[FieldTrip] EEG beamformer source analyses
Schoffelen, J.M. (Jan Mathijs)
jan.schoffelen at donders.ru.nl
Tue Sep 15 12:00:47 CEST 2020
OK, thanks for updating.
What’s the error stack now?
Also, are you sure that you don’t have a messed up matlab path (e.g. have an overloaded rusty version from EEGLAB/SPM included)?
If the error is the same, i.e. something happening in ‘ft_checkconfig, line 307’, this suggests that MATLAB still ends up using outdated code.
Best wishes,
JM
On 15 Sep 2020, at 11:53, Patrick Wiegel <patrick.wiegel at sport.uni-freiburg.de<mailto:patrick.wiegel at sport.uni-freiburg.de>> wrote:
Dear Jan-Mathijs,
thanks for the note. I updated the version but the error still appears.
I attached my script if that helps to understand the issue.
Best, Patrick
Patrick Wiegel
Department of Sport and Sport Science
University of Freiburg
Sandfangweg 4
79117 Freiburg i. Br .
phone: +49 (0)761/ 203-4550
email: patrick.wiegel at sport.uni-freiburg.de<mailto:patrick.wiegel at sport.uni-freiburg.de>
web: www.sport.uni-freiburg.de<http://www.sport.uni-freiburg.de>
Am 15.09.2020 um 11:15 schrieb Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>>:
Dear Patrick,
Just to be sure: can you get the latest release version of the code and try whether this error persists (e.g. http://github.com/fieldtrip/fieldtrip/releases/tag/20200911)? The reason I ask is that your reported line number (i.e. line 217 in ft_sourcenalasysis) that throws the error does not match the current state of the code. I’d like to be sure that this is a genuine error, or that you happen to have stumbled upon a dysfunctional version (for which we humbly apologize :) ).
Best wishes,
Jan-Mathijs
On 15 Sep 2020, at 10:55, Patrick Wiegel <patrick.wiegel at sport.uni-freiburg.de<mailto:patrick.wiegel at sport.uni-freiburg.de>> wrote:
Dear Fieldtrip community,
I am a PhD student from Germany and I am working with EEG data. I would like to do Beamformer source analyses on power data.
I don’t have individual MRIs or related electrode positions available, so I am taking the standard MRI and BEM headmodel from the fieldtrip templates. Doing the source_analyses, I am getting an error message. Can anyone tell me if I missed something and what the reason for that error is? The error appears when running the last part of the script ft_sourceanalyses:
the input is freq data with 64 channels, 1 frequencybins and no timebins
Undefined function or variable 'fieldname'.
Error in ft_checkconfig (line 307)
for i=1:length(fieldname)
Error in ft_sourceanalysis (line 217)
cfg = ft_checkconfig(cfg, 'createtopcfg', cfg.method);
Error in BEAMformer (line 116)
sourceAll = ft_sourceanalysis(cfg, frequ_all);
I added my code below. I would appreciate any help. I added information on my existing variables below the code.
Best, Patrick
%% import EEG data
EEG_Data = eeglab2fieldtrip( EEG, 'raw', 'none' );
%% define trials for frequency analyses
cfg = [];
cfg.trials = Indexes_correct{1, 1};
cfg.toilim = [0.25 0.55];
data_fed_correct = ft_redefinetrial(cfg, EEG_Data);
cfg = [];
cfg.trials = Indexes_incorrect{1, 1};
cfg.toilim = [0.25 0.55];
data_fed_incorrect = ft_redefinetrial(cfg, EEG_Data);
%% run frequenc analyses
cfg = [];
cfg.method = 'mtmfft';
cfg.output = 'powandcsd';
cfg.tapsmofrq = 4;
cfg.foilim = [25 25];
frequ_correct = ft_freqanalysis(cfg, data_fed_correct);
cfg = [];
cfg.method = 'mtmfft';
cfg.output = 'powandcsd';
cfg.tapsmofrq = 4;
cfg.foilim = [25 25];
frequ_incorrect = ft_freqanalysis(cfg, data_fed_incorrect);
cfg = [];
cfg.method = 'mtmfft';
cfg.output = 'powandcsd';
cfg.tapsmofrq = 4;
cfg.foilim = [25 25];
frequ_all = ft_freqanalysis(cfg,EEG_Data);
%% load MRI and BEM templates
load('/Users/patrickwiegel/Documents/MATLAB/Scripts/2020/TF_Data/fieldtrip-20200603/template/headmodel/standard_bem.mat')
load('/Users/patrickwiegel/Documents/MATLAB/Scripts/2020/TF_Data/fieldtrip-20200603/template/headmodel/standard_mri.mat')
%% segment mri
cfg = [];
cfg.write = 'no';
[segmentedmri] = ft_volumesegment(cfg, mri);
disp(segmentedmri)
%%
mri = ft_volumereslice(cfg, segmentedmri);
display(mri)
%% align electrodes
load('elec_aligned')
elec_aligned = ft_convert_units(elec_aligned, 'cm');
vol = ft_convert_units(vol, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.
%%
[headmodel, elec_aligned]=ft_prepare_vol_sens (vol,elec_aligned);
cfg = [];
cfg.method = 'interactive';
cfg.elec = elec_aligned;
cfg.headshape = headmodel.bnd(1);
elec_aligned = ft_electroderealign(cfg);
%%
% construct the dipole grid in the template brain coordinates
% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
cfg = [];
cfg.resolution = 1;
cfg.tight = 'yes';
cfg.inwardshift = -1.5;
cfg.headmodel = headmodel;
sourcemodel = ft_prepare_sourcemodel(cfg);
%%
cfg = [];
cfg.method = 'dics';
cfg.frequency = 25;
cfg.sourcemodel = sourcemodel;
cfg.headmodel = headmodel;
cfg.elec = elec_aligned;
cfg.dics.projectnoise = 'yes';
cfg.dics.lambda = '5%';
cfg.dics.keepfilter = 'yes';
cfg.dics.realfilter = 'yes';
sourceAll = ft_sourceanalysis(cfg, frequ_all);
sourcemodel =
struct with fields:
dim: [17 22 18]
pos: [6732×3 double]
unit: 'cm'
inside: [6732×1 logical]
cfg: [1×1 struct]
elec_aligned =
struct with fields:
chanpos: [64×3 double]
chantype: {64×1 cell}
chanunit: {64×1 cell}
elecpos: [64×3 double]
homogeneous: [4×4 double]
label: {1×64 cell}
tra: [64×64 double]
type: 'eeg1010'
unit: 'cm'
cfg: [1×1 struct]
headmodel =
struct with fields:
bnd: [1×3 struct]
cond: [0.3300 0.0041 0.3300]
mat: [64×3000 double]
type: 'dipoli'
unit: 'cm'
skin_surface: 1
inner_skull_surface: 3
source: 3
Patrick Wiegel
Department of Sport and Sport Science
University of Freiburg
Sandfangweg 4
79117 Freiburg i. Br .
phone: +49 (0)761/ 203-4550
email: patrick.wiegel at sport.uni-freiburg.de<mailto:patrick.wiegel at sport.uni-freiburg.de>
web: www.sport.uni-freiburg.de<http://www.sport.uni-freiburg.de/>
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