[FieldTrip] Specific sources and ft_sourcestatistics

[Max Cantor]

Hi Laura,

If I understand your problem correctly, what I think you need to do is
create a template grid using ft_source_model, then use ft_source_model to
create a grid using each subjects' mri with the template grid, and finally
change the .dim and .pos parameters of the source analysis output to unwarp
from the subject grid to the template grid. The following code might help,
although I think there is also a tutorial that talks about this:

    template                   = ft_read_mri(templatefile);
    template.coordsys    = 'spm';

    % segment the template brain and construct a volume conduction model
(i.e. head model)

    cfg                            = [];
    template_seg           = ft_volumesegment(cfg, template);

    cfg                            = [];
    cfg.method               = 'singleshell';
    template_vol             = ft_prepare_headmodel(cfg, template_seg);

    % construct the dipole grid in the template brain coordinates

    cfg                           = [];
    cfg.grid.xgrid           = -20:1:20;
    cfg.grid.ygrid           = -20:1:20;
    cfg.grid.zgrid           = -20:1:20;
    cfg.grid.unit             = 'cm';
    cfg.grid.tight            = 'yes';
    cfg.inwardshift        = -1.5;
    cfg.vol                     = template_vol;
    template_grid         = ft_prepare_sourcemodel(cfg);

   % Subject mri

    mri                          = ft_read_mri(mrifile);
    mri                          = ft_volumereslice([], mri);

    cfg                          = [];
    cfg.write                  = 'no';
    cfg.coordsys           = 'ctf';
    segmented             = ft_volumesegment(cfg, mri);

    cfg                          = [];
    cfg.method             = 'singleshell';
    vol                          = ft_prepare_headmodel(cfg, segmented);

    % Prepare Source Model using template grid and subject mri

    cfg                          = [];
    cfg.grid.warpmni     = 'yes';
    cfg.grid.template     = template_grid;
    cfg.grid.nonlinear    = 'yes';
    cfg.mri                     = mri;
    grid                          = ft_prepare_sourcemodel(cfg);

   % Unwarp Grid (For group analysis)

    src.dim                   = template_grid.dim;
    src.pos                   = template_grid.pos;

I hope this helps.
best,

Max



On Mon, Oct 20, 2014 at 12:17 PM, Laura Rueda Delgado <
Laura.Rueda at faber.kuleuven.be> wrote:

>  Dear all,
>
>
>
> I’m working with EEG data and the individual MRIs. I have a doubt about a
> step for defining ROIs. I have EEG data during a task with 3 conditions
> (C1, C2, C3) and during rest. I would like to know what is the main effect
> of the conditions in my source data. I was recommended to use the contrast
> of Task (C1, C2 and C3 together) vs Rest to obtain meaningful sources,
> which then are used to restrict the source and statistical analysis between
> the conditions. This is what I do:
>
>
>
> -          Estimate sources with the common filter for Task and Rest
> separately.
>
> -          Find sources that are significantly different between these
> two conditions (ft_sourcestatistics with dependent T).
>
> -          Use the position of these sources as ROIs in ft_sourceanalysis
> for C1, C2 and C3 separately (but using a common filter of these
> conditions).
>
> -          Find sources that account for the main effect between
> conditions (ft_sourcestatistics with dependent F).
>
>
>
> Now the problem is that if I use the position of the sources in
> ft_sourceanalysis, I don’t have a regular grid anymore, and this becomes a
> problem when using ft_sourcestatistics as cfg.dim needs to be specified and
> if I do not specify it (because I don’t have a regular grid with 3
> dimensions as expected), I get the following error:
>
>
>
> Error using reshape
>
> To RESHAPE the number of elements must not change.
>
>
>
> Error in clusterstat (line 185)
>
>       posclusobs = findcluster(reshape(postailobs,
> [cfg.dim,1]),channeighbstructmat,cfg.minnbchan);
>
>
>
> Error in ft_statistics_montecarlo (line 361)
>
>   [stat, cfg] = clusterstat(cfg, statrand, statobs);
>
>
>
> Error in statistics_wrapper (line 308)
>
>     [stat, cfg] = statmethod(cfg, dat, design);
>
>
>
> Error in ft_sourcestatistics (line 107)
>
>     [stat, cfg] = statistics_wrapper(cfg, varargin{:});
>
>
>
>
>
> So does anybody know a way to work around this?
>
>
>
> And what do you think of the logic of these steps?
>
>
>
> Thank you in advance for any help!
>
>
>
>
>
> Cheers,
>
>
>
> Laura Rueda Delgado
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Max Cantor
Lab Manager
Computational Neurolinguistics Lab
University of Michigan
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