[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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>         fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
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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
>
>
>
>         _______________________________________________
>         fieldtrip mailing list
>         fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>         http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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