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function ft_sourcewrite(cfg, source)
% FT_SOURCEWRITE exports source-reconstructed results to gifti or nifti format file.
% The appropriate output file depends on whether the source locations are described by
% on a cortically constrained sheet (gifti) or by a regular 3D lattice (nifti).
%
% Use as
% ft_sourcewrite(cfg, source)
% where source is a source structure obtained from FT_SOURCEANALYSIS and
% cfg is a structure that should contain
%
% cfg.filename = string, filename without the extension
% cfg.filetype = string, can be 'nifti', 'gifti' or 'cifti' (default is automatic)
% cfg.parameter = string, functional parameter to be written to file
% cfg.precision = string, can be 'single', 'double', etc.
%
% To facilitate data-handling and distributed computing you can use
% cfg.inputfile = ...
% If you specify this the input data will be read from a *.mat
% file on disk. This mat file should contain only a single variable,
% corresponding with the input data structure.
%
% See also FT_SOURCEANALYSIS, FT_SOURCEDESCRIPTIVES, FT_VOLUMEWRITE
% Copyright (C) 2011, Jan-Mathijs Schoffelen
% Copyright (C) 2011-2014, Jan-Mathijs Schoffelen, 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/>.
%
% $Id$
% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin = nargin;
ft_nargout = nargout;
% do the general setup of the function
ft_defaults
ft_preamble init
ft_preamble debug
ft_preamble loadvar source
ft_preamble provenance source
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
return
end
% ensure that the required options are present
cfg = ft_checkconfig(cfg, 'required', {'parameter', 'filename'});
% get the options
cfg.parameter = ft_getopt(cfg, 'parameter');
cfg.filename = ft_getopt(cfg, 'filename');
cfg.filetype = ft_getopt(cfg, 'filetype'); % the default is determined further down
cfg.brainstructure = ft_getopt(cfg, 'brainstructure'); % is used for cifti
cfg.parcellation = ft_getopt(cfg, 'parcellation'); % is used for cifti
cfg.precision = ft_getopt(cfg, 'precision'); % is used for cifti
% check if the input data is valid for this function
if strcmp(cfg.filetype, 'cifti')
% keep the transformation matrix
if isfield(source, 'transform')
transform = source.transform;
elseif isfield(source, 'brainordinate') && isfield(source.brainordinate, 'transform')
transform = source.brainordinate.transform;
else
transform = [];
end
if isfield(source, 'brainordinate')
% it is a parcellated source representation, i.e. the main structure one channel for each parcel
brainordinate = source.brainordinate;
source = rmfield(source, 'brainordinate');
% split them and check individually
source = ft_checkdata(source, 'datatype', {'timelock', 'freq', 'chan'}, 'feedback', 'yes');
brainordinate = ft_checkdata(brainordinate, 'datatype', 'parcellation', 'parcellationstyle', 'indexed', 'hasunit', 'yes');
% merge them again
source = copyfields(brainordinate, source, setdiff(fieldnames(brainordinate), {'cfg'}));
else
source = ft_checkdata(source, 'datatype', 'source', 'hasunit', true, 'feedback', 'yes');
end
% keep the transformation matrix
if ~isempty(transform)
source.transform = transform;
end
end % if cifti
if isempty(cfg.filetype)
if isfield(source, 'dim')
% source positions are on a regular 3D lattice, save as nifti
cfg.filetype = 'nifti';
elseif isfield(source, 'tri')
% there is a specification of a 2D cortical sheet, save as gifti
cfg.filetype = 'gifti';
else
ft_error('the input data does not look like a 2D sheet, nor as a 3D regular volume');
end
end
switch (cfg.filetype)
case 'nifti'
if numel(cfg.filename)<=4 || ~strcmp(cfg.filename(end-3:end), '.nii');
cfg.filename = cat(2, cfg.filename, '.nii');
end
% convert functional data into 4D
dat = getsubfield(source, cfg.parameter);
dat = reshape(dat, source.dim(1), source.dim(2), source.dim(3), []);
if ~isfield(source, 'transform')
source.transform = pos2transform(source.pos);
end
% this is a bit of a kludge, but ft_write_mri can write 3D and 4D nifti
ft_write_mri(cfg.filename, dat, 'dataformat', 'nifti', 'transform', source.transform);
case 'gifti'
if numel(cfg.filename)<=4 || ~strcmp(cfg.filename(end-3:end), '.gii');
cfg.filename = cat(2, cfg.filename, '.gii');
end
% this is a bit of a kludge, but ft_write_headshape can write gifti including data
ft_write_headshape(cfg.filename, source, 'data', getsubfield(source, cfg.parameter), 'format', 'gifti');
case 'cifti'
% brainstructure should represent the global anatomical structure, such as CortexLeft, Thalamus, etc.
% parcellation should represent the detailled parcellation, such as BA1, BA2, BA3, etc.
ft_write_cifti(cfg.filename, source, 'parameter', cfg.parameter, 'brainstructure', cfg.brainstructure, 'parcellation', cfg.parcellation, 'precision', cfg.precision);
otherwise
ft_error('unsupported output format "%s"', cfg.filetype);
end % switch filetype
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble previous source
ft_postamble provenance