[FieldTrip] Fwd: Source Analysis from EEG data
Kasturi Barik
kash.kgp at gmail.com
Thu Jun 1 08:27:48 CEST 2017
Dear all,
As per last suggestion, I again focus on constructing head-model to generate
a proper forward model for localization purposes.
*CODE:*
%% 1. read the anatomical data with ft_read_mri;
load('standard_mri.mat');
disp(mri)
save mri mri
%% Align the coordinate system
cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'spm';
cfg.snapshot = 'yes';
[mri_aligned] = ft_volumerealign(cfg,mri);
save mri_aligned mri_aligned
%% 2. SEGMENTATION
% set path of means go to :
D:\MATLAB\toolbox\fieldtrip-20140401\external\spm8
cfg = [];
cfg.output = {'brain','skull','scalp'};
segmentedmri = ft_volumesegment(cfg, mri_aligned);
save segmentedmri segmentedmri
%% 3. triangulate the surfaces with ft_prepare_mesh;
cfg = [];
cfg.tissue = {'brain','skull','scalp'};
cfg.numvertices = [3000 2000 1000];
bnd = ft_prepare_mesh(cfg,segmentedmri);
save bnd bnd
%% 4. Create headmodel
cfg = [];
cfg.method = 'bemcp'; % You can also specify 'openmeeg', 'bemcp', or
another method.
% cfg.conductivity = [0.3300 0.0041 0.3300];
vol1 = ft_prepare_headmodel(cfg, bnd);
*When running these settings **I am getting the following error message:*
Error using surface_nesting (line 26)
the compartment nesting cannot be determined
Error in ft_headmodel_bemcp (line 66)
order = surface_nesting(vol.bnd, 'insidefirst');
Error in ft_prepare_headmodel (line 257)
vol = ft_headmodel_bemcp(geometry, 'conductivity',
cfg.conductivity);
I am not able to detect, where is the problem. I would be very thankful if
you can help me in this regard.
On Wed, May 31, 2017 at 5:19 PM, Cristiano Micheli <michelic72 at gmail.com>
wrote:
> Dear Kastouri,
>
> My hunch is that either ft_prepare_headmodel or ft_prepare_leadfield fail
> in generating a proper forward model for localization purposes.
> I would check that ft_prepare_headmodel's vol structure contains sensible
> data by plotting both the 'bnd' triangulated surface and the EEG electrodes
> together (you should be able to find instructions on the wiki) in the same
> image. Sometimes units (mm,cm) or coregistration (left/right swap) might
> influence a good outcome.
> Accordingly the grid.leadfield structure will not make sense because it
> uses the incorrect outcome of the vol structure.
>
> So if you manage to solve the 1st problem you'll kill two bird with a stone
> Good luck!
> Cris
>
>
>
>
>
> On Wed, May 31, 2017 at 12:50 PM, Kasturi Barik <kash.kgp at gmail.com>
> wrote:
>
>> *Dear all,
>> **I am trying to perform source localization in the frequency domain *
>>
>> *from EEG data using 'DICS' . As I have no mri data of the participants, *
>>
>> *I am using **'Subject01.mri' to read the anatomical data with ft_read_mri. *
>>
>> *The **head model created with 'bemcp'.*
>>
>> *Code:*
>>
>> *%% **Read the anatomical data*
>>
>> *mri = ft_read_mri('Subject01.mri');*
>>
>> *%% **Segment the anatomical information & triangulate the surfaces*
>>
>> *load segmentedmri % load from *ftp
>> server
>> <ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/headmodel_eeg/segmentedmri.mat>
>> (segmentedmri.mat).
>> *load bnd*
>>
>> *%% **Create the headmodel*
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *cfg = [];cfg.method = 'bemcp'; vol =
>> ft_prepare_headmodel(cfg, bnd);%% Position of the
>> electrodesload('Face_sub.mat'); % data of
>> participants' electrode positions electrodes = Face_sub.elec;%% Interactive
>> alignmentcfg = [];cfg.method = 'interactive';cfg.elec =
>> electrodes;cfg.headshape = vol.bnd(3); %
>> scalpelec_aligned = ft_electroderealign(cfg);%% Compute leadfield:cfg
>> = [];cfg.elec = elec_aligned;cfg.vol =
>> vol;cfg.channel = {'EEG'};[grid] = ft_prepare_leadfield(cfg);%%
>> Source Analysiscfg = []; cfg.method =
>> 'dics';cfg.frequency = 10; cfg.grid = grid;cfg.vol =
>> vol;cfg.dics.projectnoise = 'yes';cfg.dics.lambda = 0;sourceFace =
>> ft_sourceanalysis(cfg, face_data); % face_data is obtained from the
>> FT_FREQANALYSIS % [%% time frequency analysis
>> || cfg = [];
>> || cfg.channel = 'EEG'; ||
>> cfg.method = 'mtmfft'; ||
>> cfg.output = 'powandcsd'; ||
>> cfg.tapsmofrq = 4; ||
>> cfg.foi = 1:1:40; ||
>> face_data = ft_freqanalysis(cfg, Face_sub); ]*
>>
>> *When running DICS with these settings **I am getting the following error message:*
>>
>>
>> *Error using svd
>> Input to SVD must not contain NaN or Inf.
>>
>> Error in beamformer_dics>pinv (line 650)
>> [U,S,V] = svd(A,0);
>>
>> Error in beamformer_dics (line 339)
>> filt = pinv(lf' * invCf * lf) * lf' * invCf;
>> % Gross eqn. 3, use PINV/SVD to cover rank
>> deficient leadfield
>>
>> Error in ft_sourceanalysis (line 568)
>> dip(i) = beamformer_dics(grid, sens, vol, [],
>> squeeze(Cf(i,:,:)), optarg{:});
>>
>> Error in SourceAnalysis (line 133)
>> sourceFace = ft_sourceanalysis(cfg, face_data);*
>>
>>
>> * I am not able to detect, where is the problem. Another issue I have found that 'vol.mat' or 'grid.leadfield' are all NaN value. I cannot understand how to solve it. I would be very thankful if you can help me in this regard. *
>>
>>
>>
>>
>>
>> --
>> Thanks & Regards
>>
>> *Kasturi Barik*
>>
>> MS Research Scholar
>> Audio and Bio-signal Processing Lab
>> Department of Electronics and Electrical Engineering
>> Indian Institute of Technology Kharagpur
>> Mob: +91-8902400644 <+91%2089024%2000644>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
Thanks & Regards
*Kasturi Barik*
MS Research Scholar
Audio and Bio-signal Processing Lab
Department of Electronics and Electrical Engineering
Indian Institute of Technology Kharagpur
Mob: +91-8902400644
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170601/96d64962/attachment.html>
More information about the fieldtrip
mailing list