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Hi Lilla,<br>
<br>
Yeah, the skull, I was thinking about that too. So if I understand
the pics you sent, the skull is now extended as if it's massive just
under the skin. I don't know enough about the volume conduction
model and the exact effect of the skull/skin in it to really know
what would be better: Not extended skull or massive extended skull.
But here's my 2 cents:<br>
<br>
In my case, the low electrodes are mostly on the cheek and low in
the neck. As you can see on the pic I attached to this email, the
neck bone does not extend that low, and the cheek doesn't really
have bone. So, I'm not sure the extended massive-bone one would be
better. Best would be of course to segment the real bone from the
MRI, but I have no clue how the segmentation magic takes place,
probably is not trivial. Currently it only finds the not extended
skull. And making the rest of the bone, if you could segment it,
into a mesh is not possible I think, so it has to be sort of massive
(meshable). So indeed, to extend or not to extend, that's the
question. Probably depends on the location of the low electrodes. I
think in my case I would tend to lean towards choosing not to
extend.<br>
<br>
Thanks,<br>
Ingrid <br>
<br>
<br>
<div class="moz-cite-prefix">On 4/12/2013 8:03 AM,
<a class="moz-txt-link-abbreviated" href="mailto:Lilla.Magyari@mpi.nl">Lilla.Magyari@mpi.nl</a> wrote:<br>
</div>
<blockquote
cite="mid:51507.131.174.45.70.1365778991.squirrel@131.174.45.70"
type="cite">
<pre wrap="">hi Ingrid,
I would like to comment on this because I have been discussing this with
Robert, and we thought that for the lower electrodes, it is still not
optimal when only the skin is extended which is more conductive then the
skull. I have attached two images for illustration. The FT segmentation
will produce the segmentation in origskull.jpg. This is fine when the
electrodes do not extend lower than the skull. When the electrodes are
lower, a segmentation like the one in extendedskull.jpg is probably more
useful.
I created this extended skull based on the skin segmentation with the
imerode function of the matlab image processing toolbox
(imerode(seg.skin,strel_bol(5)), strel_bol is from fieldtrip/private).
Best,
Lilla
</pre>
<blockquote type="cite">
<pre wrap="">Hi Imali,
Tzvetan shared the bem model made from the tutorial MRI with me, that
one extends to low enough, so I'm good! Thanks a lot though!
Cheers,
Ingird
--
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305
On 4/10/2013 6:14 PM, IMALI THANUJA HETTIARACHCHI wrote:
</pre>
<blockquote type="cite">
<pre wrap="">
Hi Ingrid,
I had similar issues with creating my own BEM as I too did not have
the individual MRI's nor the digitized electrode positions.
I created a BEM using the Curry (Neuroscan) software and imported in
.mat format to use with Fieldtrip. However these are also based on the
MNI template.
I am not sure whether this extends lower enough for your situation. I
am attaching here a picture of my head model showing the skull and
cortex with my registered electrodes. If you are happy with it, I am
more than happy to share it with you.
Please let me know.
Regards
Imali
*From:*fieldtrip-bounces@science.ru.nl
[<a class="moz-txt-link-freetext" href="mailto:fieldtrip-bounces@science.ru.nl">mailto:fieldtrip-bounces@science.ru.nl</a>] *On Behalf Of *Ingrid
Nieuwenhuis
*Sent:* Thursday, 11 April 2013 4:22 AM
*To:* <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>
*Subject:* Re: [FieldTrip] source analysis EEG data without MRI
Hi all,
Just had a brain wave, I'll share it for people with similar situation
that might be interested in this thread. I think I should just get a
random structural MRI that extends lower (includes ears and bit
below), optimally of a subject with a head similar to the MNI
template. Make a BEM model (hmm, have to fix these errors I mentioned
earlier then, well, should be doable on linux using dipoli). Then use
ft_electroderealign to align the electrodes to this MRI, do the source
analysis for all subjects using this model, and subsequently use
ft_volumenormalise to normalize to MNI template if I want to use any
atlas functionality.
If anyone did this already using FieldTrip and has a pre-made BEM
(just like the standard_bem), would be really nice if you're willing
to share :)
If not, I'll make my own, and people with low electrodes and no
structural MRI and or no linux access can email me if they want to use
it.
Cheers,
Ingrid
--
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305
On 4/10/2013 10:17 AM, Ingrid Nieuwenhuis wrote:
Hi Lilla and Imali,
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.
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.
*So my question is:*
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?
I'm also a bit confused about the statement on this wiki page:
<a class="moz-txt-link-freetext" href="http://fieldtrip.fcdonders.nl/template/headmodel?s">http://fieldtrip.fcdonders.nl/template/headmodel?s</a>[]=standard&s[]=bem
<a class="moz-txt-link-rfc2396E" href="http://fieldtrip.fcdonders.nl/template/headmodel?s%5b%5d=standard&s%5b%5d=bem"><http://fieldtrip.fcdonders.nl/template/headmodel?s%5b%5d=standard&s%5b%5d=bem></a>
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."
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.
Anyway, thanks for all the help, and worse case, I just get rid of
the low fellows.
Cheers,
Ingrid
--
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305
On 4/10/2013 9:05 AM, Magyari, Lilla wrote:
hi Ingrid and Imali,
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.
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).
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.
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.)
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.
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.
Lilla
IMALI THANUJA HETTIARACHCHI wrote:
Hi Ingrid,
I had a similar issue a few weeks ago, where my lower most
electrodes
started floating after electrode realign using the
ft_electroderealign
function.
I used the ft_prepare_vol_sens as,
[vol, elecR]=ft_prepare_vol_sens (col,elecR) and this did the
trick and
brought the electrodes on to the skin.
Hope this helps...!
Regards
Imali
*From:* <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>
<a class="moz-txt-link-rfc2396E" href="mailto:fieldtrip-bounces@science.ru.nl"><mailto:fieldtrip-bounces@science.ru.nl></a>
[<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>
<a class="moz-txt-link-rfc2396E" href="mailto:fieldtrip-bounces@science.ru.nl"><mailto:fieldtrip-bounces@science.ru.nl></a>] on behalf of Ingrid
Nieuwenhuis
[<a class="moz-txt-link-abbreviated" href="mailto:inieuwenhuis@berkeley.edu">inieuwenhuis@berkeley.edu</a> <a class="moz-txt-link-rfc2396E" href="mailto:inieuwenhuis@berkeley.edu"><mailto:inieuwenhuis@berkeley.edu></a>]
*Sent:* Wednesday, 10 April 2013 9:29 AM
*To:* <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a> <a class="moz-txt-link-rfc2396E" href="mailto:fieldtrip@science.ru.nl"><mailto:fieldtrip@science.ru.nl></a>
*Subject:* Re: [FieldTrip] source analysis EEG data without MRI
Hi all,
A follow up on this and some new issues:
1) I first tried Jörn's approach by creating my own BEM,
always fun to
make it yourself ;) However, I did not succeed since:
a) the dipoli method does not work on Windows
b) I downloaded the openmeeg toolbox, but got an error
"om_minverser.exe
has stopped working" I've emailed their buglist
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.
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
And away went my determination to do it myself, so I continued
using
thestandard_bem.mat
<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>
<a class="moz-txt-link-rfc2396E" href="http://fieldtrip.fcdonders.nl/template/headmodel?s%5b%5d=standard&s%5b%5d=bem"><http://fieldtrip.fcdonders.nl/template/headmodel?s%5b%5d=standard&s%5b%5d=bem></a>.
(I did not know this existed, I've added this link to note in
the
headmodel tutorial
<a class="moz-txt-link-rfc2396E" href="http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?&#background"><http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?&#background></a>
<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
make it easier to find, thanks Tzvetan for pointing this out!).
2) This worked and after some fiddling to get the electrodes
aligned it
looks okay (see attached).
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?
*So my question is:*
a) will this cause great inaccuracies?
b) if so, how can I extend the skin to go lower? The template
MRI only
goes that far to the bottom... Trick anyone?
Thanks again,
Ingrid
On 4/9/2013 9:39 AM, Ingrid Nieuwenhuis wrote:
Thanks Jörn and Tzvetan for the scripts! I'll try it out and
put it on
the wiki.
Have a great day,
Ingrid
On 4/9/2013 12:32 AM, Tzvetan Popov wrote:
Dear Ingrid,
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.
Good luck
tzvetan
%% read electrodes
elec = ft_read_sens('/your
path/fieldtrip-20130324/template/electrode/GSN-HydroCel-128.sfp');
%% read headmodel
templateheadmodel = '/your
path/fieldtrip-20130324/template/headmodel/standard_bem.mat';
load(templateheadmodel);
%% electrode realign as good as possible
% i.e. translate 0 -2 1.5
cfg=[];
cfg.method = 'interactive';
cfg.elec = elec;
cfg.headshape = vol.bnd(1).pnt;
elecR = ft_electroderealign(cfg);
%% verify how the electrodes fit toghether with the brain volume
cfg=[];
cfg.method = 'interactive';
cfg.elec = elecR;
cfg.headshape = vol.bnd(3).pnt;
elecR = ft_electroderealign(cfg);
Hi Ingrid,
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:
/% read in the template MRI
if isunix
mri =
ft_read_mri('/home/common/matlab/fieldtrip/external/spm8/templates/T1.nii');
elseif ispc
mri = ft_read_mri(fullfile('M:', 'FieldTrip', 'trunk',
'external',
'spm8', 'templates', 'T1.nii'));
end
% segment the MRI
cfg = [];
cfg.output = {'brain' 'skull' 'scalp'};
segmentedmri = ft_volumesegment(cfg, mris);
% create the headmodel (BEM)
cfg = [];
%cfg.method ='openmeeg'; % TODO FIXME download openmeeg
if isunix
cfg.method ='dipoli'; % dipoli only works under linux
else
disp('TODO FIXME stick to dipoli for now or download
openmeeg\n');
keyboard;
end
hdm = ft_prepare_headmodel(cfg, segmentedmri);
elec = ft_read_sens('standard_1020.elc');
hdm = ft_convert_units(hdm, elec.unit);
cfg = [];
cfg.grid.xgrid = -125:8:125;
cfg.grid.ygrid = -125:8:125;
cfg.grid.zgrid = -125:8:125;
cfg.grid.tight = 'yes';
cfg.grid.unit = hdm.unit;
cfg.inwardshift = -1.5;
cfg.vol = hdm;
grid = ft_prepare_sourcemodel(cfg)
grid = ft_convert_units(grid, elec.unit);
figure;
hold on;
ft_plot_mesh(hdm.bnd(1), 'facecolor',[0.2 0.2 0.2], 'facealpha',
0.3, 'edgecolor', [1 1 1], 'edgealpha', 0.05);
ft_plot_mesh(grid.pos(grid.inside, :));
% this step is not necessary, cause you will see that
everything is
already aligned
cfg = [];
cfg.method = 'interactive';
cfg.elec = elec;
cfg.headshape = hdm.bnd(1);
tmp = ft_electroderealign(cfg);
elec = tmp; % I had a bug here that I couldn't assign elec
directly
%% verify location of occipital electrodes
occ_elec = elec;
occ_chan = ft_channelselection({'O*', 'PO*', 'Cz*', 'Fz*'},
elec.label);
occ_idx = match_str(elec.label, occ_chan);
occ_elec.chanpos = occ_elec.chanpos(occ_idx, :);
occ_elec.elecpos = occ_elec.elecpos(occ_idx, :);
occ_elec.label = occ_elec.label(occ_idx, :);
figure;
ft_plot_sens(occ_elec)
hold on;
ft_plot_vol(ft_convert_units(hdm, elec.unit))/
Afair, that's all that is needed. Of course you need to adjust
folder and file names.
Greetings
Jörn
On 4/9/2013 2:04 AM, Ingrid Nieuwenhuis wrote:
Hi all,
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?
Thanks a lot!
Ingrid
--
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:
<a class="moz-txt-link-abbreviated" href="mailto:E-Mail:jm.horschig@donders.ru.nl">E-Mail:jm.horschig@donders.ru.nl</a>
<a class="moz-txt-link-rfc2396E" href="mailto:E-Mail:jm.horschig@donders.ru.nl"><mailto:E-Mail:jm.horschig@donders.ru.nl></a>
Tel:+31-(0)24-36-68493 <Tel:+31-%280%2924-36-68493>
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
_______________________________________________
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*******************************************
Tzvetan Popov
Clinical Psychology
University of Konstanz
Box 23
78457 Konstanz, GERMANY
Phone: 0049-7531-883086
Fax: 0049-7531-884601
Email: <a class="moz-txt-link-abbreviated" href="mailto:tzvetan.popov@uni-konstanz.de">tzvetan.popov@uni-konstanz.de</a>
<a class="moz-txt-link-rfc2396E" href="mailto:tzvetan.popov@uni-konstanz.de"><mailto:tzvetan.popov@uni-konstanz.de></a>
<a class="moz-txt-link-rfc2396E" href="mailto:tzvetan.popov@uni-konstanz.de"><mailto:tzvetan.popov@uni-konstanz.de></a>
<a class="moz-txt-link-rfc2396E" href="mailto:tzvetan.popov@uni-konstanz.de"><mailto:tzvetan.popov@uni-konstanz.de></a>
*******************************************
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--
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305
_______________________________________________
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--
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305
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</pre>
</blockquote>
<pre wrap="">
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<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
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</blockquote>
</blockquote>
<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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