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Hi Michael,
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</div>
<div class="">Yes, this sounds correct.</div>
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<div class="">If I do sum(atlas.tissue(:)~=0)./prod(atlas.dim), I get ~0.15, i.e. 15%. This means that 15% of the voxels in the original volume are labelled.</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 23 Aug 2023, at 22:58, Michael Glassen via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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Hi all,</div>
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I am using the template atlas for the brainetome atlas included with fieldtrip, and using it along with ft_virtualchannel to parcellate my source data(for eeg). My steps are below:</div>
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<ol data-editing-info="{"orderedStyleType":3,"unorderedStyleType":1}" data-listchain="__List_Chain_202" class="">
<li style="list-style-type: "1) ";" class=""><span class="">import eeg, project electrodes onto default headmodel</span></li><li style="list-style-type: "2) ";" class=""><span class="">create leadfield with 4mm resolution</span></li><li style="list-style-type: "3) ";" class=""><span class="">compute average sources, save filters</span></li><li style="list-style-type: "4) ";" class="">interpolate brainetome atlas onto computed leadfield using ft_sourceinterpolate</li><li style="list-style-type: "5) ";" class="">compute trial by trial source data using ft_virutal channel with eeg data, source filters, and interpolated atlas.</li></ol>
<div class="">I believe I have everything working, but ft_virtualchannel shows that I am only segmenting ~15% of the total volume, with each roi ranging from .01 to .15% of total volume(246 rois total).</div>
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<div class="">Does this seem correct, or did I make a mistake with interpolating the atlas onto my leadfield?</div>
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<div class="">Thank you!</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Michael Glassen</div>
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</div>
<div class="">Source code below:</div>
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</div>
<div class="">
<div class="rtcContent" style="padding: 30px;"><span class="lineNode" style="font-size: 10pt; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-weight: normal;"><span class=""><span class="ContentPasted0">headmodel = vol;</span></span></span>
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<span class=""><span class="ContentPasted0">atlas = ft_read_atlas(atlasLoc);</span></span></div>
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<span class=""><span class="ContentPasted0">EEG = pop_loadset(eegLoc);</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%<span class="Apple-converted-space"> </span></span></span></div>
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<span class=""><span class="ContentPasted0">EEG = pop_basicfilter( EEG, 1:size(EEG.data,1) ,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'Boundary'</span><span class="ContentPasted0">,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'boundary'</span><span class="ContentPasted0">,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'Cutoff'</span><span class="ContentPasted0">,
[ 1 100],</span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'Design'</span><span class="ContentPasted0">,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'butter'</span><span class="ContentPasted0">,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'Filter'</span><span class="ContentPasted0">,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'bandpass'</span><span class="ContentPasted0">,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'Order'</span><span class="ContentPasted0">,
2,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'RemoveDC'</span><span class="ContentPasted0">,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'on'<span class="Apple-converted-space"> </span></span><span class="ContentPasted0">);</span></span></div>
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<span class=""><span class="ContentPasted0">EEG = eeg_regepochs(EEG,</span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'recurrence'</span><span class="ContentPasted0">,1,</span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'limits'</span><span class="ContentPasted0">,[0
1],</span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'rmbase'</span><span class="ContentPasted0">,NaN);</span></span></div>
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<span class=""><span class="ContentPasted0">EEG = pop_iclabel(EEG,</span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'default'</span><span class="ContentPasted0">);</span></span></div>
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<span class=""><span class="ContentPasted0">EEG = pop_icflag(EEG, [NaN NaN;0.75 1;0.75 1;NaN NaN;NaN NaN;NaN NaN;NaN NaN]);</span></span></div>
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<span class=""><span class="ContentPasted0">EEG = pop_subcomp(EEG,[],0,0);</span></span></div>
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<span class=""><span class="ContentPasted0">header = eeglab2fieldtrip(EEG,</span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'preprocessing'</span><span class="ContentPasted0">,</span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'none'</span><span class="ContentPasted0">);</span></span></div>
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<span class=""><span class="ContentPasted0">header.hdr.chanunit = repmat({</span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'uV'</span><span class="ContentPasted0">},[size(EEG.data,1),1]);</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%% Seperate EEG and EMG data</span></span></div>
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<span class=""><span class="ContentPasted0">eegChans = {};</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(14, 0, 255);">for<span class="Apple-converted-space"> </span></span><span class="ContentPasted0">i = 1:size(EEG.data,1)</span></span></div>
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<span class=""><span class="ContentPasted0"> eegChans = [eegChans header.label{i}];</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(14, 0, 255);">end</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% emgChans = {};</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% for i = 65:EEG.nbchan</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% emgChans = [emgChans header.label{i}];</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% end</span></span></div>
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<span class=""><span class="ContentPasted0">cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.channel = eegChans;</span></span></div>
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<span class=""><span class="ContentPasted0">eegData = ft_selectdata(cfg,header);</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% cfg.channel = emgChans;</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% %</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% emgData = ft_selectdata(cfg,header);</span></span></div>
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<span class=""><span class="ContentPasted0">tempElec = ft_read_sens(electrodePos);</span></span></div>
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<span class=""><span class="ContentPasted0">newElec = tempElec;</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(14, 0, 255);">for<span class="Apple-converted-space"> </span></span><span class="ContentPasted0">i = 1:length(eegData.label)</span></span></div>
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<span class=""><span class="ContentPasted0"> checker = 0;</span></span></div>
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<span class=""><span class="ContentPasted0"> <span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(14, 0, 255);">for<span class="Apple-converted-space"> </span></span><span class="ContentPasted0">i2 = 1:length(tempElec.label)</span></span></div>
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<span class=""><span class="ContentPasted0"> <span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(14, 0, 255);">if<span class="Apple-converted-space"> </span></span><span class="ContentPasted0">strcmpi(eegData.label{i},tempElec.label{i2})</span></span></div>
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<span class=""><span class="ContentPasted0"> checker = 1;</span></span></div>
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<span class=""><span class="ContentPasted0"> newElec.chanpos(i,:) = tempElec.chanpos(i2,:);</span></span></div>
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<span class=""><span class="ContentPasted0"> newElec.chantype{i} = tempElec.chantype{i2};</span></span></div>
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<span class=""><span class="ContentPasted0"> newElec.chanunit{i} = tempElec.chanunit{i2};</span></span></div>
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<span class=""><span class="ContentPasted0"> newElec.elecpos(i,:) = tempElec.elecpos(i2,:);</span></span></div>
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<span class=""><span class="ContentPasted0"> newElec.label{i} = tempElec.label{i2};</span></span></div>
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<span class=""><span class="ContentPasted0"> <span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(14, 0, 255);">end</span></span></div>
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<span class=""><span class="ContentPasted0"> <span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(14, 0, 255);">end</span></span></div>
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<span class=""><span class="ContentPasted0"> <span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(14, 0, 255);">if<span class="Apple-converted-space"> </span></span><span class="ContentPasted0">checker == 0</span></span></div>
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<span class=""><span class="ContentPasted0"> eegData.elec.label{i}</span></span></div>
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<span class=""><span class="ContentPasted0"> <span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(14, 0, 255);">end</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(14, 0, 255);">end</span></span></div>
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<span class=""><span class="ContentPasted0">newElec.chanpos(length(eegData.label)+1:end,:) = [];</span></span></div>
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<span class=""><span class="ContentPasted0">newElec.chantype(length(eegData.label)+1:end) = [];</span></span></div>
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<span class=""><span class="ContentPasted0">newElec.chanunit(length(eegData.label)+1:end) = [];</span></span></div>
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<span class=""><span class="ContentPasted0">newElec.elecpos(length(eegData.label)+1:end,:) = [];</span></span></div>
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<span class=""><span class="ContentPasted0">newElec.label(length(eegData.label)+1:end) = [];</span></span></div>
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<span class=""><span class="ContentPasted0">eegData.elec = newElec;</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%% Project electrodes to scalp</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(14, 0, 255);">if<span class="Apple-converted-space"> </span></span><span class="ContentPasted0">strcmp(headmodel.type,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'bemcp'</span><span class="ContentPasted0">)</span></span></div>
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<span class=""><span class="ContentPasted0"> scalp_index = 3;</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(14, 0, 255);">elseif<span class="Apple-converted-space"> </span></span><span class="ContentPasted0">strcmp(headmodel.type,<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'dipoli'</span><span class="ContentPasted0">)</span></span></div>
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<span class=""><span class="ContentPasted0"> scalp_index = 1;</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(14, 0, 255);">end</span></span></div>
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<span class=""><span class="ContentPasted0">cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.method =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'project'</span><span class="ContentPasted0">;<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%
onto scalp surface</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.headshape = headmodel.bnd(scalp_index);<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(0, 128, 19);">% scalp surface</span></span></div>
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<span class=""><span class="ContentPasted0">eegData.elec = ft_electroderealign(cfg, eegData.elec);</span></span></div>
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<span class=""><span class="ContentPasted0">cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.headmodel = headmodel;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.elec = eegData.elec;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.grid.resolution = 4;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.grid.unit =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'mm'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.channel =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'all'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">grid = ft_prepare_leadfield(cfg);</span></span></div>
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<span class=""><span class="ContentPasted0">cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.covariance =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'yes'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.covariancewindow =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'all'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">timelock_allexp = ft_timelockanalysis(cfg, eegData);</span></span></div>
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<span class=""><span class="ContentPasted0">cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.covariance =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'yes'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.covariancewindow =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'all'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.keeptrials =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'yes'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">timelock_allexp_all = ft_timelockanalysis(cfg, eegData);</span></span></div>
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<span class=""><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%General source localisation</span></span></div>
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<span class=""><span class="ContentPasted0">cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.headmodel = vol;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.elec = timelock_allexp.elec;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.grid = grid;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.method =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'lcmv'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.lcmv.fixedori =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'yes'</span><span class="ContentPasted0">; </span><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%Project
onto largest variance orientation</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.lcmv.keepfilter =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'yes'</span><span class="ContentPasted0">;<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%Keep
the beamformer weights</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.lcmv.lambda =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'5%'</span><span class="ContentPasted0">;<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(0, 128, 19);">%Regularise
a little</span></span></div>
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<span class=""><span class="ContentPasted0">source_allexp = ft_sourceanalysis(cfg, timelock_allexp);</span></span></div>
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<span class=""><span class="ContentPasted0">cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.method =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'nearest'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.parameter =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'tissue'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">grid2 = ft_sourceinterpolate(cfg,atlas,grid);</span></span></div>
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<span class=""><span class="ContentPasted0">grid2.tissue = fix(grid2.tissue);</span></span></div>
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<span class=""><span class="ContentPasted0">grid2.tissuelabel = atlas.tissuelabel;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.parcellation =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'tissue'</span><span class="ContentPasted0">;</span></span></div>
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<span class=""><span class="ContentPasted0">cfg.method =<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="color: rgb(167, 9, 245);">'svd'</span><span class="ContentPasted0">;</span></span></div>
<span class="lineNode" style="font-size: 10pt; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-weight: normal;"><span class=""><span class="ContentPasted0">roiData = ft_virtualchannel(cfg,timelock_allexp_all,source_allexp,grid2);</span></span></span></div>
<br class="">
</div>
</div>
<span style="caret-color: rgb(0, 0, 0); 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; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; text-decoration: none; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" 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="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class="">
<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!8MfiFIKtdQjMkyMZdUcN7LmshWPRfmD4iH9-ablz_WARh4VUTy1Q4Z6Rf5hkNoxCt_1GwDE6GE75pQLjQVrBaYw5Gq8tPGnJtl-UkA$" 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>
</blockquote>
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