[FieldTrip] Cortical Sheet for MNE source reconstruction

Annika Thierfelder athierfelder at tuebingen.mpg.de
Thu Sep 13 13:35:23 CEST 2018


Hi Jan-Mathijs,

Thank you very much for your response! There is quite some story behind 
the reason why I extrapolated it to the 3D grid, but I'll try to explain 
shortly so you can also see how both my emails relate.

When I let the MNE algorithm run for the first time, I noticed that 
there was a consistent activity overshoot at always the same voxel in 
all my conditions. So I checked the code and I tracked it down to the 
part in the sourcemodel outside of the headmodel, as described in the 
other email. I shifted the sourcemodel a little bit upwards manually and 
got rid of the artefact (although that might not be the best solution).

However, I realized that the misalignment in the source- and the 
headmodel is, as you also said, in the left temporal cortex. But my 
artifacts were in the right temporal cortex. Also, the activation did 
not seem to be on the side where we expected it to be.

So, I found out that this might be due to the coordinate systems, so I 
wanted to make sure if it is the same if I plot it on the MRI. And this 
then looked like you saw in the image, so I got very confused if there 
was something essentially wrong in the whole pipeline I used. It is very 
reassuring to hear that this probably is not the case. Is there any way 
to check this?

So, as a final question: Is it probable that the source activity is 
mirrored in the surface sourceplots?

Best and thanks again for the help,

Annika


On 9/13/2018 12:13 PM, Schoffelen, J.M. (Jan Mathijs) wrote:
> 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
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> https://doi.org/10.1371/journal.pcbi.1002202
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202




More information about the fieldtrip mailing list