[FieldTrip] source analysis EEG data without MRI
Ingrid Nieuwenhuis
inieuwenhuis at berkeley.edu
Thu Apr 11 05:44:40 CEST 2013
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:
>
> 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 at science.ru.nl
> [mailto:fieldtrip-bounces at science.ru.nl] *On Behalf Of *Ingrid Nieuwenhuis
> *Sent:* Thursday, 11 April 2013 4:22 AM
> *To:* fieldtrip at science.ru.nl
> *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:
> http://fieldtrip.fcdonders.nl/template/headmodel?s[]=standard&s[]=bem
> <http://fieldtrip.fcdonders.nl/template/headmodel?s%5b%5d=standard&s%5b%5d=bem>
> 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:* fieldtrip-bounces at science.ru.nl
> <mailto:fieldtrip-bounces at science.ru.nl>
> [fieldtrip-bounces at science.ru.nl
> <mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Ingrid
> Nieuwenhuis
> [inieuwenhuis at berkeley.edu <mailto:inieuwenhuis at berkeley.edu>]
> *Sent:* Wednesday, 10 April 2013 9:29 AM
> *To:* fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>
> *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
> <http://fieldtrip.fcdonders.nl/template/headmodel?s[]=standard&s[]=bem>
> <http://fieldtrip.fcdonders.nl/template/headmodel?s%5b%5d=standard&s%5b%5d=bem>.
>
> (I did not know this existed, I've added this link to note in the
> headmodel tutorial
> <http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?&#background>
> <http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?&#background>
> 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:
> E-Mail:jm.horschig at donders.ru.nl
> <mailto:E-Mail:jm.horschig at donders.ru.nl>
> Tel:+31-(0)24-36-68493 <Tel:+31-%280%2924-36-68493>
> Web:http://www.ru.nl/donders
>
> 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: tzvetan.popov at uni-konstanz.de
> <mailto:tzvetan.popov at uni-konstanz.de>
> <mailto:tzvetan.popov at uni-konstanz.de>
> <mailto:tzvetan.popov at uni-konstanz.de>
> *******************************************
>
>
>
>
>
>
>
>
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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
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> --
> 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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