[FieldTrip] Issues with: Sourcegrandaverage & Spatial Common Filter

Tzvetan Popov tzvetan.popov at uni-konstanz.de
Sat Oct 10 14:53:33 CEST 2015


Hi Sara,
1. The error stems from the fact that all dipole locations and their positions are warped in individual anatomy. After each individual source reconstruction you have to specify 
source.pos = template_grid.pos
source.pnt = template_grid.pos
After this you can use ft_sourcegrandaverage, ft_sourcestatistics etc.

2.) Yes, ideally all appended.

good luck,
Tzvetan


> Dear all, 
> 
> I am working on the localization of oscillatory sources using beamforming 
> (http://www.fieldtriptoolbox.org/tutorial/beamformer). 
> The data are recorded with Elekta-Neuromag,
> the source estimations are based on individual MNI-aligned grids
> (http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space), 
> and the FT version is fieldtrip-20150701.
> 
> And I have two main issues, which would be very appreciated if someone could help me with:
> 
> 1. When SOURCEGRANDAVERAGING, "ERROR: the input sources vary in the field inside". Below this message you can see the code I am using.
> 
>  Should I make additional normalization prior to / in the creation of the individual grid? 
>  I found this link which is specific to Neuromag data but it says is outdated (?). 
>  http://www.fieldtriptoolbox.org/example/read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space
> 
>  Or should I interpolate the source estimation to the template, instead of to the individual-mri?
>  When doing so (without after normalizing it), everything works fine but my plots looks like attached (grandavg of 7 subjects). 
> 
> 2. When creating a SPATIAL COMMON FILTER for comparing the Post stimulus sources of two conditions (effects were baseline corrected within condition in sensor space), 
>  should the Allappended input data include the Post-stimulus and Pre-stimulus intervals of each condition (e.g. PrestimA + PrestimB + PoststimA + PoststimB)?
> 
> 
> Any comment would be very helpful! 
> 
> Thank you in advance, 
> 
> All the best,
> 
> Sara 
> 
> %%
> 
>    %% Interpolation, normalization and grandaverage
> 
>    load source mri_real template
> 
>    source.pos=template_grid.pos; % right(?) 
> 
>    cfg              = [];
>    cfg.downsample   = 2;
>    cfg.parameter    = 'pow';
>    sourceInt        = ft_sourceinterpolate(cfg, source, mri_real);  
> 
>    cfg = [];
>    cfg.spmversion   = 'spm8';
>    %cfg.template    = '~/fieldtrip/external/spm8/templates/T1.nii'; 
>                               % When enabling this parameter i get this error: "the head coordinate system of the template does not seem to be correspond with the mni/spm convention".
>                               % However should be one taken by default and unablinginn it works fine so it is confussing (?)
>    sourceIntNorm    = ft_volumenormalise(cfg, sourceInt);
> 
>    %% grand average for 7 subjects
> 
>    cfg=[];
>    cfg.parameter    = 'pow';
>    [grandavg]       = ft_sourcegrandaverage(cfg, sourceIntNorm{:});
> 
>    %%
> 
> %%
> <gravg_int_templ.jpg>_______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip





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