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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Dear Fieldtrip community,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">I would like to bring up the topic of ROI-based source analysis. I’ve seen that many have asked about this in the last years, but I could not find an answer that
worked.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">I would like to restrict my ft_sourcestatistics to specific ROIs taken from the aal atlas. I implemented the code as suggested in other discussions/tutorials, but
the results are identical to the ones obtained without ROI selection.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Could you please give me an advice on how to solve it?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Here is my code:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">realPrePost{1} =
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> struct with fields:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> freq: 5.5008<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg: [1×1 struct]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> dim: [15 18 15]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> inside: [4050×1 logical]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> pos: [4050×3 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> method: 'average'<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> avg: [1×1 struct]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">%
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009">Prepare cfg to run the stats</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">cfg.dim = realPrePost{1}.dim;</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.method =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'montecarlo'</span><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.statistic =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'ft_statfun_indepsamplesT'</span><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.parameter =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'pow'</span><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.correctm =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'cluster'</span><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.clusteralpha = 0.05;</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.numrandomization = 10000;</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.alpha = 0.05;</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.tail = 0;</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"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">%
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009">Atlas-related cfg options</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">aal = ft_read_atlas(</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'C:\toolbox\fieldtrip-20220317\template\atlas\aal\ROI_MNI_V4.nii'</span><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.atlas = aal;</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.roi = aal.tissuelabel(63:64);</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.avgoverroi =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'yes'</span><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.hemisphere =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'both'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">% 'combined'</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:#028009"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">%
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009">Design matrix</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009">
</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">designMatrix = [];</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">designMatrix(1,1:nReal+nSham) = [ones(1,nReal) 2*ones(1,nSham)];</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.design = designMatrix;</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.ivar = 1;</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">stat = ft_sourcestatistics(cfg, realPrePost{:}, shamPrePost{:});</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:#028009">% Load and reslice MRI</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009"> template</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 style="font-size:10.0pt;font-family:"Courier New";color:black">mri = ft_read_mri(</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'C:\toolbox\fieldtrip-20220317\template\anatomy\single_subj_T1_1mm.nii'</span><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">mri = ft_volumereslice([], mri);</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">cfg.downsample = 2;</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.parameter =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'stat'</span><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">statPlot = ft_sourceinterpolate(cfg, stat, mri);</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:#028009">% Plot source</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">close
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">all</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">maxval = max(statPlot.stat);</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">cfg.method =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'ortho'</span><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.funparameter =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'stat'</span><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.maskparameter = cfg.funparameter;</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.funcolorlim = [0.5 maxval];</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.opacitylim = [0.5 maxval];</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.opacitymap =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#AA04F9">'rampup'</span><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">ft_sourceplot(cfg, statPlot);</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:12.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Any help would be appreciated,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Giuseppe<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:2.4pt;mso-para-margin-bottom:.2gd;background:white">
<b><span lang="EN-GB" style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black;mso-fareast-language:EN-GB">Dr. Giuseppe Angelo Zito</span></b><span lang="EN-GB" style="font-size:12.0pt;font-family:"Arial",sans-serif;color:#222222;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;mso-para-margin-bottom:.2gd;background:white">
<span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:EN-GB">Principal Investigator, Swiss National Science Foundation<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;mso-para-margin-bottom:.2gd;background:white">
<span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;mso-para-margin-bottom:.2gd;background:white">
<span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:EN-GB">Decision Neuroscience Lab<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;mso-para-margin-bottom:.2gd;background:white">
<span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:EN-GB">Department of Health Sciences and Technology (D-HEST)<o:p></o:p></span></p>
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<span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:EN-GB">ETH – Swiss Federal Institute of Technology Zurich<o:p></o:p></span></p>
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<span lang="FR-CH" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:EN-GB">Winterthurerstrasse 190<o:p></o:p></span></p>
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<span lang="FR-CH" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:EN-GB">8057 Zürich
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<span lang="FR-CH" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:EN-GB">Switzerland<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:#1000">Tel: +41 44 633 05 17<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959;mso-fareast-language:#1000">mailto: giuseppeangelo.zito@hest.ethz.ch<o:p></o:p></span></p>
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