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Hi everyone,</div>
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I have added my code below for source reconstruction on a grid based on the standard_bem headmodel, and am wondering if there is an easy way to map my grid coordinates to the destrieux atlas, or another atlas (like AAL).<br>
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%% create a head model || vol is standard bem from FT<br>
load('/rcg/bcni/users/Evan/fieldtrip-20190912/template/headmodel/standard_bem.mat')<br>
headmodel = vol;<br>
headmodel = ft_convert_units(headmodel, 'm');<br>
<br>
<br>
cfg=[];<br>
cfg.resolution = .015; %headmodel resolution(was 0.008)<br>
cfg.headmodel = headmodel;<br>
source_model = ft_prepare_sourcemodel(cfg);<br>
<br>
%% align electrodes to head model<br>
elec = ft_read_sens('standard_1020.elc');<br>
elec = ft_convert_units(elec, 'm');<br>
<br>
scalp_index = 1; %scalp is 1<br>
<br>
cfg = [];<br>
cfg.method = 'project'; % onto scalp surface<br>
cfg.headshape = headmodel.bnd(scalp_index); % scalp surface<br>
elec_realigned = ft_electroderealign(cfg,elec);<br>
<br>
% end<br>
<br>
%% align electrodes<br>
% for subject<br>
[v, ix, ixx] = intersect(elec_realigned.label, interp.label);<br>
elecICA = elec_realigned;<br>
elecICA.chanpos = elecICA.chanpos(ix,:);<br>
elecICA.chantype = elecICA.chantype(ix,:);<br>
elecICA.chanunit = elecICA.chanunit(ix,:);<br>
elecICA.elecpos = elecICA.elecpos(ix,:);<br>
elecICA.label = elecICA.label(ix);<br>
elecICA.tra = elecICA.tra(ix, ix); %cant find<br>
<br>
%% leadfield<br>
<br>
cfg = [];<br>
cfg.sourcemodel = source_model; %% where are the sources?<br>
cfg.headmodel = headmodel; %% how do currents spread?<br>
cfg.elec = elecICA;% how do sources and sensors connect?<br>
cfg.normalize = 'yes'; %was no<br>
leadfield = ft_prepare_leadfield(cfg,interp);<br>
<br>
<br>
<br>
%% source estimation via LCMV<br>
cfg = [];<br>
cfg.trials = 'all';<br>
cfg.channel = 'eeg';<br>
cfg.covariance = 'yes';<br>
cfg.covariancewindow = 'all';<br>
cfg.keeptrials = 'yes';<br>
cfg.removemean = 'yes';<br>
timelock = ft_timelockanalysis(cfg, interp);<br>
<br>
%LCMV BEAMFORMER to create spatial filter<br>
cfg = [];<br>
cfg.method = 'lcmv';<br>
cfg.grid = leadfield;<br>
cfg.headmodel = headmodel;<br>
cfg.elec = elecICA;<br>
cfg.lcmv.lambda = '5%';<br>
cfg.lcmv.projectmom = 'yes';<br>
cfg.lcmv.keepfilter = 'yes';<br>
cfg.lcmv.keepori = 'yes';<br>
cfg.lcmv.projectnoise = 'yes';<br>
sfilter = ft_sourceanalysis(cfg, timelock); % use this for your source reconstruction<br>
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%% Source analysis<br>
<br>
cfg = [];<br>
cfg.trials = 'all';<br>
cfg.trials = any(interp.trialinfo == [5],2);%<br>
cfg.covariance = 'yes';<br>
cfg.covariancewindow = 'all';<br>
cfg.keeptrials = 'yes';<br>
cfg.removemean = 'yes';<br>
timelock_trl_left = ft_timelockanalysis(cfg, interp);<br>
<br>
cfg = [];<br>
cfg.trials = 'all';<br>
cfg.trials = any(interp.trialinfo == [6],2);%<br>
cfg.covariance = 'yes';<br>
cfg.covariancewindow = 'all';<br>
cfg.keeptrials = 'yes';<br>
cfg.removemean = 'yes';<br>
timelock_trl_right = ft_timelockanalysis(cfg, interp);<br>
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<br>
% no need at this point to generate and save the time series<br>
cfg = [];<br>
cfg.method = 'lcmv';<br>
cfg.grid = leadfield;<br>
cfg.headmodel = headmodel;<br>
cfg.elec = elecICA;<br>
cfg.lcmv.lambda = '5%';<br>
cfg.lcmv.projectmom = 'yes';<br>
<br>
cfg.rawtrial = 'yes';<br>
cfg.grid.filter = sfilter.avg.filter; %sfilter taken from before<br>
cfg.lcmv.projectnoise = 'yes'; % noise estimation from the single value decomposition<br>
cfg.lcmv.keepmom = 'yes'; % saves the time series<br>
cfg.lcmv.fixedori = 'yes';<br>
cfg.keeptrials = 'yes'; %'no' or 'yes<br>
cfg.keepleadfield = 'yes';<br>
cfg.keepfilter = 'no';<br>
source_left = ft_sourceanalysis(cfg,timelock_trl_left);<br>
source_right = ft_sourceanalysis(cfg,timelock_trl_right)</div>
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Cheers,</p>
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Evan</p>
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<p><b></b>Evan Hutcheon<b></b></p>
<p>PhD Candidate|<span style="font-size:12pt">Dr. </span><span style="font-size:12pt">Doesburg laboratory </span></p>
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