[FieldTrip] source analysis EEG data without MRI

Wed Apr 10 18:05:02 CEST 2013

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