[FieldTrip] ft_sourcemovie - producing 'contemporary art' instead of a brain

[Eelke Spaak]

Hi Emilie,

To add to Jan-Mathijs' explanation of why this does not work: you can
use ft_sourceinterpolate to interpolate your volumetric source data
onto a surface, which you can then plot using ft_sourcemovie (or the
newer, though still somewhat experimental, ft_sourceplot_interactive).

Best,
Eelke

On Tue, 31 Mar 2020 at 11:07, Schoffelen, J.M. (Jan Mathijs)
<jan.schoffelen at donders.ru.nl> wrote:
>
> Hi Emilie,
>
> ft_sourcemovie has been designed to operate on source level data that is defined on a cortical surface based source model.
> The code you pasted in suggests that you used a 3-dimensional grid as a sourcemodel. So this is never going to work.
> Apparently, you managed to fool the function by post-hoc including a so-called ’tri’ field, which is the hallmark that fieldtrip uses to determine whether the sourcemodel geometry was a mesh or not.
> However, there is no relation whatsoever between the specified triangulation (which you took from the headmodel) and the dipole positions at which your source activity has been estimated.
>
> Best wishes,
> Jan-Mathijs
>
>
> On 31 Mar 2020, at 10:42, Emilie Caspar <ecaspar at ulb.ac.be> wrote:
>
> Dear all,
>
> I am trying to compute a source reconstruction of different ERPs between two experimental conditions. Well, good news is that the script ‘works’, but the issue is that I am producing contemporary art instead of a brain with ft_sourcemovie (see figure in attachement). The headmodel I used is the standard one available for download. The leadfield I built seems to look like a brain with a correct positions of the electrodes (see also figure in attachement).
>
> I really have no cue about how I produced such output with ft_sourcemovie and what could possibly be the issue (code is below). If someone can help transforming this to a brain? ;-)
> The only thing that differs (I think) from the tutorial is that I don’t have a headmodel.tri but rather a headmodel.bnd.tri. Don’t know if it makes any difference. Perhaps the sourcespace defined in the tutorial is something different?
>
> Thank you,
>
> Emilie
>
> <ft_sourcemovie.png><leadfield.png><ft_plot_mesh.png>
>
> CODE
>
> q=biosim64;
> ph = cell2mat(q(:,2));
> th = cell2mat(q(:,3));
> x = sin(ph*pi/180) .* cos(th*pi/180);
> y = sin(ph*pi/180) .* sin(th*pi/180);
> z = cos(ph*pi/180);
>
> plot3(x, y, z, '.');
> elec.label = q(:,1);
> elec.pnt = [x y z];
>
> cfg.sourcemodel.pos = elec.pnt;
> sourcemodel = ft_prepare_sourcemodel(cfg);
>
> headmodel = ft_read_headmodel('headmodel/standard_bem.mat');
>
> % realign electrodes to headmodel
> cfg = [];
> cfg.method = 'interactive';
> cfg.elec = elec;
> cfg.headshape = headmodel.bnd(1); %1 = skin
> elec = ft_electroderealign(cfg);
>
> %save new electrodes
> save elec64.mat elec
>
> ERPsAll.elec = ft_read_sens('elec64.mat’);
>
> % Prepare leadfield
> cfg                 = [];
> cfg.elec            = ERPsAll.elec;
> cfg.vol             = headmodel;
> cfg.reducerank      = 3;
> cfg.grid.resolution = 1;   % use a 3-D grid with a 1 cm resolution
> cfg.grid.unit       = 'cm';
> cfg.channel ={'all'};
> leadfield = ft_prepare_leadfield(cfg);
>
>
>
> %%mne
> cfg              = [];
> cfg.method       = 'mne'; %pcc: partial cannonical correlation/coherence
> cfg.elec         = ERPsAll.elec; %grid.cfg.elec;%
> cfg.headmodel          = headmodel;
> cfg.grid = leadfield;
> %cfg.sourcemodel = sourcemodel;
> % cfg.channel ={'all'};%, '-spmnas', '-spmlpa', '-spmrpa'};
> cfg.mne.prewhiten = 'yes';
> cfg.mne.lambda    = 3;
> cfg.mne.scalesourcecov = 'yes';
> %cfg.reducerank          = 2;
>
> source_C_Shock = ft_sourceanalysis(cfg, GA_C_Shock);
> source_C_Noshock = ft_sourceanalysis(cfg, GA_C_NOshock);
>
> save source_C_Shock.mat source_C_Shock
> save source_C_Noshock.mat source_C_Noshock
>
> bnd.pos = headmodel.bnd.pos;
> bnd.tri = headmodel.bnd.tri;
>
> m=source_C_Shock.avg.pow(:,450);
> %timeN1 = [1232:1301];timeP3 = [1722:1927];timeeLPP = [1928:2356];timelLPP = [2357:2868];
> ft_plot_mesh(bnd, 'vertexcolor', m);
> view([180 0]); h = light; set(h, 'position', [0 1 0.2]); lighting gouraud; material dull
>
> cfg = [];
> cfg.projectmom = 'yes';
> sdShock  = ft_sourcedescriptives(cfg,source_C_Shock);
> sdNoShock = ft_sourcedescriptives(cfg,source_C_Noshock);
>
> sdDIFF         = sdNoShock;
> sdDIFF.avg.pow = sdNoShock.avg.pow - sdShock.avg.pow;
> sdDIFF.tri = headmodel.bnd.tri;
>
> save sd sdDIFF;
>
> cfg = [];
> cfg.funparameter = 'pow';
> %cfg.method       = 'surface';
> ft_sourcemovie(cfg,sdDIFF);
>
>
> ---------------------------------------------
> Emilie Caspar, Ph.D
>
> CO3, Centre de Recherche Cognition et Neurosciences (CRCN), ULB
> Voice : +32 2 650 32 95
> mail : ecaspar at ulb.ac.be
> office: DB10-138
>
> Social Brain Lab, Netherlands Institute for Neuroscience (NIN), KNAW
> mail : e.caspar at nin.knaw.nl
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202