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Hi Paolo,
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<div class="">My version of the fieldtrip code mentions a ‘FIXME the following needs to be reimplemented’ in line 29 of ft_sourcestatistics, which is just before the cfg options are described that you intend to use. My conclusion is therefore that the current
fieldtrip code does not support this functionality. I see in your message that you use fieldtrip(-lite) as a plugin from EEGLAB. I don’t know the state of the code that is shipped with EEGLAB so I don’t know what the help of ft_sourcestatistics in that folder
is promising the user w.r.t. certain functionality.</div>
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<div class="">If you want to do a ‘roi’ (or parcel) based postprocessing of your data (including statistics), I recommend you to look into the functions ft_sourceparcellate and/or ft_virtualchannel for this.</div>
<div class="">Note that - once the data are parcellated - one should use ft_timelockstatistics/ft_freqstatistics even if the data has been source reconstructed.</div>
<div class="">Note also that the positions at which the sources are defined should coincide meaningfully with the positions that are defined in the atlas, e.g. it does not make sense to try and parcellate data that is defined on a corticex-constrained mesh
using a volumetric (e.g. AAL) atlas.</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 10:55, Paolo PRESTI <<a href="mailto:paolo.presti@unipr.it" class="">paolo.presti@unipr.it</a>> wrote:</div>
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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 class=""> cfg.method = 'mne';</div>
<div class=""> cfg.grid = leadfield;</div>
<div class=""> cfg.headmodel = vol.vol;</div>
<div class=""> cfg.mne.lambda = 3;</div>
<div class=""> cfg.mne.scalesourcecov = 'yes';</div>
<div class=""> sourceLow = ft_sourceanalysis(cfg, dataAvgLow);</div>
sourceHigh = ft_sourceanalysis(cfg, dataAvgHigh);<br class="">
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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 class="">
brain_hlm{i} = sourceLow;<br class="">
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As concerns the statistical analysis, I have used the same script of the tutorial<a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/example/source_statistics/__;!!HJOPV4FYYWzcc1jazlU!_LkHCep6J1bmBoOHwpLMO68Ky6g7I46AYzkxnLIp-hOkDeBUNJmg2rvacBiqK0BKt3yGyBB6IyUVX-TgnBx8AQI6C3rL6zqWGBbWew$" id="LPNoLPOWALinkPreview" class="">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 class=""> cfg.method = 'montecarlo';</div>
<div class=""> cfg.latency = [0.200 0.400]; % This was the significant time interaval where I found differences at the scalp level</div>
<div class=""> cfg.avgovertime = 'yes';</div>
<div class=""> cfg.statistic = 'ft_statfun_depsamplesT';</div>
<div class=""> cfg.parameter = 'pow';</div>
<div class=""> cfg.correctm = 'cluster';</div>
<div class=""> %cfg.clusterstatistic = 'wcm';</div>
<div class=""> cfg.numrandomization = 1000;</div>
<div class=""> cfg.alpha = 0.05; % note that this only implies single-sided testing</div>
<div class=""> cfg.tail = 0;</div>
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<div class=""> nsubj=numel(brain_hlm);</div>
<div class=""> cfg.design(1,:) = [1:nsubj 1:nsubj];</div>
<div class=""> cfg.design(2,:) = [ones(1,nsubj)*1 ones(1,nsubj)*2];</div>
<div class=""> cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: subjects)</div>
<div class=""> 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 class="">
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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; background-color: rgba(0, 0, 0, 0);" class=""> aal = ft_read_atlas('D:\Matlab Analysis\Toolbox\eeglab2021.0\plugins\Fieldtrip-lite20210601\template\atlas\aal\ROI_MNI_V4.nii');</span><br class="">
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cfg.atlas = aal;
<div class=""> cfg.roi = aal.tissuelabel;</div>
cfg.avgoverroi = 'yes';<br class="">
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However, the statP200 variable returned by the <span style="background-color: rgb(255, 255, 255); display: inline !important;" class="">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;" class="">Hope I now provided more details!</span></div>
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<span style="background-color: rgb(255, 255, 255); display: inline !important;" class="">Thanks</span></div>
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<span style="background-color: rgb(255, 255, 255); display: inline !important;" class="">Paolo </span></div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">Da:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>> per conto di Schoffelen,
J.M. (Jan Mathijs) via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Inviato:</b><span class="Apple-converted-space"> </span>lunedì 13 giugno 2022 10:14<br class="">
<b class="">A:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:janmathijs.schoffelen@donders.ru.nl" class="">janmathijs.schoffelen@donders.ru.nl</a>><br class="">
<b class="">Oggetto:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] ft_sourcestatistics on restricted regions of interest</font>
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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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<blockquote type="cite" class="">
<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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<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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mailing list</span><br class="" style="font-family: Helvetica; font-size: 14px; 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; text-decoration: none;">
<a href="https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fmailman.science.ru.nl*2Fmailman*2Flistinfo*2Ffieldtrip&data=05*7C01*7Cpaolo.presti*40unipr.it*7Cc481d8194dab43075ebb08da4d15edcd*7Cbb064bc5b7a841ecbabed7beb3faeb1c*7C0*7C0*7C637907053831077986*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=Fjjahtuq*2FfAs*2FGnU*2FOAN3d*2BHhOGuV4Q*2FuD*2Bk*2F7pZ3VE*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!HJOPV4FYYWzcc1jazlU!_LkHCep6J1bmBoOHwpLMO68Ky6g7I46AYzkxnLIp-hOkDeBUNJmg2rvacBiqK0BKt3yGyBB6IyUVX-TgnBx8AQI6C3rL6zrwmWPlkw$" originalsrc="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" shash="ZUA8euCbEYWSdZshSCd1zeLroUqHQBjBY8OpX/YzcOeiJkBrlBhLVv4Kin27KERqWjDMbyYgvNdQZKB6B2vwh40eMBekmFxrhTiPKijS4Z3PMvyGc872ouGNtS7i24xQWWiqH5dfOGMHtB12yFh56aYlQXRBYkPzy0Ytx5YHD5s=" class="" style="font-family: Helvetica; font-size: 14px; 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;">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="" style="font-family: Helvetica; font-size: 14px; 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; text-decoration: none;">
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