<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Ingrid,<div><br></div><div>in addition to Jorn's approach since you don't have MR and digitized elec position's you can load and realign the electrodes to the standard bem. Subsequently you can calculate the lead field and continue with your analysis pipeline.</div><div>Good luck</div><div>tzvetan</div><div><div style="margin: 0px; font-size: 9px; font-family: Courier; color: rgb(37, 153, 45); ">%% read electrodes</div><div style="margin: 0px; font-size: 9px; font-family: Courier; color: rgb(178, 69, 243); "><span style="color: #000000">elec = ft_read_sens(</span>'/your path/fieldtrip-20130324/template/electrode/GSN-HydroCel-128.sfp'<span style="color: #000000">);</span></div><div style="margin: 0px; font-size: 9px; font-family: Courier; color: rgb(37, 153, 45); ">%% read headmodel</div><div style="margin: 0px; font-size: 9px; font-family: Courier; color: rgb(178, 69, 243); "><span style="color: #000000">templateheadmodel = </span>'/your path/fieldtrip-20130324/template/headmodel/standard_bem.mat'<span style="color: #000000">;</span></div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">load(templateheadmodel);</div><div style="margin: 0px; font-size: 9px; font-family: Courier; color: rgb(37, 153, 45); ">%% electrode realign as good as possible</div><div style="margin: 0px; font-size: 9px; font-family: Courier; color: rgb(37, 153, 45); ">% i.e. translate 0 -2 1.5</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">cfg=[];</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">cfg.method = <span style="color: #b245f3">'interactive'</span>;</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">cfg.elec = elec;</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">cfg.headshape = vol.bnd(1).pnt;</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">elecR = ft_electroderealign(cfg);</div><div style="margin: 0px; font-size: 9px; font-family: Courier; color: rgb(37, 153, 45); ">%% verify how the electrodes fit toghether with the brain volume</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">cfg=[];</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">cfg.method = <span style="color: #b245f3">'interactive'</span>;</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">cfg.elec = elecR;</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">cfg.headshape = vol.bnd(3).pnt;</div><div style="margin: 0px; font-size: 9px; font-family: Courier; ">elecR = ft_electroderealign(cfg);</div></div><div><br></div><div><div><br class="Apple-interchange-newline"><blockquote type="cite">
<meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type">
<div text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Hi Ingrid,<br>
<br>
I just happen to done this a few weeks back, I changed things in
the meanwhile, but I hope that the below steps are complete:<br>
<i><small>% read in the template MRI<br>
if isunix<br>
mri =
ft_read_mri('/home/common/matlab/fieldtrip/external/spm8/templates/T1.nii');<br>
elseif ispc<br>
mri = ft_read_mri(fullfile('M:', 'FieldTrip', 'trunk',
'external', 'spm8', 'templates', 'T1.nii'));<br>
end<br>
<br>
<br>
% segment the MRI<br>
cfg = [];<br>
cfg.output = {'brain' 'skull' 'scalp'};<br>
segmentedmri = ft_volumesegment(cfg, mris);<br>
<br>
<br>
% create the headmodel (BEM)<br>
cfg = [];<br>
%cfg.method ='openmeeg'; % TODO FIXME download openmeeg<br>
if isunix<br>
cfg.method ='dipoli'; % dipoli only works under linux<br>
else<br>
disp('TODO FIXME stick to dipoli for now or download
openmeeg\n');<br>
keyboard;<br>
end<br>
hdm = ft_prepare_headmodel(cfg, segmentedmri);<br>
<br>
elec = ft_read_sens('standard_1020.elc');<br>
hdm = ft_convert_units(hdm, elec.unit);<br>
<br>
cfg = [];<br>
cfg.grid.xgrid = -125:8:125; <br>
cfg.grid.ygrid = -125:8:125; <br>
cfg.grid.zgrid = -125:8:125;<br>
cfg.grid.tight = 'yes'; <br>
cfg.grid.unit = hdm.unit;<br>
cfg.inwardshift = -1.5;<br>
cfg.vol = hdm;<br>
grid = ft_prepare_sourcemodel(cfg)<br>
grid = ft_convert_units(grid, elec.unit);<br>
<br>
figure;<br>
hold on;<br>
ft_plot_mesh(hdm.bnd(1), 'facecolor',[0.2 0.2 0.2],
'facealpha', 0.3, 'edgecolor', [1 1 1], 'edgealpha', 0.05);<br>
ft_plot_mesh(grid.pos(grid.inside, :));<br>
<br>
% this step is not necessary, cause you will see that
everything is already aligned<br>
cfg = [];<br>
cfg.method = 'interactive';<br>
cfg.elec = elec;<br>
cfg.headshape = hdm.bnd(1);<br>
tmp = ft_electroderealign(cfg);<br>
elec = tmp; % I had a bug here that I couldn't assign elec
directly<br>
<br>
%% verify location of occipital electrodes<br>
<br>
occ_elec = elec;<br>
occ_chan = ft_channelselection({'O*', 'PO*', 'Cz*', 'Fz*'},
elec.label);<br>
occ_idx = match_str(elec.label, occ_chan);<br>
occ_elec.chanpos = occ_elec.chanpos(occ_idx, :);<br>
occ_elec.elecpos = occ_elec.elecpos(occ_idx, :);<br>
occ_elec.label = occ_elec.label(occ_idx, :);<br>
figure;<br>
ft_plot_sens(occ_elec)<br>
hold on;<br>
ft_plot_vol(ft_convert_units(hdm, elec.unit))</small></i><br>
<br>
<br>
Afair, that's all that is needed. Of course you need to adjust
folder and file names.<br>
<br>
Greetings<br>
Jörn<br>
<br>
On 4/9/2013 2:04 AM, Ingrid Nieuwenhuis wrote:<br>
</div>
<blockquote cite="mid:51635B04.7090004@berkeley.edu" type="cite">Hi
all,
<br>
<br>
I'd like to do source analysis (loreta and or DICS) on my EEG
data. I don't have anatomical MRIs and I don't have a measurement
of the scalp surface. So I'd like to use a template MRI or a
template head model that is located in the FieldTrip template
directory. I have EGI (128 channels) data and electrode positions
(not subject specific, just the standard file also available in
FieldTrip electrode template, GSN-HydroCel-128.sfp), but I'm kind
of stuck how to start. I don't see any examples on the FieldTrip
page of how to make a headmodel and volume conduction model giving
only this limited data. I'd be happy to make it into a example
Matlab script on the FieldTrip page after I got it to work. Would
someone be able to give me some pointers, or example code?
<br>
<br>
Thanks a lot!
<br>
Ingrid
<br>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Contact:
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>
Tel: +31-(0)24-36-68493
Web: <a class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands</pre>
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