html#mne.connectivity.spectral_connectivity</a>),
but I did not found any related setting to return connectivity measures value of each of the epoch.<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">But, the accompanying documentation (<a href="https://secure-web.cisco.com/16q_3CCS_-dCdBv55zRM9Mtz76ztHmZbDKvB1V5VuuUY7wPZ6_th_XEA_MU62svsGuFO3zSFw7HGe5-eDe2cjhIMP1eGhnQpK8ie_dOyqW18dgiF4GR46UwI8NEQv17PpeJbqo4Wo5GgBtHVbFjIkrR2jfLGllQ6m9lDyPho6CwrAx533ELYGNBy5NrckURLfnKW6b4edAwKIHGsW1AXKDg/https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-python%2Fblob%2F0e080a5a645b5934445ef4da6da744d7dfa7f68d%2Fmne%2Fconnectivity%2Fspectral.py%23L630%29" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><font color="red" class=""><b class="">MailScanner
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</b></font><span class="Apple-converted-space"> </span>https://github.com/mne-tools/mne-python/blob/0e080a5a645b5934445ef4da6da744d7dfa7f68d/mne/connectivity/spectral.py#L630)<span class="Apple-converted-space"> </span></a> not
explicitly mention `</span><span lang="EN-US" class=""><span class="Apple-converted-space"> </span></span><span lang="EN-US" class="">con` will be the average value of all epoch. This leads me to believe that the function can return the connectivity measures
value of each of the epoch. Appreciate for confirmation about this issue.<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">Code example lead to the above observation is as below:<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-US" class="">import mne<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">from mne import io<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">from mne.connectivity import spectral_connectivity<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">from mne.datasets import sample<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-US" class="">data_path = sample.data_path()<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">raw = io.read_raw_fif(raw_fname)<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">events = mne.read_events(event_fname)<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">ch_names =<span class="Apple-converted-space"> </span><a href="http://secure-web.cisco.com/1aFtFSijGjjMel_yKXswsCC_aPBeyZc8i-Tlqhd_dqrm7ntacmB3pF4R5TPayXofr_MA9Wop01CMVnyhbbOPanpZ7tMIPSEU1YJxS2xDprMNOkqPaQX0o6WikdIHSWfm43ic2DIa6UEnWOlj6Cdlb4gJF80fE4pm4kUDsowquzOGmUG3W4q4BV0RyN2mpJYT73PX9U9wolJBpIozSMftkNQ/http%3A%2F%2Fraw.info%2F" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><font color="red"><b>MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</b></font> raw.info</a>['ch_names']<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">picks = mne.pick_channels(ch_names=ch_names,include=['EEG 001','EEG 002','EEG 003'])<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">event_id, tmin, tmax = 1, -10, 0<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks)<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">fmin, fmax = (1.,5.),(4.,9.)<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">sfreq =<span class="Apple-converted-space"> </span><a href="http://secure-web.cisco.com/1aFtFSijGjjMel_yKXswsCC_aPBeyZc8i-Tlqhd_dqrm7ntacmB3pF4R5TPayXofr_MA9Wop01CMVnyhbbOPanpZ7tMIPSEU1YJxS2xDprMNOkqPaQX0o6WikdIHSWfm43ic2DIa6UEnWOlj6Cdlb4gJF80fE4pm4kUDsowquzOGmUG3W4q4BV0RyN2mpJYT73PX9U9wolJBpIozSMftkNQ/http%3A%2F%2Fraw.info%2F" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><font color="red"><b>MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</b></font> raw.info</a>['sfreq'] # the sampling frequency<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">tmin = 0 # exclude the baseline period<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">tmax=2<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">epochs.load_data()<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">con, freqs, times, n_epochs, n_tapers = spectral_connectivity(<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""> epochs, method='pli', mode='multitaper', sfreq=sfreq, fmin=fmin, fmax=fmax,<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""> faverage=True, tmin=tmin, tmax=tmax,mt_adaptive=False, n_jobs=1)<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">Regards<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">Rodney<o:p class=""></o:p></span></div>
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<a href="https://secure-web.cisco.com/1c4b4Bxko8iRoqpgzbYe3I-E1vUHSrzFsc738n_mp5LCiNlj7sqotCwkPJTSQZtSRGeNiNRsG1NX0oFomdh4FjsQN7RwippDDG3Ms8ujLgxyXPCss-ekzfxH54TZFEYRLtUpgCl1MWqKiLpkJv46Sys7TVFXMPYdrpsWRl7wlxTaSNyl3T6uSvuPUcjOMp5XqBN2w-2pTMG-_bO9UdGmw_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Fmne_analysis" style="color: rgb(5, 99, 193); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class=""><font color="red"><b>MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</b></font> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></div>
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