[FieldTrip] source analysis EEG data without MRI
Ingrid Nieuwenhuis
inieuwenhuis at berkeley.edu
Tue Apr 9 18:39:26 CEST 2013
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>
> *******************************************
>
>
>
>
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>
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> 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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