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<p style="margin-top:0;margin-bottom:0">Hi <span style="font-size: 12pt;">Jan-Mathijs,</span></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
Changing the interpmethod was indeed helpful. Thank you! <br>
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<div>Cheers,</div>
<div>Jane</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen@donders.ru.nl><br>
<b>Sent:</b> Tuesday, 19 February 2019 10:07:47 PM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Strange MNE source reconstruction results</font>
<div> </div>
</div>
<div class="" style="word-wrap:break-word">Hi Jane,
<div class=""><br class="">
</div>
<div class="">You may want to adjust the cfg.interpmethod in your call to ft_sourceinterpolate.</div>
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</div>
<div class="">Or alternatively, don’t use ft_sourceinterpolate, and use cfg.method = ‘surface’, in ft_sourceplot</div>
<div class=""><br class="">
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<div class="">Happy computing and good luck,</div>
<div class=""><br class="">
</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
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<div class="" style="word-wrap:break-word">
<div class="" style="word-wrap:break-word">
<div class="" style="word-wrap:break-word">J.M.Schoffelen, MD PhD<br class="">
Senior Researcher, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
<div class="" style="word-wrap:break-word">Physical location: room 00.028</div>
<div class="" style="word-wrap:break-word">Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
<br class="">
<br class="">
</div>
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<blockquote type="cite" class="">
<div class="">On 19 Feb 2019, at 14:57, Jane Tan <<a href="mailto:Jane.Tan@murdoch.edu.au" class="">Jane.Tan@murdoch.edu.au</a>> wrote:</div>
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<div class="" style="margin-top:0px; margin-bottom:0px">Dear community,</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">I am trying to run source reconstruction on EEG data using minimum source estimation, but have gotten very strange-looking results. The ortho view (via ft_sourceplot) shows source activity "shooting" from
within the cortex to outside of the head. I have attached a screen capture. I've been trying to find out what's wrong, but I can't seem to find anything amiss. I initially thought it might be an issue with the leadfield, but I use the BEM headmodel and sourcemodel
ft templates for the leadfield calculation, and have checked that the sensors (EGI 128) are properly aligned to the headmodel using ft_plot_sens, so I don't think the problem lies with the leadfield. I don't think that it is due to the dataset as well, because
previous source reconstructions with beamformers resulted in normal-looking sourceplots.. I'm really at a loss right now, and would really appreciate any suggestions or advice.</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">My code:</div>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">% Getting noise-covariance</span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg = [];</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.covariance =<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'yes'</span><span class="" style="font-size:10pt; font-family:'Courier New'">;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.covariancewindow =<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'prestim'</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">tlckSS = ft_timelockanalysis(cfg, dataSS_epoched);</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:7pt; line-height:9.986666679382324px"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt"><span class="" style="font-size:10pt; line-height:14.266666412353516px; font-family:'Courier New'">% Leadfield</span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">sourcemodel=ft_read_headshape(</span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'C:\xxxxx\xxxxx\xxxx\MATLAB\fieldtrip-20181109\template\sourcemodel\cortex_8196.surf.gii'</span><span class="" style="font-size:10pt; font-family:'Courier New'">);</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg<span class=""> <span class="x_Apple-converted-space"> </span></span>= [];</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.elec<span class=""> <span class="x_Apple-converted-space"> </span></span>= elec_aligned;</span><span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen"><span class="x_Apple-converted-space"> </span>%aligned
to BEM headmodel</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.grid<span class=""> <span class="x_Apple-converted-space"> </span></span>= sourcemodel;<span class=""> <span class="x_Apple-converted-space"> </span></span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen">%
FROM FT TEMPLATES</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.headmodel<span class=""> <span class="x_Apple-converted-space"> </span></span>= vol;<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen">%BEM
headmodel from FT templates</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">leadfield<span class=""> <span class="x_Apple-converted-space"> </span></span>= ft_prepare_leadfield(cfg);</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:7pt; line-height:9.986666679382324px"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt"><span class="" style="font-size:10pt; line-height:14.266666412353516px; font-family:'Courier New'">% Minimum norm estimation</span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg<span class=""> <span class="x_Apple-converted-space"> </span></span>= [];</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.method<span class=""> <span class="x_Apple-converted-space"> </span></span>=<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'mne'</span><span class="" style="font-size:10pt; font-family:'Courier New'">;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.grid<span class=""> <span class="x_Apple-converted-space"> </span></span>= leadfield;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.headmodel<span class=""> <span class="x_Apple-converted-space"> </span></span>= vol;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.elec<span class=""> <span class="x_Apple-converted-space"> </span></span>= elec_aligned;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.mne.prewhiten =<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'yes'</span><span class="" style="font-size:10pt; font-family:'Courier New'">;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.mne.lambda<span class=""> <span class="x_Apple-converted-space"> </span></span>= 3;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.mne.scalesourcecov =<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'yes'</span><span class="" style="font-size:10pt; font-family:'Courier New'">;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">sourceSS<span class=""> <span class="x_Apple-converted-space"> </span></span>= ft_sourceanalysis(cfg,tlckSS);</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:7pt; line-height:9.986666679382324px"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:7pt; line-height:9.986666679382324px"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:7pt; line-height:9.986666679382324px"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen">% Loading single_subj_T1 MRI template</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">mri = ft_read_mri(</span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'C:\xxxxx\xxxxx\xxxx\MATLAB\fieldtrip-20181109\template \anatomy\single_subj_T1_1mm.nii'</span><span class="" style="font-size:10pt; font-family:'Courier New'">);<span class=""> </span></span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'"><span class=""> </span></span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen">% Reslice the MRI to align voxel axes with the head coordinate axes</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">mri = ft_volumereslice([], mri);</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'"><span class=""> </span></span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen">%Interpolate the source to the MRI</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg<span class=""> <span class="x_Apple-converted-space"> </span></span>= [];</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.downsample = 2;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.parameter<span class=""> <span class="x_Apple-converted-space"> </span></span>=<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'pow'</span><span class="" style="font-size:10pt; font-family:'Courier New'">;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">sourceSSInt<span class=""> <span class="x_Apple-converted-space"> </span></span>= ft_sourceinterpolate(cfg, sourceSS , mri);</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:7pt; line-height:9.986666679382324px"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:7pt; line-height:9.986666679382324px"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen">%Plotting</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg = [];</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.method<span class=""> <span class="x_Apple-converted-space"> </span></span>=<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'ortho'</span><span class="" style="font-size:10pt; font-family:'Courier New'">;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.funparameter<span class=""> <span class="x_Apple-converted-space"> </span></span>=<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'pow'</span><span class="" style="font-size:10pt; font-family:'Courier New'">;</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.latency<span class=""> <span class="x_Apple-converted-space"> </span></span>= [0.2 0.4];<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen">%to
specify time range in seconds</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">cfg.avgovertime<span class=""> <span class="x_Apple-converted-space"> </span></span>=<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:rgb(160,32,240)">'yes'</span><span class="" style="font-size:10pt; font-family:'Courier New'">;<span class="x_Apple-converted-space"> </span></span><span class="" style="font-size:10pt; font-family:'Courier New'; color:forestgreen">%
for time range</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
<div class="" style="margin-top:0px; margin-bottom:0.0001pt; line-height:normal">
<span class="" style="font-size:10pt; font-family:'Courier New'">ft_sourceplot(cfg, sourceSSInt);</span><span class="" style="font-size:9pt; font-family:'Courier New'"></span></div>
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<div class="" style="margin-top:0px; margin-bottom:0px"><span lang="EN-SG" class="">Best regards,</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span lang="EN-SG" class=""><br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px"><span lang="EN-SG" class="">Jane</span></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">
<a href="https://clicktime.symantec.com/3TUf7pBhXvnVkC5ys8SaU4r7Vc?u=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip" class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; 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">
<a href="https://clicktime.symantec.com/3YG9crzWq1UKuff5tdoNa7t7Vc?u=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202" class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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