savenifti.m

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/NeuroJSON/jsonlab) and ZMat (http://gitlab.com/NeuroJSON/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/NeuroJSON/jnifti
%
%    License: Apache 2.0, see https://github.com/NeuroJSON/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);