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Slepi/Code/Utilities/spm12/external/mne/mne_read_source_spaces.m
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mne_read_source_spaces.m
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function [src] = mne_read_source_spaces(source,add_geom,tree)
%
% [src] = mne_read_source_spaces(source,add_geom,tree)
%
% Reads source spaces from a fif file
%
% source - The name of the file or an open file id
% add_geom - Add geometry information to the source spaces
% tree - Required if source is an open file id, search for the
% source spaces here
%
%
%
% Author : Matti Hamalainen, MGH Martinos Center
% License : BSD 3-clause
%
% Revision 1.13 2007/03/11 13:32:22 msh
% Nearest numbers had to be incremented by one to comply with the 1-based Matlab indexing
%
% Revision 1.12 2006/09/25 19:48:16 msh
% Added projection item kinds to fiff_define_constants
% Changed some fields to int32 in surface structures
%
% Revision 1.11 2006/05/22 10:44:44 msh
% Added surface and curvature reading routines.
% Fixed error in mne_read_source_spaces: triangle normals were not normalized
%
% Revision 1.10 2006/05/05 03:50:40 msh
% Added routines to compute L2-norm inverse solutions.
% Added mne_write_inverse_sol_stc to write them in stc files
% Several bug fixes in other files
%
% Revision 1.9 2006/05/03 19:05:06 msh
% Eliminated more Matlab 6.5 incompatibility
%
% Revision 1.8 2006/05/03 18:53:06 msh
% Approaching Matlab 6.5 backward compatibility
%
% Revision 1.7 2006/05/03 15:50:39 msh
% Fixed some Matlab 6.5 incompatibility.
%
% Revision 1.6 2006/04/28 18:01:27 msh
% Added mne_read_bem_surfaces
% Fixed errors in mne_read_source_spaces and improved triangle data computation.
%
% Revision 1.5 2006/04/23 15:29:41 msh
% Added MGH to the copyright
%
% Revision 1.4 2006/04/20 21:49:38 msh
% Added mne_read_inverse_operator
% Changed some of the routines accordingly for more flexibility.
%
% Revision 1.3 2006/04/18 23:21:22 msh
% Added mne_transform_source_space_to and mne_transpose_named_matrix
%
% Revision 1.2 2006/04/18 20:44:46 msh
% Added reading of forward solution.
% Use length instead of size when appropriate
%
% Revision 1.1 2006/04/17 21:05:08 msh
% Added source space reading routine.
%
%
me='MNE:mne_read_source_spaces';
global FIFF;
if isempty(FIFF)
FIFF = fiff_define_constants();
end
if nargin == 1
add_geom = false;
fid = -1;
fname = source;
elseif nargin == 2
fid = -1;
fname = source;
elseif nargin == 3
a = whos('source');
if strcmp(a.class,'char')
fname = source;
fid = -1;
else
fid = source;
end
else
error(me,'Incorrect number of arguments');
end
%
% Open the file, create directory
%
if fid < 0
[ fid, tree ] = fiff_open(fname);
open_here = true;
else
open_here = false;
end
%
% Find all source spaces
%
spaces = fiff_dir_tree_find(tree,FIFF.FIFFB_MNE_SOURCE_SPACE);
if isempty(spaces)
close_file;
error(me,'No source spaces found');
end
for k = 1:length(spaces)
fprintf(1,'\tReading a source space...');
this = read_source_space(spaces(k));
fprintf(1,'[done]\n');
if add_geom
complete_source_space_info;
end
src(k) = this;
end
fprintf(1,'\t%d source spaces read\n',length(spaces));
close_file;
return;
function [res] = read_source_space(this)
%
% Read all the interesting stuff
%
FIFF_BEM_SURF_NTRI=3104;
FIFF_BEM_SURF_TRIANGLES=3106;
tag = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_ID);
if isempty(tag)
res.id = int32(FIFF.FIFFV_MNE_SURF_UNKNOWN);
else
res.id = int32(tag.data);
end
tag = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NPOINTS);
if isempty(tag)
close_file;
error(me,'Number of vertices not found');
end
res.np = tag.data;
tag = find_tag(this,FIFF_BEM_SURF_NTRI);
if isempty(tag)
tag = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NTRI);
if isempty(tag)
res.ntri = 0;
else
res.ntri = tag.data;
end
else
res.ntri = tag.data;
end
tag = find_tag(this,FIFF.FIFF_MNE_COORD_FRAME);
if isempty(tag)
close_file;
error(me,'Coordinate frame information not found');
end
res.coord_frame = tag.data;
%
% Vertices, normals, and triangles
%
tag = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_POINTS);
if isempty(tag)
close_file;
error(me,'Vertex data not found');
end
res.rr = tag.data;
if size(res.rr,1) ~= res.np
close_file;
error(me,'Vertex information is incorrect');
end
tag = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NORMALS);
if isempty(tag)
close_file;
error(me,'Vertex normals not found');
end
res.nn = tag.data;
if size(res.nn,1) ~= res.np
close_file;
error(me,'Vertex normal information is incorrect');
end
if res.ntri > 0
tag = find_tag(this,FIFF_BEM_SURF_TRIANGLES);
if isempty(tag)
tag = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_TRIANGLES);
if isempty(tag)
close_file;
error(me,'Triangulation not found');
else
res.tris = tag.data;
end
else
res.tris = tag.data;
end
if size(res.tris,1) ~= res.ntri
close_file;
error(me,'Triangulation information is incorrect');
end
else
res.tris = [];
end
%
% Which vertices are active
%
tag = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NUSE);
if isempty(tag)
res.nuse = 0;
res.inuse = int32(zeros(1,res.nuse));
res.vertno = [];
else
res.nuse = tag.data;
tag = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_SELECTION);
if isempty(tag)
close_file;
error(me,'Source selection information missing');
end
res.inuse = int32(tag.data');
res.vertno = int32(zeros(1,res.nuse));
if length(res.inuse) ~= res.np
close_file;
error(me,'Incorrect number of entries in source space selection');
end
pp = 0;
for p = 1:res.np
if res.inuse(p)
pp = pp + 1;
res.vertno(pp) = p;
end
end
end
%
% Use triangulation
%
tag1 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NUSE_TRI);
tag2 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_USE_TRIANGLES);
if isempty(tag1) || isempty(tag2)
res.nuse_tri = int32(0);
res.use_tris = [];
else
res.nuse_tri = tag1.data;
res.use_tris = tag2.data;
end
%
% Patch-related information
%
tag1 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST);
tag2 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST_DIST);
if isempty(tag1) || isempty(tag2)
res.nearest = [];
res.nearest_dist = [];
else
res.nearest = tag1.data' + 1;
res.nearest_dist = tag2.data';
end
res.pinfo = mne_patch_info(res.nearest);
if ~isempty(res.pinfo)
fprintf(1,'Patch information added...');
end
%
% Distances
%
tag1 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_DIST);
tag2 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_DIST_LIMIT);
if isempty(tag1) || isempty(tag2)
res.dist = [];
res.dist_limit = [];
else
res.dist = tag1.data;
res.dist_limit = tag2.data;
%
% Add the upper triangle
%
res.dist = res.dist + res.dist';
end
return;
function [tag] = find_tag(node,findkind)
for p = 1:node.nent
if node.dir(p).kind == findkind
tag = fiff_read_tag(fid,node.dir(p).pos);
return;
end
end
tag = [];
return;
end
end
function complete_source_space_info
%
% Main triangulation
%
fprintf(1,'\tCompleting triangulation info...');
this.tri_area = zeros(1,this.ntri);
r1 = this.rr(this.tris(:,1),:);
r2 = this.rr(this.tris(:,2),:);
r3 = this.rr(this.tris(:,3),:);
this.tri_cent = (r1+r2+r3)/3.0;
this.tri_nn = cross((r2-r1),(r3-r1));
for p = 1:this.ntri
size = sqrt(this.tri_nn(p,:)*this.tri_nn(p,:)');
this.tri_area(p) = size/2.0;
this.tri_nn(p,:) = this.tri_nn(p,:)/size;
end
fprintf(1,'[done]\n');
%
% Selected triangles
%
fprintf(1,'\tCompleting selection triangulation info...');
if this.nuse_tri > 0
r1 = this.rr(this.use_tris(:,1),:);
r2 = this.rr(this.use_tris(:,2),:);
r3 = this.rr(this.use_tris(:,3),:);
this.use_tri_cent = (r1+r2+r3)/3.0;
this.use_tri_nn = cross((r2-r1),(r3-r1));
for p = 1:this.nuse_tri
this.use_tri_area(p) = sqrt(this.use_tri_nn(p,:)*this.use_tri_nn(p,:)')/2.0;
end
end
fprintf(1,'[done]\n');
end
function close_file
if open_here
fclose(fid);
end
end
end
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