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<div class="moz-cite-prefix">Hi Lilla and Imali,<br>
<br>
Thanks for your replies. In my case, the problem is not the
aligning. My nasion electrode is on the nasion, and Cz is on Cz,
everything is where it should be. The EGI 128 electrode net really
has these low electrodes, which are there specifically to make
source analysis better by capturing more of the electric field. So
I would have the best solution if I'd leave them there. However,
in the model as derived from the MNI template, the skin part does
not go down low enough.<br>
<br>
I looked at the picture after ft_prepare_vol_sens (see
attachement, black is before, red is after), and indeed, this is
not good. The low electrodes are squeezed up, and this will make
source analysis worse. So I should indeed remove these electrodes
(which is a pity), or find a better MNI template.<br>
<br>
<b>So my question is:</b><br>
Does anyone know of a template in MNI space that extends more
down? This template comes from SPM8, is there a version that
extends lower? Or could I extend the skin roughly downwards with
some triangular magic?<br>
<br>
I'm also a bit confused about the statement on this wiki page: <a
href="http://fieldtrip.fcdonders.nl/template/headmodel?s[]=standard&s[]=bem">http://fieldtrip.fcdonders.nl/template/headmodel?s[]=standard&s[]=bem</a><br>
under "revision information" header "skin" is says: "This skin
surface is not used in the BEM model itself for computational
reasons, but can be used for visualization."<br>
But this does not seem to be the case, since my electrode
positions are modified based on till where the skin goes. So the
skin surface does significantly influence the source analysis. <br>
<br>
Anyway, thanks for all the help, and worse case, I just get rid of
the low fellows.<br>
<br>
Cheers,<br>
Ingrid<br>
<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>
On 4/10/2013 9:05 AM, Magyari, Lilla wrote:<br>
</div>
<blockquote cite="mid:51658DAE.9080207@mpi.nl" type="cite">hi Ingrid
and Imali,
<br>
<br>
<br>
I think it is a really good question what to do in Ingrid's case.
I do not know the "right" answer, but I would like to share my
thoughts about it.
<br>
<br>
The ft_prepare_vol_sens is indeed projects the electrode positions
closer to the headsurface as Imali wrote. But this function called
automatically when you create your leadfield, so you do not have
to do it separately (unless you want to visualize the corrected
electrode positions).
<br>
<br>
However, I have been advised to rely on this projection carefully
if electrode positions are far from the skin and specially, if the
inaccuracies (distance from the skin) are not equally distributed
across the electrodes, because that can cause a spatial bias.
<br>
<br>
Therefore, my question would be: why are those electrodes so low?
Are those positions reflect the actual positions of the electrodes
during the measurement? If yes, I would not change their
positions, I would rather try to extend my headmodel e.g. by using
another template. (or another (but quite suboptimal) possibility
is maybe to exclude those electrodes (and the data) from the
analysis if they are anyway far from the brain.)
<br>
<br>
If the position of the electrodes should be higher up on the head,
then instead of relying on projection, I would try first to scale
the electrodes to fit them into the headsurface with the
ft_electroderealign function.
<br>
<br>
I looked to the standard_bem file in the template directory, and I
also load in the standard_1020.elc, and those electrodes perfectly
fit the vol. So, it seems that the extension of the standard bem
headsurface is suitable for the area which is covered by the those
template electrodes. And I do not know if the electrode set you
use should cover a larger surface of the head, or if it should be
just adjusted to the given headsurface.
<br>
<br>
Lilla
<br>
<br>
<br>
<br>
<br>
IMALI THANUJA HETTIARACHCHI wrote:
<br>
<blockquote type="cite">Hi Ingrid,
<br>
<br>
I had a similar issue a few weeks ago, where my lower most
electrodes
<br>
started floating after electrode realign using the
ft_electroderealign
<br>
function.
<br>
<br>
I used the ft_prepare_vol_sens as,
<br>
[vol, elecR]=ft_prepare_vol_sens (col,elecR) and this did the
trick and
<br>
brought the electrodes on to the skin.
<br>
<br>
Hope this helps...!
<br>
<br>
Regards
<br>
Imali
<br>
<br>
<br>
*From:* <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>
<br>
[<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>] on behalf of Ingrid
Nieuwenhuis
<br>
[<a class="moz-txt-link-abbreviated" href="mailto:inieuwenhuis@berkeley.edu">inieuwenhuis@berkeley.edu</a>]
<br>
*Sent:* Wednesday, 10 April 2013 9:29 AM
<br>
*To:* <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>
<br>
*Subject:* Re: [FieldTrip] source analysis EEG data without MRI
<br>
<br>
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
<br>
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
<br>
has stopped working" I've emailed their buglist
<br>
c) bemcp did run, but the result was not ok (see attachement). I
also
<br>
got the warning "% Warning: Matrix is singular, close to
singular or
<br>
badly scaled. Results may be inaccurate." several times, so that
might
<br>
be the problem.
<br>
d) and asa gave the following error: % Error using
ft_prepare_headmodel
<br>
(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
<br>
thestandard_bem.mat
<br>
<a class="moz-txt-link-rfc2396E" href="http://fieldtrip.fcdonders.nl/template/headmodel?s[]=standard&s[]=bem"><http://fieldtrip.fcdonders.nl/template/headmodel?s[]=standard&s[]=bem></a>.
<br>
(I did not know this existed, I've added this link to note in
the
<br>
headmodel tutorial
<br>
<a class="moz-txt-link-rfc2396E" href="http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?&#background"><http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?&#background></a>
to
<br>
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
<br>
looks okay (see attached).
<br>
However, as you can see in the figures, I have several very low
<br>
electrodes, that are lower than the skin mesh. So I was
wondering if
<br>
this is a problem? Since for accurate calculation of how the
currents
<br>
flow from these low electrodes, I assume one needs the skin to
go till
<br>
there? What happens when I have electrodes floating in thin air?
<br>
*So my question is:*
<br>
a) will this cause great inaccuracies?
<br>
b) if so, how can I extend the skin to go lower? The template
MRI only
<br>
goes that far to the bottom... Trick anyone?
<br>
<br>
Thanks again,
<br>
Ingrid
<br>
<br>
<br>
On 4/9/2013 9:39 AM, Ingrid Nieuwenhuis wrote:
<br>
<blockquote type="cite">Thanks Jörn and Tzvetan for the scripts!
I'll try it out and put it on
<br>
the wiki.
<br>
Have a great day,
<br>
Ingrid
<br>
<br>
On 4/9/2013 12:32 AM, Tzvetan Popov wrote:
<br>
<blockquote type="cite">Dear Ingrid,
<br>
<br>
in addition to Jorn's approach since you don't have MR and
digitized
<br>
elec position's you can load and realign the electrodes to
the
<br>
standard bem. Subsequently you can calculate the lead field
and
<br>
continue with your analysis pipeline.
<br>
Good luck
<br>
tzvetan
<br>
%% read electrodes
<br>
elec = ft_read_sens('/your
<br>
path/fieldtrip-20130324/template/electrode/GSN-HydroCel-128.sfp');
<br>
%% read headmodel
<br>
templateheadmodel = '/your
<br>
path/fieldtrip-20130324/template/headmodel/standard_bem.mat';
<br>
load(templateheadmodel);
<br>
%% electrode realign as good as possible
<br>
% i.e. translate 0 -2 1.5
<br>
cfg=[];
<br>
cfg.method = 'interactive';
<br>
cfg.elec = elec;
<br>
cfg.headshape = vol.bnd(1).pnt;
<br>
elecR = ft_electroderealign(cfg);
<br>
%% verify how the electrodes fit toghether with the brain
volume
<br>
cfg=[];
<br>
cfg.method = 'interactive';
<br>
cfg.elec = elecR;
<br>
cfg.headshape = vol.bnd(3).pnt;
<br>
elecR = ft_electroderealign(cfg);
<br>
<br>
<br>
<blockquote type="cite">Hi Ingrid,
<br>
<br>
I just happen to done this a few weeks back, I changed
things in the
<br>
meanwhile, but I hope that the below steps are complete:
<br>
/% read in the template MRI
<br>
if isunix
<br>
mri =
<br>
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',
<br>
'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',
<br>
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
<br>
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))/
<br>
<br>
<br>
Afair, that's all that is needed. Of course you need to
adjust
<br>
folder and file names.
<br>
<br>
Greetings
<br>
Jörn
<br>
<br>
On 4/9/2013 2:04 AM, Ingrid Nieuwenhuis wrote:
<br>
<blockquote type="cite">Hi all,
<br>
<br>
I'd like to do source analysis (loreta and or DICS) on
my EEG data.
<br>
I don't have anatomical MRIs and I don't have a
measurement of the
<br>
scalp surface. So I'd like to use a template MRI or a
template head
<br>
model that is located in the FieldTrip template
directory. I have
<br>
EGI (128 channels) data and electrode positions (not
subject
<br>
specific, just the standard file also available in
FieldTrip
<br>
electrode template, GSN-HydroCel-128.sfp), but I'm kind
of stuck
<br>
how to start. I don't see any examples on the FieldTrip
page of how
<br>
to make a headmodel and volume conduction model giving
only this
<br>
limited data. I'd be happy to make it into a example
Matlab script
<br>
on the FieldTrip page after I got it to work. Would
someone be able
<br>
to give me some pointers, or example code?
<br>
<br>
Thanks a lot!
<br>
Ingrid
<br>
<br>
</blockquote>
<br>
<br>
--
<br>
Jörn M. Horschig
<br>
PhD Student
<br>
Donders Institute for Brain, Cognition and Behaviour
<br>
Centre for Cognitive Neuroimaging
<br>
Radboud University Nijmegen
<br>
Neuronal Oscillations Group
<br>
FieldTrip Development Team
<br>
<br>
P.O. Box 9101
<br>
NL-6500 HB Nijmegen
<br>
The Netherlands
<br>
<br>
Contact:
<br>
<a class="moz-txt-link-abbreviated" href="mailto:E-Mail:jm.horschig@donders.ru.nl">E-Mail:jm.horschig@donders.ru.nl</a>
<br>
Tel:+31-(0)24-36-68493
<br>
Web:<a class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
<br>
<br>
Visiting address:
<br>
Trigon, room 2.30
<br>
Kapittelweg 29
<br>
NL-6525 EN Nijmegen
<br>
The Netherlands
<br>
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<br>
</blockquote>
<br>
*******************************************
<br>
Tzvetan Popov
<br>
Clinical Psychology
<br>
University of Konstanz
<br>
Box 23
<br>
78457 Konstanz, GERMANY
<br>
Phone: 0049-7531-883086
<br>
Fax: 0049-7531-884601
<br>
Email: <a class="moz-txt-link-abbreviated" href="mailto:tzvetan.popov@uni-konstanz.de">tzvetan.popov@uni-konstanz.de</a>
<br>
<a class="moz-txt-link-rfc2396E" href="mailto:tzvetan.popov@uni-konstanz.de"><mailto:tzvetan.popov@uni-konstanz.de></a>
<br>
*******************************************
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<br>
</blockquote>
<br>
--
<br>
Ingrid Nieuwenhuis PhD
<br>
Postdoctoral Fellow
<br>
Sleep and Neuroimaging Laboratory
<br>
Department of Psychology
<br>
University of California, Berkeley
<br>
California 94720-1650
<br>
Tolman Hall, room 5305
<br>
<br>
<br>
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<br>
</blockquote>
<br>
--
<br>
Ingrid Nieuwenhuis PhD
<br>
Postdoctoral Fellow
<br>
Sleep and Neuroimaging Laboratory
<br>
Department of Psychology
<br>
University of California, Berkeley
<br>
California 94720-1650
<br>
Tolman Hall, room 5305
<br>
<br>
<br>
<br>
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