[FieldTrip] surface plot with atlas limited template_grid.inside

[Elena Orekhova]

Dear FT experts,

I just recently started to use Fieldtrip for my MEG data source
reconstruction.


I would like to use an atlas with my source reconstruction. I limited
template_grid.inside to the atlas, as advised in the tutorial (
http://www.fieldtriptoolbox.org/tutorial/salzburg)



%% Create template grid based on the standard head model

load(strcat(fieldtripfolder, '/template/headmodel/standard_singleshell'));

step=0.7;

cfg = [];

cfg.grid.xgrid  = -20:step:20;

cfg.grid.ygrid  = -20:step:20;

cfg.grid.zgrid  = -20:step:20;

cfg.grid.unit   = 'cm';

cfg.grid.tight  = 'yes';

cfg.inwardshift = -1;

cfg.headmodel        = vol;

template_grid  = ft_prepare_sourcemodel(cfg);



%% Load atlas and create a binary mask

atlas = ft_read_atlas(strcat(fieldtripfolder,
'/template/atlas/aal/ROI_MNI_V4.nii') );

atlas = ft_convert_units(atlas,'cm');% assure that atlas and template_grid
are expressed in the %same units



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);



% create temporary mask according to the atlas entries

tmp                  = repmat(template_grid.inside,1,1);

tmp(tmp==1)          = 0;

tmp(mask)            = 1;

% define inside locations according to the atlas based mask

template_grid.inside = tmp;

%%


Then I performed the  source reconstruction using this template_grid and
plotted the result (induced visual gamma power) on the standard brain
surface.



The resulting surface image has ‘holes’ and it does not look correct to me.

When I do not limit the template_grid.inside to the atlas it looks much
better.

(figures are attached)



What am I doing wrong?



Best regards,

Elena
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