[FieldTrip] source analysis EEG data without MRI
Ingrid Nieuwenhuis
inieuwenhuis at berkeley.edu
Fri Apr 12 20:08:31 CEST 2013
Hi Lilla,
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:
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.
Thanks,
Ingrid
On 4/12/2013 8:03 AM, Lilla.Magyari at mpi.nl wrote:
> 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
>
>
>
>> 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
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>> <mailto:fieldtrip at donders.ru.nl>
>>> <mailto:fieldtrip at donders.ru.nl>
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> *******************************************
>>> 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>
>>> *******************************************
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>>
>>>
>>> --
>>> 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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>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>>
>>>
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>>>
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>>>
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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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