[FieldTrip] Issue plotting Brainnetome aligned EEG source data

Schoffelen, J.M. (Jan Mathijs) janmathijs.schoffelen at donders.ru.nl
Thu Jul 1 08:51:39 CEST 2021


Hi Jack,

Following up on my previous message: I didn’t think of the fact that you are using EEG, with a BEM volume conduction model. In this case the inwardshift is probably not going to work.
Is there a particular reason why you’d want to visualize your results on the surface?

Best wishes,
Jan-Mathijs



> On 1 Jul 2021, at 05:57, Jack Fogarty via fieldtrip <fieldtrip at science.ru.nl> wrote:
> 
> Hi everyone,
> 
> After more digging it appears I have a similar issue as to the one pointed out in this previous request to the FT mailing list although there doesn't appear to be a clear solution. See, "surface plot with atlas limited template_grid.inside ", at
> https://mailman.science.ru.nl/pipermail/fieldtrip/2017-June/024483.html
> 
> Essentially, when I use ft_sourceplot to display my source results on a surface there are 'holes' or empty vertices on the surface, where it looks like the data is missing or not interpolated to the default surface file. I've created a template grid aligned to the brainnetome atlas for my source analyses and I am wondering if it is not compatible or there is simply an issue with 'source interpolate'. 
> 
> Has anyone come across this and/or know why it occurs and if there is a solution?
> 
> It should be possible to replicate and visualise the same (or at least a visually similar) issue by plotting template grid 'inside values' with this code:
> 
>    ft_defaults
>    [ftver, ftpath] = ft_version;
> 
>    % Load the Headmodel
>    load(fullfile(ftpath, 'template/headmodel/standard_bem.mat'));
> 
>    % Prepare the template grid 'standard sourcemodel'
>    cfg = [];
>    cfg.xgrid  = 'auto';
>    cfg.ygrid  = 'auto';
>    cfg.zgrid  = 'auto';
>    cfg.unit   = 'mm';
>    cfg.tight  = 'yes';
>    cfg.resolution  = 7;
>    cfg.headmodel   = vol;
>    template_grid   = ft_prepare_sourcemodel(cfg);
> 
>    % Read in Brainnetome Atlas; ensure its units are consistent with template
>    atlas = ft_read_atlas(fullfile(ftpath, 'template/atlas/brainnetome/BNA_MPM_thr25_1.25mm.nii'));
> 
>    % Ensure units are consistent between atlas and sourcemodel
>    atlas = ft_convert_units(atlas,'mm');
>    template_grid = ft_convert_units(template_grid,'mm');
> 
>    % Check the coordsys field exists in sourcemodel
>    if ~isfield(template_grid, 'coordsys');
>        template_grid.coordsys = 'mni';
>    end
> 
>    % Create binary mask for all grid points inside the Brainnetome atlas locations
>    cfg = [];
>    cfg.atlas      = atlas;
>    cfg.roi        = atlas.tissuelabel;  % here you can also specify a single label, i.e. single ROI
>    cfg.inputcoord = 'mni';
>    mask           = ft_volumelookup(cfg, template_grid);
> 
>    template_grid.inside = false(template_grid.dim);
>    template_grid.inside(mask == 1) = true;
> 
>    cfg = [];
>    cfg.method = 'surface';
>    cfg.funparameter = 'inside';
>    cfg.funcolormap = 'hsv';
>    ft_sourceplot(cfg,template_grid);
> 
> Cheers,
> Jack
> 
> 
> 
> Message: 1
> Date: Wed, 30 Jun 2021 10:20:22 +0000
> From: Jack Fogarty <jf752 at uowmail.edu.au>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Issue plotting Brainnetome aligned EEG source
> 	data
> Message-ID:
> 	<SYBPR01MB5308E7903F7D080B1F042675C2019 at SYBPR01MB5308.ausprd01.prod.outlook.com>
> 	
> Content-Type: text/plain; charset="utf-8"
> 
> Hello Fieldtrippers!
> 
> Apologies for the long email, but I am hoping that I can get some help working with the Brainnetome atlas.
> 
> Background
> 
> Ultimately, I want to explore EEG connectivity between Brainnetome ROIs. I don't have individual MRI data, just resting EEG, so I am first trying to develop a standard template grid (sourcemodel) aligned to the Brainnetome atlas so I can explore EEG source analyses and easily examine the output in terms of the Brainnetome ROIs. I am following this Fieldtrip tutorial to create a template grid using the standard BEM and Brainnetome atlas provided by Fieldtrip. I went with this because I had trouble interpolating to the Brainnetome atlas and this seemed like an efficient way to create a standard template that I could apply to multiple subjects:
> https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_brain_atlas_based_mni_space/__;!!HJOPV4FYYWzcc1jazlU!qxNYm5UX4r247zxfCBJ131UKIxbWXgzqM0w90neZ3KOfI1PkrlTTd0PH_LB64dBWEwQgYvR3qz0yU2Q$ 
> 
> Issue
> 
> My code runs, but whenever I attempt to plot my source results using ft_sourceplot it seems that some data is not interpolated to parts of the brain surface. I'm not sure, but I believe this could be an issue in the ft_volumelookup stage; that is, when I create a binary mask of all locations in the template grid that match the atlas locations, some grid points may be missed and considered 'empty'. Is there a specific problem in my code causing this? Or a way to address it so that I am capturing all the data in the analysis and/or plotting stages?
> 
> I have attached an image of the final plot with the funny/missing data (which appears as the grey patches on some gyri) and my code is below. Any help would be really appreciated.
> 
> Thanks,
> Jack
> 
> [cid:image003.png at 01D76DED.5573FB20]
> 
> My code is here:
> 
> %% Generate standard BEM template aligned to Brainnetome atlas
> 
>    ft_defaults
>    [ftver, ftpath] = ft_version;
> 
>    % Load the Headmodel
>    load(fullfile(ftpath, 'template/headmodel/standard_bem.mat')); % Colin27
> 
>    % Prepare the template grid 'standard sourcemodel'
>    cfg = [];
>    cfg.xgrid  = 'auto';
>    cfg.ygrid  = 'auto';
>    cfg.zgrid  = 'auto';
>    cfg.unit   = 'mm';
>    cfg.tight  = 'yes';
>    cfg.resolution  = 7;
>    cfg.headmodel   = vol;
>    template_grid   = ft_prepare_sourcemodel(cfg);
> 
>    % Check alignment of the template grid and headmodel
>    figure;
>    hold on
>    ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>    ft_plot_headmodel(vol,  'facecolor', 'cortex', 'edgecolor', 'none');
>    ft_plot_axes(vol);
>    alpha 0.5
>    camlight
> 
>    % Read in Brainnetome Atlas; ensure its units are consistent with template
>    atlas = ft_read_atlas(fullfile(ftpath, 'template/atlas/brainnetome/BNA_MPM_thr25_1.25mm.nii'));
> 
>    % Ensure units are consistent between atlas and sourcemodel
>    atlas = ft_convert_units(atlas,'mm');
>    template_grid = ft_convert_units(template_grid,'mm');
> 
>    % Check the coordsys field exists in sourcemodel
>    if ~isfield(template_grid, 'coordsys');
>        template_grid.coordsys = 'mni';
>    end
> 
>    % Create binary mask for all grid points inside the Brainnetome atlas locations
>    cfg = [];
>    cfg.atlas      = atlas;
>    cfg.roi         = atlas.tissuelabel;  % here you can also specify a single label, i.e. single ROI
>    cfg.inputcoord = 'mni';
>    mask           = ft_volumelookup(cfg, template_grid);
>    template_grid.inside = false(template_grid.dim);
>    template_grid.inside(mask == 1) = true;
> 
>    % Check grid points inside the Brainnetome atlas
>    figure;
>    ft_plot_mesh(template_grid.pos(template_grid.inside,:),'vertexcolor','black','vertexalpha',0.5);
> 
>    clearvars -except atlas template_grid vol
> 
>    %% EEG source analysis and plotting
> 
>    setenv('PATH', 'C:\Program Files\OpenMEEG\bin');
>    setenv('LD_LIBRARY_PATH', 'C:\Program Files\OpenMEEG\lib');
> 
>    % Load preprocessed EEG data
>    load('C:\Users\jf752\Desktop\Processing\source_analysis\test_data');
> 
>    % Realign electrodes
>    cfg = [];
>    cfg.method = 'interactive';
>    cfg.headshape = vol.bnd(1);
>    cfg.elec = cln_data.elec;
>    elec_aligned = ft_electroderealign(cfg);
> 
>    cln_data.elec = elec_aligned;
> 
>    % Prepare the Leadfield
>    cfg = [];
>    cfg.elec      = cln_data.elec;
>    cfg.channel   = cln_data.label;
>    cfg.headmodel = vol;
>    cfg.sourcemodel.pos = template_grid.pos;
> 
>    leadfield = ft_prepare_leadfield(cfg);
> 
>    % Run Frequency Analysis
>    cfg            = [];
>    cfg.method     = 'mtmfft';
>    cfg.output     = 'powandcsd';
>    cfg.keeptrials = 'yes';
>    cfg.tapsmofrq  = 1;
>    cfg.foi        = 10;
>    freq           = ft_freqanalysis(cfg, cln_data);
> 
>    % Run eLORETA Source Localisation
>    cfg = [];
>    cfg.method       = 'eloreta';
>    cfg.frequency    = 10; % single number in Hz
>    cfg.sourcemodel  = leadfield;
>    cfg.headmodel    = vol;
>    cfg.elec         = cln_data.elec;
>    cfg.projectnoise = 'yes';
> 
>    source_freq = ft_sourceanalysis(cfg, freq);
> 
>    % Plot the 10 Hz power on surface
>    cfg = [];
>    cfg.method = 'surface';
>    cfg.funparameter = 'avg.pow';
>    ft_sourceplot(cfg,source_freq);
> 
> 
> 
> 
> 
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