[FieldTrip] Cortical Sheet for MNE source reconstruction

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Thu Sep 13 12:13:32 CEST 2018


Hi Annika,

Part of what you are looking at is an extrapolation artifact, which is caused by ft_sourceinterpolate. Is there a specific reason why you want the data visualized on a 3D grid, rather than as the original surface? Using ft_sourceplot (or ft_sourcemovie) should work with the original source data (provided it contains a description of the cortical mesh, in the fields pos and tri).

Best wishes,
Jan-Mathijs





> On 11 Sep 2018, at 15:04, Annika Thierfelder <athierfelder at tuebingen.mpg.de> wrote:
> 
> 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
> 
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