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<p class="MsoNormal">Dear FieldTrip community,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-GB">I want to compute coherence between brain sources and an EMG channel that I selected. Here is the pipeline I am using :<o:p></o:p></span></p>
<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l1 level1 lfo1"><span lang="EN-GB">Preprocess MEG and EMG data<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l1 level1 lfo1"><span lang="EN-GB">Process single subject MRI data to get (a) the head model, (b) the source model with leadfields<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l1 level1 lfo1"><span lang="EN-GB">Reconstruct MEG data using beamformer techniques in the time domain.
<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l1 level1 lfo1"><span lang="EN-GB">Compute coherence between source data and EMG data<o:p></o:p></span></li></ul>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">To be able to compute coherence, I need to reconstruct data for all trials and not as an average of trials. But I encountered a problem at this level.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Here is the code I used first :<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% Compute noise-covariance matrix
</span><span style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg = [];</span><span style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.covariance =
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">;
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">%default takes the whole time window to estimate the noise covariance matrix</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.keeptrials =
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> tlcontr_MEG = ft_timelockanalysis(cfg, MEG_contr);</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% Compute inverse modelling with mne : source data averaged over</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% trails</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg = [];</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.method =
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'mne'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.sourcemodel = leadfield;</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.headmodel = headmodel;</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.mne.lambda = 3;
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">%%????</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.mne.keepfilter =
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.rawtrial =
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'no'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> source_MEG_contr = ft_sourceanalysis(cfg,tlcontr_MEG);</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% Get source data for all trials : project trials by hand
</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> FILTER = source_MEG_contr.avg.filter(cellfun(@(a) ~isempty(a),source_MEG_contr.avg.filter));</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:blue">for</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
triali = 1 : length(MEG_contr.trial)</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> source_MEG_contr_trials.pow{triali} = cell2mat(cellfun(@(a) sum((a*MEG_contr.trial{triali}).^2,1),FILTER,</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'UniformOutput'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">,false)');</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> disp([</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'Trial n° '</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
num2str(triali) </span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">' out of '</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> num2str(length(MEG_contr.trial))])</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:blue">end</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">source_MEG_contr_trials</span><span lang="EN-GB"> is to be the structure that contains source data for all trials. As you can see I computed it by hand,
following a thread that I found on the website. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Then I found it was possible to use ft_sourceanalysis again, to project all trials through the filter computed at the first use of the function. So I replaced the last paragraph of code with the following :<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% project all trials through common spatial filter to get source data</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% for separate trials</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg=[];</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.method =
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'mne'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.sourcemodel = leadfield;
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% previously computed grid</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.headmodel = headmodel;
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% previously computed volume conduction model</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.rawtrial =
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">;
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% project each single trial through the filter to reconstruct single trial data</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.sourcemodel.filter = source_MEG_contr.avg.filter;
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% use the common filter computed in the previous step!</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> source_MEG_contr_trials = ft_sourceanalysis(cfg, tlcontr_MEG);
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#34C03C">% contains the source estimates for all trials/both conditions</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I preferred this “automatic” way rather than the manual one because it allows me to keep the FieldTrip shape of structures more easily and display results using FieldTrip functions.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">However, I realized that it returned completely different results. After trying to understand the steps performed in the second use of ft_sourceanalysis, I realized that filters used to compute trial source data from
trial channel data (l. 295 in ft_inverse_mne of fieldtrip-20210921 : <b>estimate.mom{i} = sourcemodel.filter{i}*dat</b>) were different from filters in cfg.sourcemodel.filter. <br>
In fact, channel labels are taken from the leadfield structure. Lines (channel dimension) in filter matrices (in cfg.sourcemodel.filter) are reorganized so that it matches channel order from data.label (= tlcontr_MEG.label).
<br>
See l.404-410 in ft_sourceanalysis of fieldtrip-20210921 : <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">[dum, chansel] = match_str(data.label, sourcemodel.label);</span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">sourcemodel.label = sourcemodel.label(chansel);<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:blue">for</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> i=1:numel(sourcemodel.filter)</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:blue">if</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> ~isempty(sourcemodel.filter{i})</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black"> sourcemodel.filter{i} = sourcemodel.filter{i}(:, chansel);</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:blue">end</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:blue">end</span><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-GB" style="font-size:12.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Thus, if I understand it correctly, this step assumes that lines in filter matrices (which come from source_MEG_contr structure) are organized in the same way as channels in leadfields. However, this is not actually the
case here because<o:p></o:p></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo2"><span lang="EN-GB">source_MEG_contr.avg.label and data.label (= tlcontr_MEG.label) are equal. <o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo2"><span lang="EN-GB">I don’t understand why but leadfields.label is different from the original alphanumerical channel organization – A1 A2 A3 etc…- found in raw data (as well as in
source_MEG_contr, and in tlcontr_MEG).<o:p></o:p></span></li></ol>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">So I think that in my case, lines in filter matrices should not be reorganized (when they are not, I get the same results as by hand) but as leadfield structure is also used when I compute source_MEG_contr from tlcontr_MEG,
I am not sure I can trust source_MEG_contr either. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I would truly appreciate if someone could proofread and pinpoint some problems in this reasoning to help me solve this annoying problem. In the meantime I will try to recompute the leadfield structure so that channel
order is the same everywhere. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Thank you in advance for your help and the time you will spend reading through this message!
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal">Manon Châteaux<o:p></o:p></p>
<p class="MsoNormal">phD Student at Aix-Marseille University<o:p></o:p></p>
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