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ENH - something went wrong with a previous change to ft_read_headshape
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@schoffelen
schoffelen committed Nov 26, 2024
1 parent 1b00ef6 commit c0858c3
Showing 1 changed file with 72 additions and 64 deletions.
136 changes: 72 additions & 64 deletions fileio/ft_read_headshape.m
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@
%
% See also FT_READ_HEADMODEL, FT_READ_SENS, FT_READ_ATLAS, FT_WRITE_HEADSHAPE

% Copyright (C) 2008-2023, Robert Oostenveld
% Copyright (C) 2008-2024, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
Expand Down Expand Up @@ -440,74 +440,82 @@
case 'mne_source'
% read the source space from an MNE file
ft_hastoolbox('mne', 1);

try
% a fif-file can also contain a source space that is volumetric, in which case the below function call will fail (due to the add_geom
% being specified as true, but the file does not contain triangulation information. strictly speaking, the fif-file then
% does not represent a headshape, but as a service to the casual user, let's support the reading of this type of file
src = mne_read_source_spaces(filename, 1);
catch
src = mne_read_source_spaces(filename);
end

src = mne_read_source_spaces(filename, 1);
if numel(src)==2
if ~isempty(annotationfile)
ft_hastoolbox('freesurfer', 1);
if numel(annotationfile)~=2
ft_error('two annotationfiles expected, one for each hemisphere');
end
for k = 1:numel(annotationfile)
[v{k}, label{k}, c(k)] = read_annotation(annotationfile{k}, 1);
end

if ~isempty(annotationfile)
ft_hastoolbox('freesurfer', 1);
if numel(annotationfile)~=2
ft_error('two annotationfiles expected, one for each hemisphere');
end
for k = 1:numel(annotationfile)
[v{k}, label{k}, c(k)] = read_annotation(annotationfile{k}, 1);
% match the annotations with the src structures
if src(1).np == numel(label{1}) && src(2).np == numel(label{2})
src(1).labelindx = label{1};
src(2).labelindx = label{2};
elseif src(1).np == numel(label{2}) && src(1).np == numel(label{1})
src(1).labelindx = label{2};
src(2).labelindx = label{1};
else
ft_warning('incompatible annotation with triangulations, not using annotation information');
end
if ~isequal(c(1),c(2))
ft_error('the annotation tables differ, expecting equal tables for the hemispheres');
end
c = c(1);
end

% match the annotations with the src structures
if src(1).np == numel(label{1}) && src(2).np == numel(label{2})
src(1).labelindx = label{1};
src(2).labelindx = label{2};
elseif src(1).np == numel(label{2}) && src(1).np == numel(label{1})
src(1).labelindx = label{2};
src(2).labelindx = label{1};
else
ft_warning('incompatible annotation with triangulations, not using annotation information');
shape = [];
% only keep the points that are in use
inuse1 = src(1).inuse==1;
inuse2 = src(2).inuse==1;
shape.pos=[src(1).rr(inuse1,:); src(2).rr(inuse2,:)];

% only keep the triangles that are in use; these have to be renumbered
newtri1 = src(1).use_tris;
newtri2 = src(2).use_tris;
for i=1:numel(src(1).vertno)
newtri1(newtri1==src(1).vertno(i)) = i;
end
for i=1:numel(src(2).vertno)
newtri2(newtri2==src(2).vertno(i)) = i;
end
shape.tri = [newtri1; newtri2 + numel(src(1).vertno)];
if isfield(src(1), 'use_tri_area')
shape.area = [src(1).use_tri_area(:); src(2).use_tri_area(:)];
end
if isfield(src(1), 'use_tri_nn')
shape.nn = [src(1).use_tri_nn; src(2).use_tri_nn];
end
if ~isequal(c(1),c(2))
ft_error('the annotation tables differ, expecting equal tables for the hemispheres');
shape.orig.pos = [src(1).rr; src(2).rr];
shape.orig.tri = [src(1).tris; src(2).tris + src(1).np];
shape.orig.inuse = [src(1).inuse src(2).inuse]';
shape.orig.nn = [src(1).nn; src(2).nn];
if isfield(src(1), 'labelindx')
shape.orig.labelindx = [src(1).labelindx;src(2).labelindx];
shape.labelindx = [src(1).labelindx(inuse1); src(2).labelindx(inuse2)];
shape.label = c.struct_names;
shape.annotation = c.orig_tab; % to be able to recover which one
shape.ctable = c.table;
end
c = c(1);
end

shape = [];
% only keep the points that are in use
inuse1 = src(1).inuse==1;
inuse2 = src(2).inuse==1;
shape.pos=[src(1).rr(inuse1,:); src(2).rr(inuse2,:)];

% only keep the triangles that are in use; these have to be renumbered
newtri1 = src(1).use_tris;
newtri2 = src(2).use_tris;
for i=1:numel(src(1).vertno)
newtri1(newtri1==src(1).vertno(i)) = i;
end
for i=1:numel(src(2).vertno)
newtri2(newtri2==src(2).vertno(i)) = i;
end
shape.tri = [newtri1; newtri2 + numel(src(1).vertno)];
if isfield(src(1), 'use_tri_area')
shape.area = [src(1).use_tri_area(:); src(2).use_tri_area(:)];
end
if isfield(src(1), 'use_tri_nn')
shape.nn = [src(1).use_tri_nn; src(2).use_tri_nn];
end
shape.orig.pos = [src(1).rr; src(2).rr];
shape.orig.tri = [src(1).tris; src(2).tris + src(1).np];
shape.orig.inuse = [src(1).inuse src(2).inuse]';
shape.orig.nn = [src(1).nn; src(2).nn];
if isfield(src(1), 'labelindx')
shape.orig.labelindx = [src(1).labelindx;src(2).labelindx];
shape.labelindx = [src(1).labelindx(inuse1); src(2).labelindx(inuse2)];
% ulabelindx = unique(c.table(:,5));
% for k = 1:c.numEntries
% % the values are really high (apart from the 0), so I guess it's safe to start
% % numbering from 1
% shape.orig.labelindx(shape.orig.labelindx==ulabelindx(k)) = k;
% shape.labelindx(shape.labelindx==ulabelindx(k)) = k;
% end
% FIXME the above screws up the interpretation of the labels, because the color table is not sorted
shape.label = c.struct_names;
shape.annotation = c.orig_tab; % to be able to recover which one
shape.ctable = c.table;
else
ft_warning('the fif-file did not seem to contain triangulation information, probably you try to read a volumetric source space');

shape = [];
shape.pos = src.rr;
shape.inside = src.inuse(:)>0;
shape.dim = pos2dim3d(src.rr);
end

case {'neuromag_fif' 'neuromag_mne'}
Expand Down Expand Up @@ -1103,7 +1111,7 @@
if ~isempty(attr)
shape.data = attr;
end

case 'vtk_xml'
data = read_vtk_xml(filename);
shape.orig = data;
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