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Hi Jane,
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<div class="">You may want to adjust the cfg.interpmethod in your call to ft_sourceinterpolate.</div>
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<div class="">Or alternatively, don’t use ft_sourceinterpolate, and use cfg.method = ‘surface’, in ft_sourceplot</div>
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<div class="">Happy computing and good luck,</div>
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<div class="">Jan-Mathijs</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
J.M.Schoffelen, MD PhD<br class="">
Senior Researcher, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<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 style="margin-top: 0px; margin-bottom: 0px;" class="">Dear community,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">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>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">My code:</div>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">% Getting noise-covariance<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg = [];</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.covariance =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'yes'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.covariancewindow =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'prestim'</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">tlckSS = ft_timelockanalysis(cfg, dataSS_epoched);</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 7pt; line-height: 9.986666679382324px;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt;" class=""><span style="font-size: 10pt; line-height: 14.266666412353516px; font-family: 'Courier New';" class="">% Leadfield<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">sourcemodel=ft_read_headshape(</span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'C:\xxxxx\xxxxx\xxxx\MATLAB\fieldtrip-20181109\template\sourcemodel\cortex_8196.surf.gii'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">);</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg<span class=""> <span class="Apple-converted-space"> </span></span>= [];</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.elec<span class=""> <span class="Apple-converted-space"> </span></span>= elec_aligned;</span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""><span class="Apple-converted-space"> </span>%aligned
to BEM headmodel</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.grid<span class=""> <span class="Apple-converted-space"> </span></span>= sourcemodel;<span class=""> <span class="Apple-converted-space"> </span></span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">%
FROM FT TEMPLATES</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.headmodel<span class=""> <span class="Apple-converted-space"> </span></span>= vol;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">%BEM
headmodel from FT templates</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">leadfield<span class=""> <span class="Apple-converted-space"> </span></span>= ft_prepare_leadfield(cfg);</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 7pt; line-height: 9.986666679382324px;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt;" class=""><span style="font-size: 10pt; line-height: 14.266666412353516px; font-family: 'Courier New';" class="">% Minimum norm estimation<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg<span class=""> <span class="Apple-converted-space"> </span></span>= [];</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.method<span class=""> <span class="Apple-converted-space"> </span></span>=<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'mne'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.grid<span class=""> <span class="Apple-converted-space"> </span></span>= leadfield;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.headmodel<span class=""> <span class="Apple-converted-space"> </span></span>= vol;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.elec<span class=""> <span class="Apple-converted-space"> </span></span>= elec_aligned;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.mne.prewhiten =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'yes'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.mne.lambda<span class=""> <span class="Apple-converted-space"> </span></span>= 3;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.mne.scalesourcecov =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'yes'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">sourceSS<span class=""> <span class="Apple-converted-space"> </span></span>= ft_sourceanalysis(cfg,tlckSS);</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 7pt; line-height: 9.986666679382324px;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 7pt; line-height: 9.986666679382324px;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 7pt; line-height: 9.986666679382324px;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% Loading single_subj_T1 MRI template</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">mri = ft_read_mri(</span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'C:\xxxxx\xxxxx\xxxx\MATLAB\fieldtrip-20181109\template \anatomy\single_subj_T1_1mm.nii'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">);<span class=""> </span></span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""><span class=""> </span></span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% Reslice the MRI to align voxel axes with the head coordinate axes</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">mri = ft_volumereslice([], mri);</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""><span class=""> </span></span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">%Interpolate the source to the MRI</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg<span class=""> <span class="Apple-converted-space"> </span></span>= [];</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.downsample = 2;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.parameter<span class=""> <span class="Apple-converted-space"> </span></span>=<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'pow'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">sourceSSInt<span class=""> <span class="Apple-converted-space"> </span></span>= ft_sourceinterpolate(cfg, sourceSS , mri);</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 7pt; line-height: 9.986666679382324px;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 7pt; line-height: 9.986666679382324px;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">%Plotting</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg = [];</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.method<span class=""> <span class="Apple-converted-space"> </span></span>=<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'ortho'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.funparameter<span class=""> <span class="Apple-converted-space"> </span></span>=<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'pow'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.latency<span class=""> <span class="Apple-converted-space"> </span></span>= [0.2 0.4];<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">%to
specify time range in seconds</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg.avgovertime<span class=""> <span class="Apple-converted-space"> </span></span>=<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'yes'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">%
for time range</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0.0001pt; line-height: normal;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">ft_sourceplot(cfg, sourceSSInt);</span><span style="font-size: 9pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-SG" class="">Best regards,</span></div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-SG" class="">Jane</span></div>
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<span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br 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; -webkit-text-stroke-width: 0px;" class="">
<span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br 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; -webkit-text-stroke-width: 0px;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br 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; -webkit-text-stroke-width: 0px;" class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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