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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">just to answer my own question: my mistake was not to apply a template grid on individual subjects.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">See tutorial step: </span>
<a href="http://www.fieldtriptoolbox.org/tutorial/sourcemodel/#performing-group-analysis-on-3-dimensional-source-reconstructed-data"><span lang="EN-US">Performing group analysis on 3-dimensional source-reconstructed data</span></a><span lang="EN-US">.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">However, I have a <b>
follow-up question:</b><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">When I plot the sourcemodel/grid (calculated by a template and the individual mri) not the brain as shown in the tutorial but the scalp is plotted. The “scalp –sourcemodel” plot remains, even when
using the example mri. Should I use the segmented mri as input to ft_prepare_sourcemodel instead?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE">FROM FIELDTRIP tutorial:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE">%% compute the source model<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE">cfg.warpmni = 'yes';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE">cfg.template =
<span style="color:red">template.sourcemodel</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE">cfg.nonlinear = 'yes'; % use non-linear normalization<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE">cfg.mri =
<span style="color:red">mri</span>; ## HERE Use segementedmri?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:DE">sourcemodel = ft_prepare_sourcemodel(cfg);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Thanks and Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Alexandra<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="mso-fareast-language:DE">Von:</span></b><span style="mso-fareast-language:DE"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>Im Auftrag von </b>Korzeczek, Alexandra<br>
<b>Gesendet:</b> Mittwoch, 19. Februar 2020 18:14<br>
<b>An:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Betreff:</b> [FieldTrip] Sourcegrandaverage error due to different "inside" values<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">Dear Fieldtrip community,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">has anyone a suggestion what might be my mistake for not being able to run ft_sourcegrandaverage over several subjects?</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">I am using FT version (20180906) applying beamformer on each individual subject prior to normalize individual subjects to MNI space.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">I receive the error message: Error using ft_sourcegrandaverage (line 116), the input sources vary in the field.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">This error is due to different values of my “src.inside” field. Some years ago (<a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2015-October/009709.html">https://mailman.science.ru.nl/pipermail/fieldtrip/2015-October/009709.html</a>)
</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">the same error was solved by adding the pos of a template. However, this does not work with my data.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Am I using a wrong template maybe? My original dimensions after using sourceinterpolate are [160,160,128].</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">The datainput to sourcegrandaverage (and output of ft_volumenormalise) looks like that:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.anatomy [181x217x181] double</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.pow [181x217x181] double</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.inside [181x217x181] logical</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.transform 4x4 double</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.dim [181,217,181]</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.params 1x1 struct</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.initial 4x4 double</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.coordsys ‘spm’</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni.cfg 1x1 struct</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">My script is:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">% source interpolate</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">cfg = [];</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">cfg.parameter = 'pow';</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_interp = ft_sourceinterpolate(cfg, src , realmri);</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">% normalize to MNI</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">cfg = [];</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">cfg.nonlinear = 'no';</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">src_mni = ft_volumennormalise(cfg, src_interp);</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Thanks,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Alexandra</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#3B3838;mso-fareast-language:DE">_____________________________________</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#3B3838;mso-fareast-language:DE">Alexandra Korzeczek
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#3B3838;mso-fareast-language:DE">PhD Student | BeCog Geog-August-Universität Göttingen</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;color:#3B3838;mso-fareast-language:DE">University Medicine Göttingen | Dept. of Clinical Neurophysiology</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;mso-fareast-language:DE"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;mso-fareast-language:DE"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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