[FieldTrip] source analysis EEG data without MRI

Wed Apr 10 19:17:04 CEST 2013

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
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
>> [fieldtrip-bounces at science.ru.nl] on behalf of Ingrid Nieuwenhuis
>> [inieuwenhuis at berkeley.edu]
>> *Sent:* Wednesday, 10 April 2013 9:29 AM
>> *To:* 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>.
>> (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> 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
>>>>> Tel:+31-(0)24-36-68493
>>>>> 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>
>>>>> 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>
>>>> *******************************************
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> 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
>>> 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
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
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> fieldtrip at donders.ru.nl
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