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Hey guys,
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<div class="">I have six within-subject conditions, where subjects saw a different visual stimulus for each condition. I am running ft_sourceanalysis with a lcmv beamformer on the conditions separately, using the filters computed over all conditions. When I
plot the grand average absolute dipole moments that I compute from ft_sourceanalysis .mom output, I get sensible looking ERFs that ‘ramp up’ at stimulus presentation for each condition. </div>
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<div class="">However, I noticed that when I call ft_sourceanalysis on 5 conditions combined (using the same filters), and compare the resulting ERF to the ERFs for the individual conditions, it has a significantly reduced baseline. I have attached an image
of this plot. You can see the outlier ERF at the bottom of the plot. Could someone explain why it is not simply a rough average of the ERFs belonging to the conditions that it itself is computed from?</div>
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<div class="">The only reason I can think of is that there is a greater number of trials going into the source analysis with 5 conditions (roughly 5 times the number), and perhaps that reduces the noise within the source analysis, bringing the dipole moments'
baselines closer to 0? If this is correct, how can you meaningfully compare source level ERFs if conditions have a different number of trials? I’m unsure of this, though, as I’m taking the average over all trials prior to calling ft_sourceanalysis(). I attach
my code below for your reference.</div>
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<div class="">Thanks,</div>
<div class="">Benjy</div>
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conditions = 0:6;</div>
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<span class="" style="color: rgb(14, 0, 255);">for </span>subj = 1:length(subjects)</div>
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subject = subjects{subj};</div>
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<span class="" style="color: rgb(0, 0, 0);"> </span></div>
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%Create Forward Model</div>
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disp(subject)</div>
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cfg = [];</div>
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<span class="" style="color: rgb(0, 0, 0);"> cfg.rawDir = </span>'D:\Raw'<span class="" style="color: rgb(0, 0, 0);">;</span></div>
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cfg.trim = false;</div>
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[headmodel,sourcemodel,grad,~,~,M] = ForwardModel(cfg,subject);</div>
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<span class="" style="color: rgb(0, 0, 0);"> load(fullfile(</span>'D:\trials.mat'<span class="" style="color: rgb(0, 0, 0);">));</span></div>
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cfg = [];</div>
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cfg.channel = <span class="" style="color: rgb(170, 4, 249);">'meg'</span>;</div>
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<span class="" style="color: rgb(0, 0, 0);"> cfg.latency = [0.1 0.45]; </span>%select latency used to compute filters in contrasts</div>
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meg_data = ft_selectdata(cfg,trials);</div>
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meg_data.grad = grad;</div>
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<span class="" style="color: rgb(0, 0, 0);"> </span>% Compute Covariance Matrix</div>
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cfg = [];</div>
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cfg.covariance = <span class="" style="color: rgb(170, 4, 249);">'yes'</span>;</div>
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cfg.channel = <span class="" style="color: rgb(170, 4, 249);">'MEG'</span>;</div>
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cfg.covariancewindow = <span class="" style="color: rgb(170, 4, 249);">'all'</span>;</div>
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avg = ft_timelockanalysis(cfg,meg_data);</div>
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<span class="" style="color: rgb(0, 0, 0);"> </span>% Warp the MNI co-orindates of a significant cluster to the subject specific grid.pos.</div>
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gridpos= ft_warp_apply(M,stat.pos(stat.mask,:));</div>
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<span class="" style="color: rgb(0, 0, 0);"> </span>%figure; ft_plot_headmodel(headmodel,'facealpha',0.01); hold on; ft_plot_mesh(gridpos,'vertexcolor','r','vertexsize',30);</div>
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<span class="" style="color: rgb(0, 0, 0);"> </span>%Calculate spatial filter for each voxel over all data</div>
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cfg = [];</div>
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cfg.method = <span class="" style="color: rgb(170, 4, 249);">'lcmv'</span>;</div>
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cfg.sourcemodel = sourcemodel;</div>
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cfg.sourcemodel.pos = gridpos;</div>
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cfg.sourcemodel.inside = true(size(gridpos,1),1);</div>
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cfg.headmodel = headmodel;</div>
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cfg.unit = sourcemodel.unit;</div>
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cfg.lcmv.fixedori = <span class="" style="color: rgb(170, 4, 249);">'yes'</span>;</div>
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cfg.lcmv.keepfilter = <span class="" style="color: rgb(170, 4, 249);">'yes'</span>;</div>
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cfg.lcmv.lambda = <span class="" style="color: rgb(170, 4, 249);">'1%'</span>;</div>
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cfg.channel = {<span class="" style="color: rgb(170, 4, 249);">'MEG'</span>};</div>
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cfg.senstype = <span class="" style="color: rgb(170, 4, 249);">'MEG'</span>;</div>
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source_idx = ft_sourceanalysis(cfg, avg);</div>
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<font face="Courier" class=""><span class="" style="font-size: 11px;"> </span>
</font><font color="#028009" face="Courier" class=""><span class="" style="font-size: 11px;">%Perform source analysis on each condition separately, and also on the combined conditions 1-5.</span></font></div>
</div>
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<span class="" style="color: rgb(14, 0, 255);">for </span>cond = 1:length(conditions)</div>
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Condition = conditions(cond);</div>
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<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
<span class="" style="color: rgb(14, 0, 255);">if </span>condition < 6 </div>
<div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="Courier" class=""><span class="" style="font-size: 11px;"> </span></font><font color="#028009" face="Courier" class=""><span class="" style="font-size: 11px;">%Here
we take the precomputed filters and run source analysis on each of the six conditions separately </span></font></div>
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cfg = [];</div>
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cfg.channel = <span class="" style="color: rgb(170, 4, 249);">'meg'</span>;</div>
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cfg.trials = meg_data.trialinfo(:,5) == cond & meg_data.trialinfo(:,4) == 1;</div>
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datacond = ft_selectdata(cfg,trials);</div>
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<span class="" style="color: rgb(14, 0, 255);">elseif </span>condition == 6</div>
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<span class="" style="caret-color: rgb(2, 128, 9); color: rgb(2, 128, 9);">%Here we take 5 conditions all together, so roughly 5x number of trials </span></div>
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cfg = [];</div>
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cfg.channel = <span class="" style="color: rgb(170, 4, 249);">'meg'</span>;</div>
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cfg.trials = meg_data.trialinfo(:,5) > 0 & meg_data.trialinfo(:,4) == 1;</div>
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datacond = ft_selectdata(cfg,trials);</div>
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<span class="" style="color: rgb(14, 0, 255);">end</span></div>
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cfg = [];</div>
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avgcond = ft_timelockanalysis(cfg,datacond);</div>
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<span class="" style="color: rgb(0, 0, 0);"> </span>%Now apply these filters to the data</div>
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cfg = [];</div>
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cfg.method = <span class="" style="color: rgb(170, 4, 249);">'lcmv'</span>;</div>
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cfg.sourcemodel = sourcemodel;</div>
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cfg.sourcemodel.pos = gridpos;</div>
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cfg.sourcemodel.inside = true(size(gridpos,1),1);</div>
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cfg.sourcemodel.filter = source_idx.avg.filter;</div>
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cfg.headmodel = headmodel;</div>
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cfg.senstype = <span class="" style="color: rgb(170, 4, 249);">'meg'</span>;</div>
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VCs{subj,cond} = ft_sourceanalysis(cfg, avgcond);</div>
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<span class="" style="color: rgb(14, 0, 255);">end</span></div>
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<span class="" style="color: rgb(14, 0, 255);">end</span></div>
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<span class="" style="color: rgb(0, 0, 0);"> </span></div>
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<span class="" style="caret-color: rgb(2, 128, 9); color: rgb(2, 128, 9);">%Plot source level ERFs</span></div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
zero_mom = {VCs{:,1}};</div>
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one_mom = {VCs{:,2}};</div>
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two_mom = {VCs{:,3}};</div>
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three_mom = {VCs{:,4}};</div>
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four_mom = {VCs{:,5}};</div>
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five_mom = {VCs{:,6}};</div>
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notzero_mom = {VCs{:,end}};</div>
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grpzero = [];</div>
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grpnotzero = [];</div>
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grpone = [];</div>
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grptwo = [];</div>
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grpthree = [];</div>
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grpfour = [];</div>
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grpfive = [];</div>
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<span class="" style="color: rgb(14, 0, 255);">for </span>subj = 1:length(zero_mom)</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
<span class="" style="caret-color: rgb(2, 128, 9); color: rgb(2, 128, 9);">%subject level ERFs by calculating mean absolute dipole moments across voxels</span></div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
zero_momsubj = mean(abs(vertcat(zero_mom{subj}.avg.mom{:})));</div>
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one_momsubj = mean(abs(vertcat(one_mom{subj}.avg.mom{:})));</div>
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two_momsubj = mean(abs(vertcat(two_mom{subj}.avg.mom{:})));</div>
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three_momsubj = mean(abs(vertcat(three_mom{subj}.avg.mom{:})));</div>
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four_momsubj = mean(abs(vertcat(four_mom{subj}.avg.mom{:})));</div>
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five_momsubj = mean(abs(vertcat(five_mom{subj}.avg.mom{:})));</div>
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notzero_momsubj = mean(abs(vertcat(notzero_mom{subj}.avg.mom{:})));</div>
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<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
grpzero = [grpzero; zero_momsubj];</div>
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grpone = [grpone; one_momsubj];</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
grptwo = [grptwo; two_momsubj];</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
grpthree = [grpthree; three_momsubj];</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
grpfour = [grpfour; four_momsubj];</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
grpfive = [grpfive; five_momsubj];</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
grpnotzero = [grpnotzero; notzero_momsubj];</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(14, 0, 255);">
end</div>
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<span class="" style="caret-color: rgb(2, 128, 9); color: rgb(2, 128, 9);">%grand average ERFs</span></div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
meanzero = mean(grpzero,1);</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
meanone = mean(grpone,1);</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
meantwo = mean(grptwo,1);</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
meanthree = mean(grpthree,1);</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
meanfour = mean(grpfour,1);</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
meanfive = mean(grpfive,1);</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
meannotzero = mean(grpnotzero,1);</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;">
<br class="">
</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
figure; plot(zero_mom{1}.time,meanzero,<span class="" style="color: rgb(170, 4, 249);">'r'</span>); hold <span class="" style="color: rgb(170, 4, 249);">on</span>;</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
plot(zero_mom{1}.time,meanone); hold <span class="" style="color: rgb(170, 4, 249);">on</span>;</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
plot(zero_mom{1}.time,meantwo); hold <span class="" style="color: rgb(170, 4, 249);">on</span>;</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
plot(zero_mom{1}.time,meanthree); hold <span class="" style="color: rgb(170, 4, 249);">on</span>;</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
plot(zero_mom{1}.time,meanfour); hold <span class="" style="color: rgb(170, 4, 249);">on</span>;</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
plot(zero_mom{1}.time,meanfive); hold <span class="" style="color: rgb(170, 4, 249);">on</span>;</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;">
plot(zero_mom{1}.time,meannotzero)</div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;">
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legend;</div>
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<img apple-inline="yes" id="A91F7F2C-E96A-4CD8-98BF-586B9E109289" class="" src="cid:A71611F8-1548-406B-8BF7-0B4D85398C53@cust.communityfibre.co.uk"></div>
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