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Hi,</div>
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yes, sure I can give some further details.</div>
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I have recorded EEG data and extracted ERPs for two different conditions. At the scalp level, I have found significant differences between conditions in two separate time intervals: one over central electrodes around 250 ms after the stimulus presentations
(P200), and the second one over occipital electrodes after 190 ms (N190). Then, I wanted to look for the source generators of these differences. </div>
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For each participant, I reconstructed the source activity using the ft_sourceanalysis function, with the mne method. </div>
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Here you can fine the line of codes:</div>
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cfg = [];
<div> cfg.method = 'mne';</div>
<div> cfg.grid = leadfield;</div>
<div> cfg.headmodel = vol.vol;</div>
<div> cfg.mne.lambda = 3;</div>
<div> cfg.mne.scalesourcecov = 'yes';</div>
<div> sourceLow = ft_sourceanalysis(cfg, dataAvgLow);</div>
sourceHigh = ft_sourceanalysis(cfg, dataAvgHigh);<br>
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Thus, I created a cell array with data of all subjects:</div>
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brain_lhh{i} = sourceHigh;<br>
brain_hlm{i} = sourceLow;<br>
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As concerns the statistical analysis, I have used the same script of the tutorial
<a href="https://www.fieldtriptoolbox.org/example/source_statistics/" id="LPNoLPOWALinkPreview">
https://www.fieldtriptoolbox.org/example/source_statistics/</a>, just adding information about the time range that I wanted to test:</div>
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cfg=[];
<div> cfg.method = 'montecarlo';</div>
<div> cfg.latency = [0.200 0.400]; % This was the significant time interaval where I found differences at the scalp level</div>
<div> cfg.avgovertime = 'yes';</div>
<div> cfg.statistic = 'ft_statfun_depsamplesT';</div>
<div> cfg.parameter = 'pow';</div>
<div> cfg.correctm = 'cluster';</div>
<div> %cfg.clusterstatistic = 'wcm';</div>
<div> cfg.numrandomization = 1000;</div>
<div> cfg.alpha = 0.05; % note that this only implies single-sided testing</div>
<div> cfg.tail = 0;</div>
<div> </div>
<div> nsubj=numel(brain_hlm);</div>
<div> cfg.design(1,:) = [1:nsubj 1:nsubj];</div>
<div> cfg.design(2,:) = [ones(1,nsubj)*1 ones(1,nsubj)*2];</div>
<div> cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: subjects)</div>
<div> cfg.ivar = 2; % row of design matrix that contains independent variable (the conditions)</div>
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statP200 = ft_sourcestatistics(cfg, brain_hlm{:}, brain_lhh{:});<br>
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This function returned the "statP200" variable where I can find information about the significant dipoles over the whole areas of the cortex.</div>
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What I want to do now is try to restrict the area of analysis to specific regions of interest. I see that the function ft_sourcestatistics gives the user the possibility to specify the ROIs, by populating the field cfg.atlas and cfg.roi. Hence, I added to the
previous lines of code the following ones: </div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgba(0, 0, 0, 0);"> aal = ft_read_atlas('D:\Matlab Analysis\Toolbox\eeglab2021.0\plugins\Fieldtrip-lite20210601\template\atlas\aal\ROI_MNI_V4.nii');</span><br>
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cfg.atlas = aal;
<div> cfg.roi = aal.tissuelabel;</div>
cfg.avgoverroi = 'yes';<br>
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However, the statP200 variable returned by the <span style="background-color:rgb(255, 255, 255);display:inline !important">ft_sourcestatistics did not contain any kind of information about differences over ROIs. Even if I try to specify some ROIs in the cfg.roi,
it does not change anything in the results</span></div>
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<span style="background-color:rgb(255, 255, 255);display:inline !important">Hope I now provided more details!</span></div>
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<span style="background-color:rgb(255, 255, 255);display:inline !important">Thanks</span></div>
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<span style="background-color:rgb(255, 255, 255);display:inline !important">Paolo </span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Da:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> per conto di Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip@science.ru.nl><br>
<b>Inviato:</b> lunedì 13 giugno 2022 10:14<br>
<b>A:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Oggetto:</b> Re: [FieldTrip] ft_sourcestatistics on restricted regions of interest</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Ciao Paolo,
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<div class="">Can you please expand a little bit? From the formulation of your question I get the impression that you already tried out a few things, but probably you ran into problems. At this point, it is a bit random guessing to the readership as to in which
direction the for you optimal answer would go.</div>
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<div class="">So, some details as to what you have tried in terms of cfg, data objects etc. would be helpful.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 13 Jun 2022, at 09:44, Paolo PRESTI via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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Hi all,</div>
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I want to perform some statistical comparisons between ROIs using the function ft_sourcestatistics. I see that one can specify the cfg.atlas and cfg.roi fields to restrict the analysis on specific ROIs. However, I am not sure that such a configuration has been
already implemented. </div>
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Does anyone know if this function actually permits performing such an analysis? Does exist an alternative way?</div>
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Thanks,</div>
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Paolo</div>
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<div class="" style="color:rgb(34,34,34); font-family:Arial,Helvetica,sans-serif; font-size:small; text-align:start; background-color:rgb(255,255,255)">
<span class="" style="font-family:monospace; font-size:9pt; background-color:rgba(0,0,0,0)">Paolo Presti, PhD Student</span></div>
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<font face="monospace" class=""><span class="" style="font-family:monospace; font-size:9pt; background-color:rgba(0,0,0,0)">Department of Medicine and Surgery, Unit of Neuroscience</span></font></div>
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<font face="monospace" class=""><span class="" style="font-family:monospace; font-size:9pt; background-color:rgba(0,0,0,0)">Via Volturno 39/E, 43125</span></font></div>
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<font face="monospace" class=""><span class="" style="font-family:monospace; font-size:9pt; background-color:rgba(0,0,0,0)">Parma</span></font></div>
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Firma il tuo 5xmille all’Università di Parma, aiutaci a essere sempre più accoglienti e inclusivi verso le nostre studentesse e i nostri studenti - Indica 00308780345 nella tua denuncia dei redditi.</div>
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