<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; color: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif, "EmojiFont", "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
<p><font size="3" face="Calibri,Helvetica,sans-serif" color="black"><span id="divtagdefaultwrapper" style="font-size:12pt"></span></font></p>
<font size="3" face="Calibri,Helvetica,sans-serif" color="black">
<div><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px">Hi everyone,</span></font></div>
<div><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px"><br>
</span></font></div>
<div><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px">I was wondering if anyone could help me
<div>perform a transformation from </div>
<div>
<div style="margin:14pt 30pt;"><font style="font-family: Calibri, Helvetica, sans-serif, serif, "EmojiFont";" size="2" face="Calibri,Helvetica,sans-serif" color="black"><span style="font-size:16px;">
<div id="gmail-m_3061653227071342799divtagdefaultwrapper"><font size="3"><span style="font-size:12pt;" id="gmail-m_3061653227071342799divtagdefaultwrapper">
<div><font face="Calibri,Helvetica,sans-serif,serif,EmojiFont">cfg.headmodel = headmodel;</font></div>
</span></font></div>
</span></font></div>
to an atlas in the MNI space?</div>
<br>
</span></font></div>
<div><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px"><br>
</span></font></div>
<div><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px"><br>
</span></font></div>
<div><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px"><br>
</span></font></div>
<div><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px">%% 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>
<br>
%% 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>
<br>
<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)</span></font></div>
<br>
<div style="margin-top:0; margin-bottom:0"><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px"> </span></font></div>
<div style="margin-top:0; margin-bottom:0"><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px">Cheers,</span></font></div>
<div style="margin-top:0; margin-bottom:0"><font size="2" face="Calibri,Helvetica,sans-serif,serif,EmojiFont"><span style="font-size:16px">Evan</span></font></div>
</font><br>
<p></p>
<p><br>
</p>
<div id="Signature">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif,"EmojiFont","Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<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>
</div>
</div>
</div>
</body>
</html>