[FieldTrip] Issue plotting Brainnetome aligned EEG source data
Jack Fogarty
jf752 at uowmail.edu.au
Thu Jul 1 05:57:10 CEST 2021
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://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_brain_atlas_based_mni_space/
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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