[FieldTrip] Cortical Sheet for MNE source reconstruction

[Annika Thierfelder]

Dear everyone,

I'm still encountering problems with my source analysis that I don't 
know how to solve. When I try to interpolate the source back to the MRI, 
it does not look at all the way it should (the sources seem to explode 
outside of the brain). You can have a look at it here: 
https://drive.google.com/file/d/1WZ2WYkKkI8FfyNHmCgk7OnbPLb6iCZYT/view?usp=sharing

I'm using the cortical sheet provided by fieldtrip 
(cortex_5124.surf.gii), along with the standard MRI and BEM. When I 
construct a source model from the BEM (which is not what I want since it 
distributes the sources evenly spaced but I tried it for testing), the 
sources are all neatly inside the brain, so I seem to be using that 
cortical sheet in a wrong way. Do I have to process it further? All 
tutorials I found just do it like this.

Below you can find the processing pipeline I am currently using. Any 
help is appreciated!

Best and thank you,

Annika

=======================================================================================

sourcemodel =  load('cortex_5124.surf.gii');

% compute the leadfield
leadfield = [];
cfg = [];
cfg.grid = sourcemodel;
cfg.headmodel = headmodel;
cfg.elec = chanlocs;
leadfield = ft_prepare_leadfield(cfg);

% I put the data through ft_timelockanalysis to have it in the right 
format, although it doesn't do anything.
% The data I work with is resting state data, that's why I don't compute 
the noise covariance here.
cfg = [];
data_prepared = ft_timelockanalysis(cfg, data);

% source reconstruction with MNE
cfg = [];
cfg.method = 'mne';
cfg.grid = leadfield;
cfg.headmodel = headmodel;
cfg.mne.prewhiten = 'yes';
cfg.mne.lambda = 0.1;
cfg.mne.scalesourcecov = 'yes';
cfg.elec = chanlocs;
source = ft_sourceanalysis(cfg, data_prepared);

% save into single structure to save memory
source = ft_struct2single(source);

% interpolate to the template MRI
cfg = [];
cfg.interpmethod = 'nearest';
cfg.parameter = 'avg.pow';
interp = ft_sourceinterpolate(cfg, source, mri);

% and do the source plot
cfg = [];
cfg.funparameter = 'pow';
cfg.method = 'ortho';
ft_sourceplot(cfg, interp);
On 9/7/2018 12:50 PM, Annika Thierfelder wrote:
> Dear fieldtrippers,
>
> I have a short question about the template files provided by 
> fieldtrip. I am doing MNE source reconstruction with the template BEM 
> headmodel and the cortical sheets provided in the sourcemodel 
> templates. However, I noticed that the sourcemodel is outside of the 
> BEM brain surface at some points. So I plotted it against the MRI 
> template and it doesn't really seem to fit. It seems quite small and 
> shifted, so it's hard to judge the shape.
>
> Are those not produced from the same template MRI? And would it 
> therefore make sense to go through the process of producing a 
> sourcemodel from the standard MRI myself as described here 
> [http://www.fieldtriptoolbox.org/tutorial/sourcemodel#construction_of_a_source_model_based_on_a_surface_description_of_the_cortical_sheet] 
> ?
>
> Thanks in advance for your advice,
>
> Best,
>
> Annika
>
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> https://doi.org/10.1371/journal.pcbi.1002202