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<body lang="FR" link="#0563C1" vlink="#954F72"><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>
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<p class="MsoPlainText"><span lang="EN-US">Dear MNE users,<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">We are trying to perform source localization at the single trial. For a reason we don't understand, the results we obtain when applying the inverse operator on each trial and then computing the average across trials
do not really make sense when compared to applying the inverse operator to the averaged epochs. In other words, applying the inverse operator on the evoked object doesn't seem to be equivalent to averaging across trials the sources from each trial. We expected
the two to be equivalent since the inverse operation is linear, but perhaps due to regularization, or another reason, the two shouldn't be the same.<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">If any of you had an example script for source localization at the single trial level it would help us to understand what we are doing wrong.<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">We have also looked at this example on mne website: "Compute MNE-dSPM inverse solution on single epochs", but didn't find the solution there.<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">Many thanks in advance<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">Best<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">Sébastien & Yair<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">Some details:<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">mne version: 0.16.dev0<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">OS: Ubuntu 16.04<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">Code:<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> '''<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> apply inverse operator and compare conditions<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> '''<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> import sys<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> import os<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> from os.path import join<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> import mne<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> from mne import morph_data<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> from mne.source_space import (setup_source_space, morph_source_spaces,<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">add_source_space_distances)<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> from mne.minimum_norm import (make_inverse_operator, read_inverse_operator, apply_inverse_epochs)<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> from sentcomp_epoching import get_condition<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> import numpy as np<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> import numpy.matlib<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> data_path = '/neurospin/meg/meg_tmp/sentcomp_Marti_2016/Seb/data'<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> subjects_dir = join(data_path, 'anatomy', 'subjects')<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> meg_dir = join(data_path, 'sss')<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> os.environ['SUBJECTS_DIR'] = subjects_dir<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> os.environ['MEG_DIR'] = meg_dir<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> speed_oi = 4<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> if speed_oi==1:<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> real_speed = .083<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> elif speed_oi==2:<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> real_speed = .116<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> elif speed_oi==3:<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> real_speed = .166<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> elif speed_oi==4:<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> real_speed = .301<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> # read epochs<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> epochs = mne.read_epochs(join(data_path, 'epochs', subject + '_speed'<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">+ str(speed) + '_V2-epo.fif'))<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> epochs.apply_baseline(baseline=(-0.76,-0.3), verbose=None)<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> # read inverse operator<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> inv_meg = read_inverse_operator(join(data_path, 'sources', subject +<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">'-meg-oct-6-meg-inv.fif'))<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> # get conditions<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> knames2, ep2 = get_condition(conditions=c2,epochs=epochs,startTime=-.2,<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">duration=1.5,real_speed=real_speed)<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> if timelock_to_word==True:<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> ev2 = ep2.average()<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> else:<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> ev2 = epochs[knames2].average()<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> ep2 = epochs[knames2]<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> snr = 3.0<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> lambda2 = 1./snr**2<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> # apply inverse operator<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> stc_meg2 = apply_inverse_epochs(ep2, inv_meg, lambda2=lambda2, method='MNE', pick_ori=None, nave=1)<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> av_stc_meg2 = np.mean(stc_meg2) # average of inverse<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> ev_stc_meg2 = apply_inverse(ev2, inv_meg, lambda2=lambda2, method='MNE', pick_ori=None) # inverse of average<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> av_stc_meg2.plot(subject='am150105', surface='inflated', hemi='lh', smoothing_steps=12, time_viewer=True, subjects_dir=subjects_dir, figure=None, views='lat', backend='mayavi', time_unit='ms', spacing='oct6')<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"> ev_stc_meg2.plot(subject='am150105', surface='inflated', hemi='lh', smoothing_steps=12, time_viewer=True, subjects_dir=subjects_dir, figure=None, views='lat', backend='mayavi', time_unit='ms', spacing='oct6')<o:p></o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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