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ft_read_headshape.m
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function [shape] = ft_read_headshape(filename, varargin)
% FT_READ_HEADSHAPE reads the fiducials and/or the measured headshape and/or meshes
% that describe headsurfaces, headmodels or cortical sheets from a variety of files
% (like CTF and Polhemus). The headshape and fiducials can for example be used for
% coregistration.
%
% Use as
% [shape] = ft_read_headshape(filename, ...)
% or
% [shape] = ft_read_headshape({filename1, filename2}, ...)
%
% If you specify the filename as a cell-array, the following situations are supported:
% - a two-element cell-array with the file names for the left and right hemisphere,
% e.g., FreeSurfer's {'lh.orig' 'rh.orig'}, or Caret's {'X.L.Y.Z.surf.gii' 'X.R.Y.Z.surf.gii'}
% - a two-element cell-array points to files that represent the coordinates and topology
% in separate files, e.g., Caret's {'X.L.Y.Z.coord.gii' 'A.L.B.C.topo.gii'}
% By default all information from the two files will be assumed to correspond to the
% left and right hemispeheres and concatenated. The option 'concatenate' can be set
% to 'no' to prevent them from being concatenated in a single structure.
%
% Additional options should be specified in key-value pairs and can include
% 'format' = string, see below
% 'coordsys' = string, e.g. 'head' or 'dewar' (only supported for CTF)
% 'unit' = string, e.g. 'mm' (default is the native units of the file)
% 'concatenate' = 'yes' or 'no' (default = 'yes')
% 'image' = path to corresponding image/jpg file
% 'surface' = specific surface to be read (only for Caret spec files)
% 'refine' = number, used for refining Structure Sensor meshes (default = 1)
% 'jmeshopt' = cell-array with {'name', 'value'} pairs, options for reading JSON/JMesh files
%
% Supported input file formats include
% 'gifti' see https://www.nitrc.org/projects/gifti/
% 'gmsh_ascii' see https://gmsh.info
% 'gmsh_binary' see https://gmsh.info
% 'matlab' containing FieldTrip or BrainStorm headshapes or cortical meshes
% 'mne_tri' MNE surface description in ASCII format
% 'mne_pos' MNE source grid in ascii format, described as 3D points
% 'neurojson_jmesh' NeuroJSON ascii JSON-based format
% 'neurojson_bmesh' NeuroJSON binary JSON-based format
% 'obj' Wavefront .obj file obtained with the Structure Sensor
% 'off' see http://www.geomview.org/docs/html/OFF.html
% 'ply' Stanford Polygon file format, for use with Paraview or Meshlab
% 'stl' STereoLithography file format, for use with CAD and/or generic 3D mesh editing programs
% 'tck' Mrtrix track file
% 'trk' Trackvis trk file
% 'vista' see http://www.cs.ubc.ca/nest/lci/vista/vista.html
% 'vtk' Visualization ToolKit file format, for use with Paraview
% 'vtk_xml' Visualization ToolKit file format
% 'itab_asc'
% 'ctf_*'
% '4d_*'
% 'neuromag_*'
% 'yokogawa_*'
% 'yorkinstruments_hdf5'
% 'polhemus_*'
% 'freesurfer_*'
% 'mne_source'
% 'spmeeg_mat'
% 'netmeg'
% 'tet'
% 'tetgen_ele'
% 'caret_surf'
% 'caret_coord'
% 'caret_topo'
% 'caret_spec'
% 'brainvisa_mesh'
% 'brainsuite_dfs'
%
% See also FT_READ_HEADMODEL, FT_READ_SENS, FT_READ_ATLAS, FT_WRITE_HEADSHAPE
% Copyright (C) 2008-2024, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% FieldTrip is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
% get the options
annotationfile = ft_getopt(varargin, 'annotationfile');
useimage = ft_getopt(varargin, 'useimage', true); % use image if hasimage
concatenate = ft_getopt(varargin, 'concatenate', 'yes');
coordsys = ft_getopt(varargin, 'coordsys', 'head'); % for ctf or neuromag_mne coil positions, the alternative is dewar
fileformat = ft_getopt(varargin, 'format');
unit = ft_getopt(varargin, 'unit');
image = ft_getopt(varargin, 'image'); % path to .jpg file
surface = ft_getopt(varargin, 'surface');
refine_ = ft_getopt(varargin, 'refine', 1); % do not confuse with the private/refine function
% Check the input, if filename is a cell-array, call FT_READ_HEADSHAPE recursively and combine the outputs.
% This is used to read the left and right hemisphere of a Freesurfer cortical segmentation.
if iscell(filename)
for i = 1:numel(filename)
tmp = ft_read_headshape(filename{i}, varargin{:});
haspos(i) = isfield(tmp, 'pos') && ~isempty(tmp.pos);
hastri(i) = isfield(tmp, 'tri') && ~isempty(tmp.tri);
if ~haspos(i), tmp.pos = []; end
if ~hastri(i), tmp.tri = []; end
if ~isfield(tmp, 'unit'), tmp.unit = 'unknown'; end
bnd(i) = tmp;
end
% Concatenate the meshes (only if 'concatenate' = 'yes' ) and if all
% structures have non-empty vertices and triangles. If not, the input filenames
% may have been caret-style coord and topo, which needs combination of
% the pos and tri.
if numel(filename)>1 && all(haspos==1) && strcmp(concatenate, 'yes')
if length(bnd)>2
ft_error('Cannot concatenate more than two files') % no more than two files are taken for cancatenation
else
fprintf('Concatenating the meshes in %s and %s\n', filename{1}, filename{2});
shape = [];
shape.pos = cat(1, bnd.pos);
npos = size(bnd(1).pos,1);
if isfield(bnd(1), 'tri') && isfield(bnd(2), 'tri')
shape.tri = cat(1, bnd(1).tri, bnd(2).tri + npos);
elseif ~isfield(bnd(1), 'tri') && ~isfield(bnd(2), 'tri')
% this is ok
else
ft_error('not all input files seem to contain a triangulation');
end
% concatenate any other fields
fnames = {'sulc' 'curv' 'area' 'thickness' 'atlasroi'};
for k = 1:numel(fnames)
if isfield(bnd(1), fnames{k}) && isfield(bnd(2), fnames{k})
shape.(fnames{k}) = cat(1, bnd.(fnames{k}));
elseif ~isfield(bnd(1), fnames{k}) && ~isfield(bnd(2), fnames{k})
% this is ok
else
ft_error('not all input files seem to contain a "%s"', fnames{k});
end
end
shape.brainstructure = []; % keeps track of the order of files in concatenation
for h = 1:length(bnd)
shape.brainstructure = [shape.brainstructure; h*ones(length(bnd(h).pos), 1)];
[p,f,e] = fileparts(filename{h});
% do an educated guess, otherwise default to the filename
iscortexright = contains(f,'rh');
iscortexright = iscortexright || contains(f,'.R.');
iscortexright = iscortexright || contains(f,'Right');
iscortexright = iscortexright || contains(f,'RIGHT');
iscortexleft = contains(f,'lh');
iscortexleft = iscortexleft || contains(f,'.L.');
iscortexleft = iscortexleft || contains(f,'Left');
iscortexleft = iscortexleft || contains(f,'LEFT');
if iscortexright && iscortexleft
% something strange is going on, default to the filename and let the user take care of this
shape.brainstructurelabel{h,1} = f;
elseif iscortexleft
shape.brainstructurelabel{h,1} = 'CORTEX_LEFT';
elseif iscortexright
shape.brainstructurelabel{h,1} = 'CORTEX_RIGHT';
else
% nothing to be guessed
shape.brainstructurelabel{h,1} = f;
end
end
end
elseif numel(filename)>1 && ~all(haspos==1)
if numel(bnd)>2
ft_error('Cannot combine more than two files') % no more than two files are taken for cancatenation
else
shape = [];
if sum(haspos==1)==1
fprintf('Using the vertex positions from %s\n', filename{haspos==1});
shape.pos = bnd(haspos==1).pos;
shape.unit = bnd(haspos==1).unit;
else
ft_error('Don''t know what to do');
end
if sum(hastri==1)==1
fprintf('Using the faces definition from %s\n', filename{hastri==1});
shape.tri = bnd(hastri==1).tri;
end
if max(shape.tri(:))~=size(shape.pos,1)
ft_error('mismatch in number of points in pos and tri');
end
end
else
% in case numel(filename)==1, or strcmp(concatenate, 'no')
shape = bnd;
end
return
end % if iscell
% some of the code does not work well on matlab strings, (i.e. "" vs ''),
% specifically ["a" "b"] yields something different than ['a' 'b'].
if isstring(filename)
filename = char(filename);
end
% optionally get the data from the URL and make a temporary local copy
filename = fetch_url(filename);
if isempty(fileformat)
% only do the autodetection if the format was not specified
fileformat = ft_filetype(filename);
end
% checks if there exists a .jpg file of 'filename'
[pathstr,name] = fileparts(filename);
if useimage
if exist(fullfile(pathstr,[name,'.jpg']), 'file')
image = fullfile(pathstr,[name,'.jpg']);
hasimage = true;
elseif exist(fullfile(pathstr,[name,'.JPG']), 'file')
image = fullfile(pathstr,[name,'.JPG']);
hasimage = true;
elseif exist(fullfile(pathstr,[name,'.png']), 'file')
image = fullfile(pathstr,[name,'.png']);
hasimage = true;
elseif exist(fullfile(pathstr,[name,'.PNG']), 'file')
image = fullfile(pathstr,[name,'.PNG']);
hasimage = true;
else
hasimage = false;
end
else
hasimage = false;
end
if ~isempty(annotationfile) && ~strcmp(fileformat, 'mne_source')
ft_error('extracting annotation information only works for ''mne_source'' files');
end
% start with an empty structure
shape = [];
shape.pos = [];
switch fileformat
case {'ctf_ds', 'ctf_hc', 'ctf_meg4', 'ctf_res4', 'ctf_old'}
[p, f, x] = fileparts(filename);
if strcmp(fileformat, 'ctf_old')
fileformat = ft_filetype(filename);
end
if strcmp(fileformat, 'ctf_ds')
filename = fullfile(p, [f x], [f '.hc']);
elseif strcmp(fileformat, 'ctf_meg4')
filename = fullfile(p, [f '.hc']);
elseif strcmp(fileformat, 'ctf_res4')
filename = fullfile(p, [f '.hc']);
end
orig = read_ctf_hc(filename);
switch coordsys
case 'head'
shape.fid.pos = cell2mat(struct2cell(orig.head));
shape.coordsys = 'ctf';
case 'dewar'
shape.fid.pos = cell2mat(struct2cell(orig.dewar));
shape.coordsys = 'dewar';
otherwise
ft_error('incorrect coordsys specified');
end
shape.fid.label = fieldnames(orig.head);
case 'ctf_shape'
orig = read_ctf_shape(filename);
shape.pos = orig.pos;
% The file also contains fiducial information, but those are in MRI voxels and
% inconsistent with the headshape itself.
%
% shape.fid.label = {'NASION', 'LEFT_EAR', 'RIGHT_EAR'};
% shape.fid.pos = zeros(0,3); % start with an empty array
% for i = 1:numel(shape.fid.label)
% shape.fid.pos = cat(1, shape.fid.pos, getfield(orig.MRI_Info, shape.fid.label{i}));
% end
case {'4d_xyz', '4d_m4d', '4d_hs', '4d', '4d_pdf'}
[p, f, x] = fileparts(filename);
if ~strcmp(fileformat, '4d_hs')
filename = fullfile(p, 'hs_file');
end
[shape.pos, fid] = read_bti_hs(filename);
% I'm making some assumptions here
% which I'm not sure will work on all 4D systems
% fid = fid(1:3, :);
[junk, NZ] = max(fid(1:3,1));
[junk, L] = max(fid(1:3,2));
[junk, R] = min(fid(1:3,2));
rest = setdiff(1:size(fid,1),[NZ L R]);
shape.fid.pos = fid([NZ L R rest], :);
shape.fid.label = {'NZ', 'L', 'R'};
if ~isempty(rest)
for i = 4:size(fid,1)
shape.fid.label{i} = ['fiducial' num2str(i)];
% in a 5 coil configuration this corresponds with Cz and Inion, or
% wherever the researcher has placed the coils
end
end
shape.coordsys = '4d';
case 'itab_asc'
shape = read_itab_asc(filename);
case 'gifti'
ft_hastoolbox('gifti', 1);
g = gifti(filename);
if ~isfield(g, 'vertices')
ft_error('%s does not contain a tesselated surface', filename);
end
shape.pos = ft_warp_apply(g.mat, g.vertices);
shape.tri = g.faces;
shape.unit = 'mm'; % defined in the GIFTI standard to be milimeter
if isfield(g, 'cdata')
shape.mom = g.cdata;
end
case {'caret_surf' 'caret_topo' 'caret_coord'}
ft_hastoolbox('gifti', 1);
g = gifti(filename);
if ~isfield(g, 'vertices') && strcmp(fileformat, 'caret_topo')
try
% do a clever guess by replacing topo with coord
g2 = gifti(strrep(filename, '.topo.', '.coord.'));
vertices = ft_warp_apply(g2.mat, g2.vertices);
catch
vertices = [];
end
else
vertices = ft_warp_apply(g.mat, g.vertices);
end
if ~isfield(g, 'faces') && strcmp(fileformat, 'caret_coord')
try
% do a clever guess by replacing topo with coord
g2 = gifti(strrep(filename, '.coord.', '.topo.'));
faces = g2.faces;
catch
faces = [];
end
else
faces = g.faces;
end
shape.pos = vertices;
shape.tri = faces;
if isfield(g, 'cdata')
shape.mom = g.cdata;
end
% check whether there is curvature info etc
filename = strrep(filename, '.surf.', '.shape.');
filename = strrep(filename, '.topo.', '.shape.');
filename = strrep(filename, '.coord.', '.shape.');
[p,f,e] = fileparts(filename);
tok = tokenize(f, '.');
if length(tok)>2
tmpfilename = strrep(filename, tok{3}, 'sulc');
if exist(tmpfilename, 'file'), g = gifti(tmpfilename); shape.sulc = g.cdata; end
if exist(strrep(tmpfilename, 'sulc', 'curvature'), 'file'), g = gifti(strrep(tmpfilename, 'sulc', 'curvature')); shape.curv = g.cdata; end
if exist(strrep(tmpfilename, 'sulc', 'thickness'), 'file'), g = gifti(strrep(tmpfilename, 'sulc', 'thickness')); shape.thickness = g.cdata; end
if exist(strrep(tmpfilename, 'sulc', 'atlasroi'), 'file'), g = gifti(strrep(tmpfilename, 'sulc', 'atlasroi')); shape.atlasroi = g.cdata; end
end
case 'caret_spec'
[p, f, e] = fileparts(filename);
[spec, headerinfo] = read_caret_spec(filename);
fn = fieldnames(spec);
% concatenate the filenames that contain coordinates
% concatenate the filenames that contain topologies
coordfiles = {};
topofiles = {};
for k = 1:numel(fn)
if ~isempty(strfind(fn{k}, 'topo'))
topofiles = cat(1,topofiles, fullfile(p,spec.(fn{k})));
end
if ~isempty(strfind(fn{k}, 'coord'))
coordfiles = cat(1,coordfiles, fullfile(p,spec.(fn{k})));
end
end
if isempty(surface)
[selcoord, ok] = listdlg('ListString',coordfiles,'SelectionMode','single','PromptString','Select a file describing the coordinates');
else
selcoord = find(contains(coordfiles, surface));
end
if numel(topofiles)>1
[seltopo, ok] = listdlg('ListString',topofiles,'SelectionMode','single','PromptString','Select a file describing the topology');
else
seltopo = 1;
end
% recursively call ft_read_headshape
tmp1 = ft_read_headshape(coordfiles{selcoord});
tmp2 = ft_read_headshape(topofiles{seltopo});
% quick and dirty sanity check to see whether the indexing of the
% points in the topology matches the number of points
if max(tmp2.tri(:))~=size(tmp1.pos,1)
ft_error('there''s a mismatch between the number of points used in the topology, and described by the coordinates');
end
shape = tmp1;
shape.tri = tmp2.tri;
case 'neuromag_mex'
[co,ki,nu] = hpipoints(filename);
fid = co(:,ki==1)';
[junk, NZ] = max(fid(:,2));
[junk, L] = min(fid(:,1));
[junk, R] = max(fid(:,1));
shape.fid.pos = fid([NZ L R], :);
shape.fid.label = {'NZ', 'L', 'R'};
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
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
% 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
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)];
shape.label = c.struct_names;
shape.annotation = c.orig_tab; % to be able to recover which one
shape.ctable = c.table;
end
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'}
orig = read_neuromag_hc(filename);
switch coordsys
case 'head'
fidN=1;
posN=1;
for i=1:size(orig.head.pos,1)
if strcmp(orig.head.label{i}, 'LPA') || strcmp(orig.head.label{i}, 'Nasion') || strcmp(orig.head.label{i}, 'RPA')
shape.fid.pos(fidN,1:3) = orig.head.pos(i,:);
shape.fid.label{fidN} = orig.head.label{i};
fidN = fidN + 1;
else
shape.pos(posN,1:3) = orig.head.pos(i,:);
shape.label{posN} = orig.head.label{i};
posN = posN + 1;
end
end
shape.coordsys = orig.head.coordsys;
case 'dewar'
fidN=1;
posN=1;
for i=1:size(orig.dewar.pos,1)
if strcmp(orig.dewar.label{i}, 'LPA') || strcmp(orig.dewar.label{i}, 'Nasion') || strcmp(orig.dewar.label{i}, 'RPA')
shape.fid.pos(fidN,1:3) = orig.dewar.pos(i,:);
shape.fid.label{fidN} = orig.dewar.label{i};
fidN = fidN + 1;
else
shape.pos(posN,1:3) = orig.dewar.pos(i,:);
shape.label{posN} = orig.dewar.label{i};
posN = posN + 1;
end
end
shape.coordsys = orig.dewar.coordsys;
otherwise
ft_error('incorrect coordinates specified');
end
case {'ricoh_mrk', 'ricoh_ave', 'ricoh_con'}
hdr = read_ricoh_header(filename);
%% An exported file or an original one
isexported = hdr.orig.digitize.info.done;
%% Marker-coil positions
mrk_pnt = hdr.orig.coregist.hpi;
if any([mrk_pnt(:).meg_pos])
mrk_pos = cat(1, mrk_pnt(1:end).meg_pos);
mrk_label = transpose({mrk_pnt(1:end).label});
sw_ind = [3 1 2];
mrk_pos(1:3,:)= mrk_pos(sw_ind, :);
mrk_pos = mrk_pos * 100; % unit: cm
mrk_label(1:3,:)= mrk_label(sw_ind, :);
else
ft_error('No coil information found in the file');
end
%% Digitized points
if ~isexported
ft_info('The input file is an original one: only marker-coil positions are loaded\n');
% The fiducial points are represented by the marker-coil positions.
if any([mrk_pnt(:).meg_pos])
shape.fid.pos = mrk_pos; % unit: cm
shape.fid.label = {'nas'; 'lpa'; 'rpa'; 'Marker4'; 'Marker5'};
end
else
ft_info('The input file is a third-party-exported one including the digitized points\n');
% All digitized points
dig_pnt = hdr.orig.digitize.point;
digitizer2meg = hdr.orig.digitize.info.digitizer2meg;
R = digitizer2meg(1:3,1:3);
T = digitizer2meg(1:3,4);
% Transform to MEG coordinate:
shape.pos = transpose( R * [[dig_pnt.x]; [dig_pnt.y]; [dig_pnt.z]] + repmat(T, 1, numel(dig_pnt))).*100; % unit: cm
shape.label = transpose( deblank({dig_pnt(1:end).name}));
% Fiducial points
nas = find(strcmpi(shape.label, 'fidnz'));
lpa = find(strcmpi(shape.label, 'fidt9'));
rpa = find(strcmpi(shape.label, 'fidt10'));
if ~isempty(nas) && ~isempty(lpa) && ~isempty(rpa)
anatfid_pos = [ shape.pos(nas,:) ; shape.pos(lpa,:) ; shape.pos(rpa,:) ];
anatfid_label = {'nas'; 'lpa'; 'rpa'};
end
% HPIs
HPI_1 = find(strcmpi(shape.label, 'HPI_1'));
HPI_2 = find(strcmpi(shape.label, 'HPI_2'));
HPI_3 = find(strcmpi(shape.label, 'HPI_3'));
HPI_4 = find(strcmpi(shape.label, 'HPI_4'));
HPI_5 = find(strcmpi(shape.label, 'HPI_5'));
if ~isempty(HPI_1) && ~isempty(HPI_2) && ~isempty(HPI_3) && ~isempty(HPI_4) && ~isempty(HPI_5)
HPI_pos = [ shape.pos(HPI_3,:) ;...
shape.pos(HPI_1,:) ;...
shape.pos(HPI_2,:) ;...
shape.pos(HPI_4,:) ;...
shape.pos(HPI_5,:) ];
HPI_label = { 'HPI_3'; 'HPI_1'; 'HPI_2'; 'HPI_4'; 'HPI_5' };
end
shape.fid.pos = [ anatfid_pos; HPI_pos; mrk_pos ];
shape.fid.label = [ anatfid_label; HPI_label; mrk_label ];
end
% 'cm' as a unit for 'pos':
shape.unit = 'cm';
case {'yokogawa_mrk', 'yokogawa_ave', 'yokogawa_con'}
if ft_hastoolbox('yokogawa_meg_reader')
hdr = read_yokogawa_header_new(filename);
%% Marker-coil positions
mrk_pnt = hdr.orig.coregist.hpi;
% markers 1-3 identical to zero: try *.mrk file
if ~any([mrk_pnt(:).meg_pos])
ft_info('Reading marker-coil positions from a .mrk file\n');
[p, f, x] = fileparts(filename);
filename = fullfile(p, [f '.mrk']);
if exist(filename, 'file')
hdr_tmp = read_yokogawa_header_new(filename);
mrk_pnt = hdr_tmp.orig.coregist.hpi;
end
end
if any([mrk_pnt(:).meg_pos])
mrk_pos = cat(1, mrk_pnt(1:end).meg_pos);
mrk_label = transpose({mrk_pnt(1:end).label});
sw_ind = [3 1 2];
mrk_pos(1:3,:)= mrk_pos(sw_ind, :);
mrk_pos = mrk_pos * 100; % unit: cm
mrk_label(1:3,:)= mrk_label(sw_ind, :);
else
ft_error('No coil information found in the file');
end
%% An exported file or an original one
isexported = hdr.orig.digitize.info.done;
%% Digitized points
if ~isexported
ft_info('The input file is an original one: only marker-coil positions are loaded\n');
% The fiducial points are represented by the marker-coil positions.
if any([mrk_pnt(:).meg_pos])
shape.fid.pos = mrk_pos; % unit: cm
shape.fid.label = {'nas'; 'lpa'; 'rpa'; 'Marker4'; 'Marker5'};
end
else
ft_info('The input file is a third-party-exported one including the digitized points\n');
% All digitized points
dig_pnt = hdr.orig.digitize.point;
digitizer2meg = hdr.orig.digitize.info.digitizer2meg;
R = digitizer2meg(1:3,1:3);
T = digitizer2meg(1:3,4);
% Transform to MEG coordinate:
shape.pos = transpose( R * [[dig_pnt.x]; [dig_pnt.y]; [dig_pnt.z]] + repmat(T, 1, numel(dig_pnt))).*100; % unit: cm
shape.label = transpose( deblank({dig_pnt(1:end).name}));
% Fiducial points
nas = find(strcmpi(shape.label, 'fidnz'));
lpa = find(strcmpi(shape.label, 'fidt9'));
rpa = find(strcmpi(shape.label, 'fidt10'));
if ~isempty(nas) && ~isempty(lpa) && ~isempty(rpa)
anatfid_pos = [ shape.pos(nas,:) ; shape.pos(lpa,:) ; shape.pos(rpa,:) ];
anatfid_label = {'nas'; 'lpa'; 'rpa'};
end
% HPIs
HPI_1 = find(strcmpi(shape.label, 'HPI_1'));
HPI_2 = find(strcmpi(shape.label, 'HPI_2'));
HPI_3 = find(strcmpi(shape.label, 'HPI_3'));
HPI_4 = find(strcmpi(shape.label, 'HPI_4'));
HPI_5 = find(strcmpi(shape.label, 'HPI_5'));
if ~isempty(HPI_1) && ~isempty(HPI_2) && ~isempty(HPI_3) && ~isempty(HPI_4) && ~isempty(HPI_5)
HPI_pos = [ shape.pos(HPI_3,:) ;...
shape.pos(HPI_1,:) ;...
shape.pos(HPI_2,:) ;...
shape.pos(HPI_4,:) ;...
shape.pos(HPI_5,:) ];
HPI_label = { 'HPI_3'; 'HPI_1'; 'HPI_2'; 'HPI_4'; 'HPI_5' };
end
shape.fid.pos = [ anatfid_pos; HPI_pos; mrk_pos ];
shape.fid.label = [ anatfid_label; HPI_label; mrk_label ];
end
% 'cm' as a unit for 'pos':
shape.unit = 'cm';
else % the case that "yokogawa_meg_reader" is not available
hdr = read_yokogawa_header(filename);
marker = hdr.orig.matching_info.marker;
% markers 1-3 identical to zero: try *.mrk file
if ~any([marker(:).meg_pos])
[p, f, x] = fileparts(filename);
filename = fullfile(p, [f '.mrk']);
if exist(filename, 'file')
hdr = read_yokogawa_header(filename);
marker = hdr.orig.matching_info.marker;
end
end
% non zero markers 1-3
if any([marker(:).meg_pos])
shape.fid.pos = cat(1, marker(1:5).meg_pos);
sw_ind = [3 1 2];
shape.fid.pos(1:3,:)= shape.fid.pos(sw_ind, :);
shape.fid.label = {'nas'; 'lpa'; 'rpa'; 'Marker4'; 'Marker5'};
else
ft_error('no coil information found in Yokogawa file');
end
% convert to the units of the grad, the desired default for yokogawa is centimeter.
shape = ft_convert_units(shape, 'cm');
end
case 'yokogawa_raw'
if ft_hastoolbox('yokogawa_meg_reader')
hdr = read_yokogawa_header_new(filename);
marker = hdr.orig.coregist.hpi;
else
hdr = read_yokogawa_header(filename);
marker = hdr.orig.matching_info.marker;
end
% markers 1-3 identical to zero: try *.mrk file
if ~any([marker(:).meg_pos])
[p, f, x] = fileparts(filename);
filename = fullfile(p, [f '.mrk']);
if exist(filename, 'file')
if ft_hastoolbox('yokogawa_meg_reader')
hdr = read_yokogawa_header_new(filename);
marker = hdr.orig.coregist.hpi;
else
hdr = read_yokogawa_header(filename);
marker = hdr.orig.matching_info.marker;
end
end
end
% non zero markers 1-3
if any([marker(:).meg_pos])
shape.fid.pos = cat(1, marker(1:5).meg_pos);
sw_ind = [3 1 2];
shape.fid.pos(1:3,:)= shape.fid.pos(sw_ind, :);
shape.fid.label = {'nas'; 'lpa'; 'rpa'; 'Marker4'; 'Marker5'};
else
ft_error('no coil information found in Yokogawa file');
end
% convert to the units of the grad, the desired default for yokogawa is centimeter.
shape = ft_convert_units(shape, 'cm');
% case {'yokogawa_mrk', 'yokogawa_ave', 'yokogawa_con', 'yokogawa_raw' }
% if ft_hastoolbox('yokogawa_meg_reader')
% hdr = read_yokogawa_header_new(filename);
% marker = hdr.orig.coregist.hpi;
% else
% hdr = read_yokogawa_header(filename);
% marker = hdr.orig.matching_info.marker;
% end
%
% % markers 1-3 identical to zero: try *.mrk file
% if ~any([marker(:).meg_pos])
% [p, f, x] = fileparts(filename);
% filename = fullfile(p, [f '.mrk']);
% if exist(filename, 'file')
% if ft_hastoolbox('yokogawa_meg_reader')
% hdr = read_yokogawa_header_new(filename);
% marker = hdr.orig.coregist.hpi;
% else
% hdr = read_yokogawa_header(filename);
% marker = hdr.orig.matching_info.marker;
% end
% end
% end
%
% % non zero markers 1-3
% if any([marker(:).meg_pos])
% shape.fid.pos = cat(1, marker(1:5).meg_pos);
% sw_ind = [3 1 2];
% shape.fid.pos(1:3,:)= shape.fid.pos(sw_ind, :);
% shape.fid.label = {'nas'; 'lpa'; 'rpa'; 'Marker4'; 'Marker5'};
% else
% ft_error('no coil information found in Yokogawa file');
% end
%
% % convert to the units of the grad, the desired default for yokogawa is centimeter.
% shape = ft_convert_units(shape, 'cm');
case 'yokogawa_coregis'
in_str = textread(filename, '%s');
nr_items = size(in_str,1);
ind = 1;
coil_ind = 1;
shape.fid.pos = [];
shape.fid.label = {};
while ind < nr_items
if strcmp(in_str{ind},'MEG:x=')
shape.fid.pos = [shape.fid.pos; str2num(strtok(in_str{ind+1},[',','['])) ...
str2num(strtok(in_str{ind+3},[',','['])) str2num(strtok(in_str{ind+5},[',','[']))];
shape.fid.label = [shape.fid.label ; ['Marker',num2str(coil_ind)]];
coil_ind = coil_ind + 1;
ind = ind + 6;
else
ind = ind +1;
end
end
if size(shape.fid.label,1) ~= 5
ft_error('Wrong number of coils');
end
sw_ind = [3 1 2];
shape.fid.pos(1:3,:)= shape.fid.pos(sw_ind, :);
shape.fid.label(1:3)= {'nas', 'lpa', 'rpa'};
case 'yokogawa_hsp'
fid = fopen_or_error(filename, 'rt');
fidstart = false;
hspstart = false;
% try to locate the fiducial positions
while ~fidstart && ~feof(fid)
line = fgetl(fid);
if ~isempty(strmatch('//Position of fiducials', line))
fidstart = true;
end
end
if fidstart
line_xpos = fgetl(fid);
line_ypos = fgetl(fid);
line_yneg = fgetl(fid);
xpos = sscanf(line_xpos(3:end), '%f');
ypos = sscanf(line_ypos(3:end), '%f');
yneg = sscanf(line_yneg(3:end), '%f');
shape.fid.pos = [
xpos(:)'
ypos(:)'
yneg(:)'
];
shape.fid.label = {
'X+'
'Y+'
'Y-'
};
end
% try to locate the fiducial positions
while ~hspstart && ~feof(fid)
line = fgetl(fid);
if ~isempty(strmatch('//No of rows', line))
hspstart = true;
end
end
if hspstart
line = fgetl(fid);
siz = sscanf(line, '%f');
shape.pos = zeros(siz(:)');
for i=1:siz(1)
line = fgetl(fid);
shape.pos(i,:) = sscanf(line, '%f');
end
end
fclose(fid);
case 'yorkinstruments_hdf5'
acquisition='default';
try
shape.pos=transpose(h5read(filename, '/geometry/head_shape/head_shape'));
catch
error('Headshape data not found.');
end
shape.unit='mm';
temp=h5info(filename, '/geometry/fiducials/');
Nfids=length(temp.Groups);
for i=1:Nfids
[null, shape.fid.label{i}, null]= fileparts(temp.Groups(i).Name);
shape.fid.pos(i,1:3)=h5read(filename, strcat('/geometry/fiducials/',shape.fid.label{i} ,'/location'));
end
if isempty(coordsys)
coordsys='dewar'
end
if strcmp(coordsys,'dewar')
try
tCCStoMegscanScs = h5read(filename,[strcat('/acquisitions/',char(string(acquisition))) '/ccs_to_scs_transform']);
T = maketform('affine',tCCStoMegscanScs);
shape.pos=tforminv(T,shape.pos(:,1),shape.pos(:,2),shape.pos(:,3));
shape.fid.pos=tforminv(T,shape.fid.pos(:,1),shape.fid.pos(:,2),shape.fid.pos(:,3));
catch
error('No head to dewar transform available in hdf5 file');
end
end
case 'ply'
[vert, face] = read_ply(filename);
shape.pos = [vert.x vert.y vert.z];
if isfield(vert, 'red') && isfield(vert, 'green') && isfield(vert, 'blue')
shape.color = double([vert.red vert.green vert.blue])/255;
end
switch size(face,2)
case 3
shape.tri = face;
case 4
shape.tet = face;
case 8
shape.hex = face;
end
case 'polhemus_fil'
[shape.fid.pos, shape.pos, shape.fid.label] = read_polhemus_fil(filename, 0);
case 'polhemus_pos'
[shape.fid.pos, shape.pos, shape.fid.label] = read_ctf_pos(filename);
case 'spmeeg_mat'
tmp = load(filename);
if isfield(tmp.D, 'fiducials') && ~isempty(tmp.D.fiducials)
shape = tmp.D.fiducials;
else
ft_error('no headshape found in SPM EEG file');
end
case 'matlab'
% determine which variables are contained in the file
tmp = load(filename);
if isfield(tmp, 'shape')
shape = tmp.shape;
elseif isfield(tmp, 'headshape')
shape = tmp.headshape;
elseif isfield(tmp, 'surface')
shape = tmp.surface;
elseif isfield(tmp, 'bnd')
% the variable in the file is most likely a precomputed triangulation of some sort
shape = tmp.bnd;
elseif isfield(tmp, 'mesh')
% the variable in the file is most likely a precomputed triangulation of some sort
shape = tmp.mesh;
elseif isfield(tmp, 'elec')
% represent the electrodes as headshape
tmp.elec = ft_datatype_sens(tmp.elec);
shape.fid.pos = tmp.elec.chanpos;
shape.fid.label = tmp.elec.label;
elseif isfield(tmp, 'Vertices')
% this applies to BrainStorm cortical meshes
shape.pos = tmp.Vertices;
% copy some optional fields over with a new name
shape = copyfields(tmp, shape, {'Faces', 'Curvature', 'SulciMap'});
shape = renamefields(shape, {'Faces', 'Curvature', 'SulciMap'}, {'tri', 'curv', 'sulc'});
elseif numel(fieldnames(tmp))==1
fn = fieldnames(tmp);
shape = tmp.(fn{1});
% check that it has vertices and triangles
assert(isfield(shape, 'pos') && isfield(shape, 'tri'), 'no headshape found in MATLAB file')
else
ft_error('no headshape found in MATLAB file');
end
case {'freesurfer_triangle_binary', 'freesurfer_quadrangle'}
% the freesurfer toolbox is required for this
ft_hastoolbox('freesurfer', 1);
[pos, tri] = read_surf(filename);
if min(tri(:)) == 0
% start counting from 1
tri = tri + 1;
end
shape.pos = pos;
shape.tri = tri;
% for the left and right
[path,name,ext] = fileparts(filename);
if strcmp(ext, '.inflated') % does the shift only for inflated surface
if strcmp(name, 'lh')
% assume freesurfer inflated mesh in mm, mni space
% move the mesh a bit to the left, to avoid overlap with the right
% hemisphere
shape.pos(:,1) = shape.pos(:,1) - max(shape.pos(:,1)) - 10;
elseif strcmp(name, 'rh')
% id.
% move the mesh a bit to the right, to avoid overlap with the left
% hemisphere
shape.pos(:,1) = shape.pos(:,1) - min(shape.pos(:,1)) + 10;