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<p class="MsoNormal">Dear List,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have run group-level source statistics on my data and extracted the labels of regions showing statistically significant differences at a group-level. I now wish to extract the average mni coordinates for these regions, but do not how
to transform voxel coordinates to mni coordinates. I would be grateful if anyone could help with this?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have pasted my code below.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Many thanks in advance, <o:p></o:p></p>
<p class="MsoNormal">Kathryn <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">%% run source statistics - compare average source coherence for exp vs control</span><span style="font-size:10.0pt;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">cd
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">D:\DICsModel</span><span style="font-size:10.0pt;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">atlas = ft_read_atlas(</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'ROI_MNI_V4.nii'</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:#3C763D">% MNI</span><span style="font-size:10.0pt;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:#3C763D">% for TAL:</span><span style="font-size:10.0pt;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:#3C763D">%afni = ft_read_atlas('C:\Users\Kat\Documents\NPMK\fieldtrip-20200607\template\atlas\afni\TTatlas+tlrc.HEAD');</span><span style="font-size:10.0pt;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:#3C763D"></span><span style="font-size:10.0pt;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:10.0pt;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 = AllExp{1}.dim;</span><span style="font-size:10.0pt;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:#A020F0">'montecarlo'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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:#A020F0">'avg.coh'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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:#A020F0">'ft_statfun_depsamplesT'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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:#A020F0">'cluster'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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:10.0pt;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.computecritval =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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.computeprob =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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 = 50000;</span><span style="font-size:10.0pt;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:10.0pt;font-family:"Courier New";color:#3C763D">% one-tailed right sided rather than 2 tailed, 0=two-sided</span><span style="font-size:10.0pt;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:#3C763D"></span><span style="font-size:10.0pt;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">nsubj=numel(AllExp);</span><span style="font-size:10.0pt;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(1,:) = [1:nsubj 1:nsubj];</span><span style="font-size:10.0pt;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(2,:) = [ones(1,nsubj)*1 ones(1,nsubj)*2];</span><span style="font-size:10.0pt;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.uvar = 1;
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% row of design matrix that contains unit variable (in this case: subjects)</span><span style="font-size:10.0pt;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 = 2;
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% row of design matrix that contains independent variable (the conditions)</span><span style="font-size:10.0pt;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:#3C763D"></span><span style="font-size:10.0pt;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, AllExp{:},AllCntrl{:});</span><span style="font-size:10.0pt;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:#3C763D">% stat.prob with the p values for each grid point</span><span style="font-size:10.0pt;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:#3C763D">% stat.mask with a 1 for each grid point if it is significant and a 0 if it is not significant</span><span style="font-size:10.0pt;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:#3C763D">% stat.posclusters and stat.negclusters you will find for each cluster the p and cluster-t values</span><span style="font-size:10.0pt;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:#3C763D">% cirange = confidence interval of p-value</span><span style="font-size:10.0pt;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:#3C763D">% stddev = st. dev of the p-value</span><span style="font-size:10.0pt;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:#3C763D">%% interpolate the t maps to the structural MRI of the subject %</span><span style="font-size:10.0pt;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:10.0pt;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:#A020F0">'all'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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, template_mri);</span><span style="font-size:10.0pt;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:#3C763D">% plot the t values on the MRI %</span><span style="font-size:10.0pt;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:10.0pt;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:#A020F0">'ortho'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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.location =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'max'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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:#3C763D">%cfg.method = 'slice';</span><span style="font-size:10.0pt;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:#A020F0">'stat'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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.funcolormap =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'jet'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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 = atlas;</span><span style="font-size:10.0pt;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 =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'mask'</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:#3C763D">% only show significant regions</span><span style="font-size:10.0pt;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.colormap =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'jet'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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.colorbartext =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'\fontsize{16}t-statistic'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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.axisfontsize = 16;</span><span style="font-size:10.0pt;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:10.0pt;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:#3C763D">%% list identified brain regions</span><span style="font-size:10.0pt;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.mask = ((statplot.mask >0));</span><span style="font-size:10.0pt;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:10.0pt;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 = atlas;</span><span style="font-size:10.0pt;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 =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'mask'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:10.0pt;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">labels = ft_volumelookup(cfg,statplot);</span><span style="font-size:10.0pt;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:#3C763D">%%</span><span style="font-size:10.0pt;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">n=1;</span><span style="font-size:10.0pt;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:blue">for</span><span style="font-size:10.0pt;font-family:"Courier New";color:black"> i = 1:size(labels.name,1)</span><span style="font-size:10.0pt;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:10.0pt;font-family:"Courier New";color:blue">if</span><span style="font-size:10.0pt;font-family:"Courier New";color:black"> labels.count(i) >0</span><span style="font-size:10.0pt;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"> labels.unique(n,1) = labels.name(i);</span><span style="font-size:10.0pt;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"> labels.uniquecount(n,1) = labels.count(i);</span><span style="font-size:10.0pt;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"> n=n+1;</span><span style="font-size:10.0pt;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:10.0pt;font-family:"Courier New";color:blue">end</span><span style="font-size:10.0pt;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:blue">end</span><span style="font-size:10.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
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