[FieldTrip] Issues with: Sourcegrandaverage & Spatial Common Filter

[Tzvetan Popov]

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  I found this link which is specific to Neuromag data but it says is outdated (?).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>_______________________________________________
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