function bytestream=savenifti(img, filename, varargin)
%
% savenifti(img, filename)
% or
% savenifti(img, filename, rawhdr)
% savenifti(img, filename, 'nifti2')
% bytestream=savenifti(img)
%
% Write an image to a NIfTI (*.nii) or compressed NIfTI file (.nii.gz)
%
% author: Qianqian Fang (q.fang <at> neu.edu)
%
% input:
% img: this is a numerical array to be stored in the NIfTI file
% filename: output file name, can have a suffix of '.nii' or '.nii.gz'
% if a .gz suffix is used, this function needs the JSONLab
% (http://gitlab.com/fangq/jsonlab) and ZMat (http://gitlab.com/fangq/zmat)
% to perform the compression.
% rawhdr (optional): a struct, as a pre-created/loaded NIfTI header data structure
% if rawhdr is 'nifti1' or 'nifti2', this function calls
% nifticreate to create a default header.
% output:
% bytestream (optional): the output file byte stream. it only returns this output if
% no filename is given.
%
% example:
% a=single(rand(10,20,30));
% savenifti(a,'randnii.nii');
% savenifti(a,'randnii2.nii.gz','nifti2'); % needs zmat
%
%
% this file is part of JNIfTI specification: https://github.com/fangq/jnifti
%
% License: Apache 2.0, see https://github.com/fangq/jnifti for details
%
if(~isempty(varargin))
if(isstruct(varargin{1}))
header=varargin{1};
elseif(ischar(varargin{1}))
header=nifticreate(img,varargin{1});
end
else
header=nifticreate(img);
end
names=fieldnames(header);
buf=[];
for i=1:length(names)
buf=[buf,typecast(header.(names{i}),'uint8')];
end
if(length(buf)~=352 && length(buf)~=544)
error('incorrect nifti-1/2 header %d',length(buf));
end
buf=[buf,typecast(img(:)','uint8')];
if(nargout>1 && nargin<2)
bytestream=buf;
return;
end
if(regexp(filename,'\.[Gg][Zz]$'))
buf=gzipencode(buf);
end
fid=fopen(filename,'wb');
if(fid==0)
error('can not write to the specified file');
end
fwrite(fid,buf);
fclose(fid);
