[FieldTrip] how to transform cfg.headmodel to an atlas in MNI space

[Evan Hutcheon]

Hi everyone,

I was wondering if anyone could help me
perform a  transformation from
cfg.headmodel           = headmodel;
to an atlas in the MNI space?




%% create a head model || vol is standard bem from FT
        load('/rcg/bcni/users/Evan/fieldtrip-20190912/template/headmodel/standard_bem.mat')
        headmodel        =  vol;
        headmodel = ft_convert_units(headmodel, 'm');


        cfg=[];
        cfg.resolution = .015;  %headmodel resolution(was 0.008)
        cfg.headmodel = headmodel;
        source_model = ft_prepare_sourcemodel(cfg);

        %% align electrodes to head model
        elec = ft_read_sens('standard_1020.elc');
        elec = ft_convert_units(elec, 'm');

        scalp_index = 1; %scalp is 1

        cfg = [];
        cfg.method = 'project'; % onto scalp surface
        cfg.headshape = headmodel.bnd(scalp_index); % scalp surface
        elec_realigned = ft_electroderealign(cfg,elec);

   % end

    %% align electrodes
    % for subject
    [v, ix, ixx] = intersect(elec_realigned.label, interp.label);
    elecICA = elec_realigned;
    elecICA.chanpos = elecICA.chanpos(ix,:);
    elecICA.chantype = elecICA.chantype(ix,:);
    elecICA.chanunit = elecICA.chanunit(ix,:);
    elecICA.elecpos = elecICA.elecpos(ix,:);
    elecICA.label = elecICA.label(ix);
    elecICA.tra = elecICA.tra(ix, ix); %cant find

    %% leadfield

    cfg = [];
    cfg.sourcemodel = source_model;    %% where are the sources?
    cfg.headmodel   = headmodel;      %% how do currents spread?
    cfg.elec        = elecICA;% how do sources and sensors connect?
    cfg.normalize   = 'yes'; %was no
    leadfield = ft_prepare_leadfield(cfg,interp);



    %% source estimation via LCMV
    cfg = [];
    cfg.trials              = 'all';
    cfg.channel             = 'eeg';
    cfg.covariance          = 'yes';
    cfg.covariancewindow    = 'all';
    cfg.keeptrials          = 'yes';
    cfg.removemean          = 'yes';
    timelock                = ft_timelockanalysis(cfg, interp);

    %LCMV BEAMFORMER to create spatial filter
    cfg = [];
    cfg.method              = 'lcmv';
    cfg.grid                = leadfield;
    cfg.headmodel           = headmodel;
    cfg.elec                = elecICA;
    cfg.lcmv.lambda         = '5%';
    cfg.lcmv.projectmom     = 'yes';
    cfg.lcmv.keepfilter     = 'yes';
    cfg.lcmv.keepori        = 'yes';
    cfg.lcmv.projectnoise   = 'yes';
    sfilter                 = ft_sourceanalysis(cfg, timelock); % use this for your source reconstruction

    %% Source analysis

    cfg = [];
    cfg.trials              = 'all';
    cfg.trials = any(interp.trialinfo == [5],2);%
    cfg.covariance          = 'yes';
    cfg.covariancewindow    = 'all';
    cfg.keeptrials          = 'yes';
    cfg.removemean          = 'yes';
    timelock_trl_left          = ft_timelockanalysis(cfg, interp);

       cfg = [];
    cfg.trials              = 'all';
    cfg.trials = any(interp.trialinfo == [6],2);%
    cfg.covariance          = 'yes';
    cfg.covariancewindow    = 'all';
    cfg.keeptrials          = 'yes';
    cfg.removemean          = 'yes';
    timelock_trl_right         = ft_timelockanalysis(cfg, interp);


    % no need at this point to generate and save the time series
    cfg = [];
    cfg.method              = 'lcmv';
    cfg.grid                = leadfield;
    cfg.headmodel           = headmodel;
    cfg.elec                = elecICA;
    cfg.lcmv.lambda         = '5%';
    cfg.lcmv.projectmom     = 'yes';

    cfg.rawtrial            = 'yes';
    cfg.grid.filter         = sfilter.avg.filter; %sfilter taken from before
    cfg.lcmv.projectnoise   = 'yes';  % noise estimation from the single value decomposition
    cfg.lcmv.keepmom        = 'yes';  % saves the time series
    cfg.lcmv.fixedori       = 'yes';
    cfg.keeptrials          = 'yes'; %'no' or 'yes
    cfg.keepleadfield       = 'yes';
    cfg.keepfilter          = 'no';
    source_left                  = ft_sourceanalysis(cfg,timelock_trl_left);
    source_right                 = ft_sourceanalysis(cfg,timelock_trl_right)


Cheers,
Evan



Evan Hutcheon

PhD Candidate|Dr. Doesburg laboratory
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20220828/0a4100ac/attachment.htm>