[FieldTrip] Signal drop out in plotting stats results

[Schoffelen, J.M. (Jan Mathijs)]

Hi Monalisa,

Rather than calling this a ’normalization’ issue, I’d call it an ‘interpolation’ issue.
The anatomical image that you use for the interpolation is most likely (well actually 100% sure) defined in a coordinate system that is different from the coordinates in which the functional data is defined.

If your main goal is to have a higher resolution anatomical in the background, you either need to align the single subject anatomical image to the template’s coordinate system, or use a high resolution template image, such as the one you can find in the fieldtrip/template/anatomy directory.

Good luck,
Jan-Mathijs



On 20 Jun 2024, at 08:36, MONALISA CHIKEZIE via fieldtrip <fieldtrip at science.ru.nl> wrote:

Hi All,
I am Monalisa, a neuroscience master's student doing research for my thesis. I am relatively new to fieldtrip. I have a dataset obtained from stats results (obtained after using dics beamformer and parametric permutation test) which I am trying to plot the brain activations during the experiment. My experiment had 100 participants and I used one participant's anatomical brain as my template. However, most activations are outside the brain. I do not know if this is a normalization issue. Below is an example of the images I generate.
<image.png>

I used the code from this tutorial : https://www.fieldtriptoolbox.org/tutorial/plotting/#plotting-data-at-the-source-level<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fplotting%2F%23plotting-data-at-the-source-level&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cee7abd47e79a4448683608dc92f4db68%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638546827537308225%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=G0M0Heesakdii6xSn%2FgISC4QHjL0P2qv1BOFdKn6HuU%3D&reserved=0>:

My code
% Load results - get standard stat-results
load('statresults/t_statres.mat');

% Interpolation - get standard MRI
mri = ft_read_mri('Z:\EEG\sub-1_T1w.mat');


%Reslice
cfg = [];
mri = ft_volumereslice(cfg, mri);

% Interpolate the statistical data onto the resliced MRI template
cfg            = [];
cfg.downsample = 2;
cfg.parameter  = 'stat';
cfg.interpmethod    = 'nearest';
Stat_source  = ft_sourceinterpolate(cfg, t_statres , mri);

% spatially normalize the data to brain sample
cfg            = [];
cfg.nonlinear  = 'no';
cfg.spmversion = 'spm12' ;
Stat_source  = ft_volumenormalise(cfg, Stat_source);


save('statresults/Stat_source.mat', 'Stat_source');
%% DONE
fprintf('DONE\n');

Plot code
cfg = [];
cfg.method = 'ortho';
cfg.funparameter = 'stat';
cfg.maskparameter = cfg.funparameter;
cfg.funcolorlim = [-2 2];  % Adjust the color limits if needed
cfg.opacitylim = [-2 2];  % Adjust the opacity limits if needed
cfg.opacitymap = 'rampup';
cfg.anaparameter = 'anatomy';
cfg.funcolormap = 'jet';

ft_sourceplot(cfg, Stat_source);

% Add title and save the plot
title('Theta_SEMxAGE');
saveas(gcf, 'Theta_EMxAGE.png');
fprintf('DONE\n');

Previously, I used the template mri in fieldtrip; mri = ft_read_mri('Z:\EEG\software\fieldtrip\external\spm12\toolbox\OldNorm\T1.nii');

Using the template, I got this image. However, I wanted a sharper anatomical underlay. How do I resolve the error above?
<image.png>
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https://doi.org/10.1371/journal.pcbi.1002202

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