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<p class="MsoNormal">Dear Fieldtrip community,<br>
<br>
My name is Brilliant (yes, it’s my real name <span style="font-family:Wingdings">
J</span>) and I am a PhD Student at Kral Lab at Hannover Medical School, Germany.
<br>
I am currently doing Time-Frequency Analysis on EEG-Data and am trying to compute the Source Reconstruction with the Beamforming in Fieldtrip.
<br>
The EEG-Data were collected in experiments, which the participants listened to auditory stimuli and had to respond by pressing a button.
<br>
In the Grand-Mean of the Time-Frequency Plot Alpha desynchronization were observed and we would like to know the source/s.<br>
<br>
When observing the figures from the result of Source Reconstruction via Beamforming, it seems like the 3D-Surface Figure (Figure A) does not correspond well with the 2D-Slice Figure (Figure B).
<br>
For example in the 3D-Surface Figure, we could not see the strong projection on left occipital hemisphere although in the 2D-Ortho Figure it can be seen (Figure C).<br>
I play around with the parameter of the ‘cfg.projthresh’, but still cannot see the source activation in the 3D-Surface Figure as clearly as in the 2D-Figures.
<o:p></o:p></p>
<p class="MsoNormal">Another question related to this is why we don’t see much activation in the auditory cortex.<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal">The code that I use to plot the results are as follow.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any feedbacks and suggestions would be appreciated.<o:p></o:p></p>
<p class="MsoNormal">Thank you and kindest regards.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Brilliant<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">---<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">source_diff_mni = source_diff;
<span style="color:#00B050">%Calculated power difference<o:p></o:p></span></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">source_diff_mni.coordsys = 'mni';
<span style="color:#00B050">%Label the coordinate system as 'mni'</span><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">absPows = abs(source_diff_mni.avg.pow);
<span style="color:#00B050">%Check the maximum power</span><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">maxPow = max(absPows);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">maxPow = round (maxPow,2);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas;color:#00B050">% Plot 3D<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.method = 'surface';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.funparameter = 'pow';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.projmethod = 'nearest';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.surfinflated = 'surface_inflated_both_caret.mat';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">%cfg.projthresh = 0.5;
<span style="color:#00B050">%more mean less projection</span><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.funcolorlim = [-maxPow maxPow];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.camlight = 'no';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">ft_sourceplot(cfg, source_diff_mni);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">brainnetome = ft_read_atlas('BNA_MPM_thr25_1.25mm.nii')
<span style="color:#00B050">%Load Atlas</span><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">atlas = brainnetome;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">mri = ft_read_mri('Subject01.mri');
<span style="color:#00B050">%Load MRI</span><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas;color:#00B050">% Interpolate the source_diff_mni to the MRI<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.voxelcoord = 'yes';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.parameter = 'pow';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.interpmethod = 'cubic';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">source_diff_mri = ft_sourceinterpolate(cfg, source_diff_mni, mri);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas;color:#00B050">% Plot 2D<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">threshold = 0.3*maxPow;
<span style="color:#00B050">%Masking to not show any power below 30% max power<o:p></o:p></span></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">threshold = round(threshold,2);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">source_diff_mri_mask = source_diff_mri;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">source_diff_mri_mask.mask = (source_diff_mri_mask.pow>threshold & source_diff_mri_mask.pow<maxPow) | (source_diff_mri_mask.pow<-threshold & source_diff_mri_mask.pow>-maxPow);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas;color:#00B050">% Slice 2D-Plot<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.method = 'slice';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.atlas = atlas;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.anparameter = 'tissue';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.maskparameter = 'mask'<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.funparameter = 'pow';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.interpmethod = 'cubic';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.funcolorlim = [-maxPow maxPow];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.nslices = 9;
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.slicedim = 1;
<span style="color:#00B050">%Slice Sagital<o:p></o:p></span></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">ft_sourceplot(cfg,source_diff_mri_mask);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas;color:#00B050">% Ortho 2D-Plot<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.method = 'ortho';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.atlas = atlas;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.maskparameter = 'mask'<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.funparameter = 'pow';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.interpmethod = 'cubic';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.location = [-3 -47 68];
<span style="color:#00B050">%Right STG 41/42<o:p></o:p></span></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">cfg.funcolorlim = [-maxPow maxPow];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:Consolas">ft_sourceplot(cfg,source_diff_mri_mask);<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:#404040;mso-fareast-language:DE">---<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:#404040;mso-fareast-language:DE"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:#404040;mso-fareast-language:DE">Brilliant, M.Sc.<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Calibri Light",sans-serif;color:#404040;mso-fareast-language:DE">Pronouns: he, him, his<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:#404040;mso-fareast-language:DE"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">Medizinische Hochschule Hannover<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">Institut für AudioNeuroTechnologie (VIANNA)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">OE 8891, M20, Ebene 01, Raum 1640<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">Stadtfelddamm 34<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">30625 Hannover<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">Tel.: +49 511 532-1532 (EEG-Labor)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">Email:
</span><a href="mailto:brilliant.OE8891@mh-hannover.de"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:blue;mso-fareast-language:DE">brilliant.OE8891@mh-hannover.de</span></a><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">Web:
</span><a href="http://www.neuroprostheses.com/"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE">www.neuroprostheses.com</span></a><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#595959;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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