[FieldTrip] Group analysis on cortical-sheet based source-reconstructed data - sourcemodel.pos are different

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Fri Jul 17 16:21:55 CEST 2020


Hi Matteo,

Dear Fieldtrip users,

I am trying to perform grand-average and group statistics of source-reconstructed data (minimum-norm estimation) for my EEG study. In particular, I performed source reconstruction as outlined in the tutorial (http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate/), creating a source model based on a surface description of the cortical sheet. However, when I try to average data from multiple subjects I get the following error message: “Error using ft_sourcegrandaverage (line 116) : the input sources vary in the field pos”.

The tutorial on the source-model preparation (http://www.fieldtriptoolbox.org/tutorial/sourcemodel/) explains that “if you performed source reconstruction on the cortical surface, and you used the recipe explained earlier in this tutorial, single-subject data can be directly compared across subjects, because the dipole locations are surface-registered to a template”. Indeed the registration to a template surface should be accomplished by the function ft_postfreesurferscript.sh (see also http://www.fieldtriptoolbox.org/workshop/paris2019/handson_anatomy/#creation-of-a-cortex-based-source-model).

If I compare the sourcemodels constructed from the output of ft_postfreesurferscript.sh for two different subjects, I can see that their sourcemodel.tri are identical but their sourcemodel.pos are different. I think that the problem at the grand-average level stems from this difference.
   subjectname = ‘sub01’  and ‘sub02’
   datapath = fullfile(mripath,subjectname,'workbench');
   filename = fullfile(datapath,[subjectname,'.L.midthickness.8k_fs_LR.surf.gii']);
   sourcemodel = ft_read_headshape({filename, strrep(filename, '.L.', '.R.')});

My question is: does this difference in the sourcemodel.pos field between subjects mean that some step in the preparation of the source models went wrong (as they should be registered to the same template)? I am asking this because at the end of the section “Performing group analysis on 3-dimensional source-reconstructed data - Subject-specific grids that are equivalent across subjects in normalized space”  a warning is present:

Don’t worry, everything went OK. The same reasoning applies as in the 3D grid case: the individual positions are different, yet thanks to the ’normalization procedure’, the points are equivalent in normalised space. It seems indeed that you got confused by the ‘warning’ message missing in this section of the tutorial. Feel free to add an equivalent section at the relevant location that describes the group level approach for cortical sheets. I believe you can even directly edit the page, which eventually creates a PR for us to merge to the website’s repository.


“Keep in mind that the .pos field in the source models are subject specific. When you want to do group analysis across subjects, which now in principle is allowed due to the equivalence of the dipole positions in normalized space, you need to replace the positions with the normalized positions of the template sourcemodel. Otherwise, FieldTrip will throw an error” (http://www.fieldtriptoolbox.org/tutorial/sourcemodel/#subject-specific-grids-that-are-equivalent-across-subjects-in-normalized-space).

Therefore, I am not sure if there is a problem in my source models after ft_postfreesurferscript, or if the same procedure from the warning should be applied to cortical-sheet based source-reconstructed data. In that case, which .pos should be used for the replacement?

You can pick any! This information will not be used in the inferential decision process (but is used in the data bookkeeping).

Best wishes,
Jan-Mathijs




Thank you in advance for your help.


Matteo

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