[FieldTrip] Fixing headmodel vertices

[Hassan Aleem]

Hi Everyone,

New to fieldtrip. My headmodel looks pretty good except for a couple
vertices that are poking in. Is there any way to address them specifically?
The code I used is similar to one provided by someone who was successful.
As follows

mri.coordsys        ='SPM'
cfg                 = [];
cfg.brainthreshold  = 0.15;
cfg.scalpthreshold  = 0.3;
cfg.downsample      = 1; %no downsampling
cfg.output          = {'brain' 'scalp' 'skull'};
segment                 = ft_volumesegment(cfg, mri);

cfg = [];
cfg.method = 'projectmesh';
cfg.numvertices = 10000;
bnd = ft_prepare_mesh( cfg, seg);

% fix mesh
[ bnd( 1).pnt, bnd( 1).tri] = meshresample( bnd( 1).pnt, bnd( 1).tri,
1000/size( bnd( 1).pnt, 1));
[ bnd( 2).pnt, bnd( 2).tri] = meshresample( bnd( 2).pnt, bnd( 2).tri,
2000/size( bnd( 2).pnt, 1));
[ bnd( 3).pnt, bnd( 3).tri] = meshresample( bnd( 3).pnt, bnd( 3).tri,
3000/size( bnd( 3).pnt, 1));
for ii = 1:size( bnd),
    [ bnd( ii).pnt, bnd( ii).tri] = meshcheckrepair( bnd( ii).pnt, bnd(
ii).tri, 'dup');
    [ bnd( ii).pnt, bnd( ii).tri] = meshcheckrepair( bnd( ii).pnt, bnd(
ii).tri, 'isolated');
    [ bnd( ii).pnt, bnd( ii).tri] = meshcheckrepair( bnd( ii).pnt, bnd(
ii).tri, 'deep');
    [ bnd( ii).pnt, bnd( ii).tri] = meshcheckrepair( bnd( ii).pnt, bnd(
ii).tri, 'meshfix');
end

% calculate headmodel % reordered to brain skull scalp
cfg = [];
cfg.method = 'bemcp'; %openmeeg doesnt work with multiple output from
ft_volumesegment
vol = ft_prepare_headmodel(cfg, bnd);
clear bnd


Thanks!
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