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Hi all,<br>
<br>
A follow up on this and some new issues:<br>
<br>
1) I first tried Jörn's approach by creating my own BEM, always fun
to make it yourself ;) However, I did not succeed since:<br>
a) the dipoli method does not work on Windows<br>
b) I downloaded the openmeeg toolbox, but got an error
"om_minverser.exe has stopped working" I've emailed their buglist<br>
c) bemcp did run, but the result was not ok (see attachement). I
also got the warning "% Warning: Matrix is singular, close to
singular or badly scaled. Results may be inaccurate." several times,
so that might be the problem.<br>
d) and asa gave the following error: % Error using
ft_prepare_headmodel (line 201) % You must supply a valid
cfg.hdmfile for use with ASA headmodel<br>
<br>
And away went my determination to do it myself, so I continued using
the<a
href="http://fieldtrip.fcdonders.nl/template/headmodel?s[]=standard&s[]=bem">
standard_bem.mat</a>. (I did not know this existed, I've added
this link to note in the <a
href="http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?&#background">headmodel
tutorial</a> to make it easier to find, thanks Tzvetan for
pointing this out!).<br>
<br>
2) This worked and after some fiddling to get the electrodes aligned
it looks okay (see attached). <br>
However, as you can see in the figures, I have several very low
electrodes, that are lower than the skin mesh. So I was wondering if
this is a problem? Since for accurate calculation of how the
currents flow from these low electrodes, I assume one needs the skin
to go till there? What happens when I have electrodes floating in
thin air? <br>
<b>So my question is:</b><br>
a) will this cause great inaccuracies?<br>
b) if so, how can I extend the skin to go lower? The template MRI
only goes that far to the bottom... Trick anyone?<br>
<br>
Thanks again,<br>
Ingrid<br>
<br>
<br>
<div class="moz-cite-prefix">On 4/9/2013 9:39 AM, Ingrid Nieuwenhuis
wrote:<br>
</div>
<blockquote cite="mid:5164443E.5040909@berkeley.edu" type="cite">
<meta content="text/html; charset=ISO-8859-1"
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Thanks Jörn and Tzvetan for the scripts! I'll try it out and put
it on the wiki.<br>
Have a great day,<br>
Ingrid<br>
<br>
<div class="moz-cite-prefix">On 4/9/2013 12:32 AM, Tzvetan Popov
wrote:<br>
</div>
<blockquote
cite="mid:43CC12AA-D78E-4374-A201-FD4F7B2C8736@uni-konstanz.de"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
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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>
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<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 moz-do-not-send="true" 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 moz-do-not-send="true" 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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<div>*******************************************</div>
<div>Tzvetan Popov </div>
<div>Clinical Psychology </div>
<div>University of Konstanz</div>
<div>Box 23</div>
<div>78457 Konstanz, GERMANY</div>
<div>Phone: 0049-7531-883086</div>
<div>Fax: 0049-7531-884601</div>
<div>Email: <a moz-do-not-send="true"
href="mailto:tzvetan.popov@uni-konstanz.de">tzvetan.popov@uni-konstanz.de</a></div>
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<pre class="moz-signature" cols="72">--
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305 </pre>
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<br>
<pre class="moz-signature" cols="72">--
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305 </pre>
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