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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Dear Jan-Mathijs,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Yes, that’s unfortunate, thank you for the hint.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US">I tried to walk around this issue. I modified the field “inside” from each subject, so that it only contains values within my ROI. Here
is the code:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><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 atlas and select supramarginal gyrus (labels 63 and 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">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">SMG = 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">SMG.tissue = zeros(aal.dim(1),aal.dim(2),aal.dim(3));</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">SMG.tissue(aal.tissue==63) = 1;
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">% supramarginal gyrus</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">SMG.tissue(aal.tissue==64) = 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">SMG.tissue = logical(SMG.tissue);</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">% Interpolate subjects' data so that they match the size of the atlas</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 = 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">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:#0E00FF">for</span><span style="font-size:10.0pt;font-family:"Courier New";color:black"> i = 1:nReal</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"> realPrePostInt{i,1} = ft_sourceinterpolate(cfg, realPrePost{i}, 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"> realPrePostInt{i,1}.inside = SMG.tissue;</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:#0E00FF">end</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:#0E00FF">for</span><span style="font-size:10.0pt;font-family:"Courier New";color:black"> i = 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"> shamPrePostInt{i,1} = ft_sourceinterpolate(cfg, shamPrePost{i}, 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"> shamPrePostInt{i,1}.inside = SMG.tissue;</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:#0E00FF">end</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;mso-fareast-language:EN-US">This seems to restrict the analysis only to the specific ROI, however, in the later plot, it seems that the activity maps do not match
with each other in the ortho-view (see picture attached). In other words, when I center the axes over a cluster in the coronal view, I do not see any cluster in the sagittal/axial views. Any input of what could have gone wrong?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Here is the code I use to run the stats and the plot.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><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">% run statistics [(post-pre)/pre]real vs [(post-pre)/pre]sham</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 = 1000;</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"></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, realPrePostInt{:}, shamPrePostInt{:});</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 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;mso-fareast-language:EN-US">Thank you again, and have a nice week end,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Giuseppe<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>Schoffelen, J.M. (Jan Mathijs) via fieldtrip<br>
<b>Sent:</b> 26 August 2022 10:16<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] ROI-based source analysis with ft_sourcestatistics<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Giuseppe, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If you open ft_sourcestatistics and read the help documentation, it states:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">% FIXME the following needs to be reimplemented<o:p></o:p></p>
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<p class="MsoNormal">%<o:p></o:p></p>
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<p class="MsoNormal">% You can restrict the statistical analysis to regions of interest (ROIs)<o:p></o:p></p>
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<p class="MsoNormal">% or to the average value inside ROIs using the following options:<o:p></o:p></p>
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<p class="MsoNormal">% cfg.atlas = filename of the atlas<o:p></o:p></p>
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<p class="MsoNormal">% cfg.roi = string or cell of strings, region(s) of interest from anatomical atlas<o:p></o:p></p>
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<p class="MsoNormal">% cfg.avgoverroi = 'yes' or 'no' (default = 'no')<o:p></o:p></p>
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<p class="MsoNormal">% cfg.hemisphere = 'left', 'right', 'both', 'combined', specifying this is required when averaging over regions<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If I subsequently search the code for the term ‘roi’ or ‘avgoverroi’, I only get a hit for the occurrences in the help documention, so that means that there is no functional consequence of specifying those options. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">In other words: it is not so surprising that it doesn’t work, at least not in the way that you implemented it in your scripts. This also means that the documentation you used to create your scripts is out of sync with the code. That’s unfortunate,
and it would be helpful if propose a change to the website (it could be as minimal as inserting a disclaimer or so) that flags the non-functionality of that snippet of code (for the time being).<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This being said, there have been various code/workflow improvements over the past years, which in principle would make it possible for you to achieve what you want, using a different route.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This requires the use of ft_sourceparcellate (or ft_virtualchannel), followed by a call to ft_timelockstatistics/ft_freqstatistics. If the documentation online proves insufficient, then it would be helpful if you were to write a bit of
documentation once you find out how to do it.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Good luck and best wishes,<o:p></o:p></p>
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<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 24 Aug 2022, at 15:53, Zito Giuseppe Angelo via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Dear Fieldtrip community,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<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.</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<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.</span><o:p></o:p></p>
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<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?</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Here is my code:</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">realPrePost{1} =</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> struct with fields:</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> freq: 5.5008</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg: [1×1 struct]</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> dim: [15 18 15]</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> inside: [4050×1 logical]</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> pos: [4050×3 double]</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> method: 'average'</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> avg: [1×1 struct]</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">%<span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009">Prepare cfg to run the stats</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.dim = realPrePost{1}.dim;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.method =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'montecarlo'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.statistic =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'ft_statfun_indepsamplesT'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.parameter =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'pow'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.correctm =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'cluster'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.clusteralpha = 0.05;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.numrandomization = 10000;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.alpha = 0.05;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.tail = 0;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">%<span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009">Atlas-related cfg options</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">aal = ft_read_atlas(<span style="color:#AA04F9">'C:\toolbox\fieldtrip-20220317\template\atlas\aal\ROI_MNI_V4.nii'</span>);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.atlas = aal;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.roi = aal.tissuelabel(63:64);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.avgoverroi =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'yes'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.hemisphere =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'both'</span>;<span class="apple-converted-space"> </span><span style="color:#028009">% 'combined'</span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">%<span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009">Design matrix</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">designMatrix = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">designMatrix(1,1:nReal+nSham) = [ones(1,nReal) 2*ones(1,nSham)];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.design = designMatrix;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.ivar = 1;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">stat = ft_sourcestatistics(cfg, realPrePost{:}, shamPrePost{:});</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">% Load and reslice MRI</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#028009">template</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">mri = ft_read_mri(<span style="color:#AA04F9">'C:\toolbox\fieldtrip-20220317\template\anatomy\single_subj_T1_1mm.nii'</span>);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">mri = ft_volumereslice([], mri);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.downsample = 2;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.parameter =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'stat'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">statPlot = ft_sourceinterpolate(cfg, stat, mri);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#028009">% Plot source</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">close<span class="apple-converted-space"> </span><span style="color:#AA04F9">all</span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">maxval = max(statPlot.stat);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.method =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'ortho'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.funparameter =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'stat'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.maskparameter = cfg.funparameter;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.funcolorlim = [0.5 maxval];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.opacitylim = [0.5 maxval];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">cfg.opacitymap =<span class="apple-converted-space"> </span><span style="color:#AA04F9">'rampup'</span>;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">ft_sourceplot(cfg, statPlot);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Any help would be appreciated,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Arial",sans-serif">Giuseppe</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><b><span lang="EN-GB" style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black">Dr. Giuseppe Angelo Zito</span></b><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">Principal Investigator, Swiss National Science Foundation</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">Decision Neuroscience Lab</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">Department of Health Sciences and Technology (D-HEST)</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">ETH – Swiss Federal Institute of Technology Zurich</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="FR-CH" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="FR-CH" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">Winterthurerstrasse 190</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="FR-CH" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">8057 Zürich</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:2.4pt;background:white"><span lang="FR-CH" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">Switzerland</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt;font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">Tel: +41 44 633 05 17</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#595959">mailto:<span class="apple-converted-space"> </span><a href="mailto:giuseppeangelo.zito@hest.ethz.ch">giuseppeangelo.zito@hest.ethz.ch</a></span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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