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Dear Fieldtrip community,
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<div class="">I am working with EEG data from a Biosemi 64 channel system from a reinforcement motor learning task. I would like to do Beamformer source analyses on power data. I don’t have individual MRIs or related electrode positions available, so I am taking
the standard MRI and BEM headmodel from the fieldtrip templates. I am following the tutorial/examples on the website (<a href="http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem/" class="">http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem/</a>). </div>
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<div class="">I am currently struggling on how to continue with the step electrode alignment. According to the tutorials, I need to align the electrode positions to the MRI in the next step with ft_electrodes_realign. However, it seems that I need to have information
on the fiducial which I don’t have. Is there anyone who knows how to do that with biosemi EEG data? I already found this example but cannot relate as there are information on the fiducial and more/other channels available (<a href="http://www.fieldtriptoolbox.org/example/biosemi/" class="">http://www.fieldtriptoolbox.org/example/biosemi/</a>). </div>
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<div class="">I added my code below. I would appreciate any help. If anyone needs more information on my data or an example set, let me know. I added information on my existing variables below the code.</div>
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<div class="">Best, Patrick</div>
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<div class=""> <span style="color: rgb(34, 139, 34); font-family: Courier; font-size: 10px;" class="">%% load MRI and BEM templates</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(160, 32, 240);" class="">
<span style="color: #000000" class="">load(</span>'/Users/patrickwiegel/Documents/MATLAB/Scripts/2020/TF_Data/fieldtrip-20200603/template/headmodel/standard_bem.mat'<span style="color: #000000" class="">)</span></div>
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<span style="color: #000000" class="">load(</span>'/Users/patrickwiegel/Documents/MATLAB/Scripts/2020/TF_Data/fieldtrip-20200603/template/headmodel/standard_mri.mat'<span style="color: #000000" class="">)</span></div>
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%% show Biosemi electrode layout</div>
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cfg = [];</div>
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<span style="color: #000000" class="">cfg.layout = (</span>'/Users/patrickwiegel/Documents/MATLAB/Scripts/2020/TF_Data/fieldtrip-20200603/template/layout/biosemi64.lay'<span style="color: #000000" class="">);</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
ft_layoutplot(cfg)</div>
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%% import EEG data</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
EEG_Data = eeglab2fieldtrip( EEG, <span style="color: #a020f0" class="">'raw'</span>,
<span style="color: #a020f0" class="">'none'</span> );</div>
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%% define trials for frequency analyses</div>
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cfg = [];</div>
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cfg.trials = Indexes_correct{1, 1};</div>
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cfg.toilim = [0.25 0.55];</div>
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data_fed_correct = ft_redefinetrial(cfg, EEG_Data);</div>
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cfg = [];</div>
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cfg.trials = Indexes_incorrect{1, 1};</div>
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cfg.toilim = [0.25 0.55];</div>
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data_fed_incorrect = ft_redefinetrial(cfg, EEG_Data);</div>
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%% run frequenc analyses</div>
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cfg = [];</div>
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cfg.method = <span style="color: #a020f0" class="">'mtmfft'</span>;</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
cfg.output = <span style="color: #a020f0" class="">'powandcsd'</span>;</div>
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cfg.tapsmofrq = 4;</div>
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cfg.foilim = [25 25];</div>
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frequ_correct = ft_freqanalysis(cfg, data_fed_correct);</div>
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cfg = [];</div>
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cfg.method = <span style="color: #a020f0" class="">'mtmfft'</span>;</div>
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cfg.output = <span style="color: #a020f0" class="">'powandcsd'</span>;</div>
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cfg.tapsmofrq = 4;</div>
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cfg.foilim = [25 25];</div>
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frequ_incorrect = ft_freqanalysis(cfg, data_fed_incorrect);</div>
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%% define head model</div>
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mri = ft_volumereslice(cfg, mri);</div>
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display(mri)</div>
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%% plot mesh </div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
ft_plot_mesh(vol.bnd(1), <span style="color: #a020f0" class="">'facecolor'</span>,[0.2 0.2 0.2],
<span style="color: #a020f0" class="">'facealpha'</span>, 0.3, <span style="color: #a020f0" class="">
'edgecolor'</span>, [1 1 1], <span style="color: #a020f0" class="">'edgealpha'</span>, 0.05);</div>
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hold <span style="color: #a020f0" class="">on</span>;</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
ft_plot_mesh(vol.bnd(2),<span style="color: #a020f0" class="">'edgecolor'</span>,<span style="color: #a020f0" class="">'none'</span>,<span style="color: #a020f0" class="">'facealpha'</span>,0.4);</div>
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hold <span style="color: #a020f0" class="">on</span>;</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
ft_plot_mesh(vol.bnd(3),<span style="color: #a020f0" class="">'edgecolor'</span>,<span style="color: #a020f0" class="">'none'</span>,<span style="color: #a020f0" class="">'facecolor'</span>,[0.4 0.6 0.4]);</div>
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%% extract electrode posiitons from Biosemi file and convert to fieldtrip struc</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
sens.label = EEG_Data.elec.label;</div>
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sens.chanpos = EEG_Data.elec.elecpos;</div>
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sens.elecpos = EEG_Data.elec.pnt;</div>
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elec = ft_datatype_sens(sens);</div>
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elec = ft_convert_units(elec, <span style="color: #a020f0" class="">'mm'</span>);</div>
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display(elec)</div>
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<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(34, 139, 34);" class="">
%% plot mesh and electrode positions</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
figure;</div>
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% head surface (scalp)</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
ft_plot_mesh(vol.bnd(1), <span style="color: #a020f0" class="">'edgecolor'</span>,<span style="color: #a020f0" class="">'none'</span>,<span style="color: #a020f0" class="">'facealpha'</span>,0.8,<span style="color: #a020f0" class="">'facecolor'</span>,[0.6
0.6 0.8]);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
hold <span style="color: #a020f0" class="">on</span>;</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(34, 139, 34);" class="">
% electrodes</div>
<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier;" class="">
ft_plot_sens(elec);</div>
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<div style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(34, 139, 34);" class="">
%% align electrodes</div>
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<div class="">variables:</div>
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<div class="">mri = </div>
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<div class=""> struct with fields:</div>
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</div>
<div class=""> anatomy: [256×256×256 double]</div>
<div class=""> coordsys: 'spm'</div>
<div class=""> dim: [256 256 256]</div>
<div class=""> transform: [4×4 double]</div>
<div class=""> unit: 'mm'</div>
<div class=""> inside: [256×256×256 logical]</div>
<div class=""> cfg: [1×1 struct]</div>
</div>
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</div>
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<div class="">
<div class="">elec = </div>
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</div>
<div class=""> struct with fields:</div>
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</div>
<div class=""> chanpos: [64×3 double]</div>
<div class=""> chantype: {64×1 cell}</div>
<div class=""> chanunit: {64×1 cell}</div>
<div class=""> elecpos: [64×3 double]</div>
<div class=""> label: {1×64 cell}</div>
<div class=""> type: 'eeg1010'</div>
<div class=""> unit: ‚mm'</div>
</div>
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</div>
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<div class="">vol = </div>
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</div>
<div class=""> struct with fields:</div>
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</div>
<div class=""> bnd: [1×3 struct]</div>
<div class=""> cond: [0.3300 0.0041 0.3300]</div>
<div class=""> mat: [3000×3000 double]</div>
<div class=""> type: 'dipoli'</div>
<div class=""> unit: 'mm'</div>
</div>
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<div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<b class="">Patrick Wiegel</b><br class="">
<font color="#680823" class="">Department of Sport and Sport Science</font>
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University of Freiburg <br class="">
Sandfangweg 4<br class="">
79117 Freiburg i. Br . <br class="">
<br class="">
<div class="">phone: +49 (0)761/ 203-4550<br class="">
<a href="mailto:patrick.wiegel@sport.uni-freiburg.de" class="">email: patrick.wiegel@sport.uni-freiburg.de</a><br class="">
web: www.sport.uni-freiburg.de</div>
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