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% Copyright (c) 2008-2025 the MRtrix3 contributors.
%
% This Source Code Form is subject to the terms of the Mozilla Public
% License, v. 2.0. If a copy of the MPL was not distributed with this
% file, You can obtain one at http://mozilla.org/MPL/2.0/.
%
% Covered Software is provided under this License on an "as is"
% basis, without warranty of any kind, either expressed, implied, or
% statutory, including, without limitation, warranties that the
% Covered Software is free of defects, merchantable, fit for a
% particular purpose or non-infringing.
% See the Mozilla Public License v. 2.0 for more details.
%
% For more details, see http://www.mrtrix.org/.
function write_mrtrix (image, filename)
% function: write_mrtrix (image, filename)
%
% write the data contained in the structure 'image' in the MRtrix
% format image 'filename' (i.e. files with the extension '.mif' or '.mih').
%
% 'image' is either a N-dimensional array (N <= 16), or a structure containing
% the following fields:
% image.data: a N-dimensional array (N <= 16)
% image.vox: N-vector of voxel sizes (in mm) (default: { 2 }) [optional]
% image.comments: a cell array of strings [optional]
% image.datatype: the datatype specifier (default: float32) [optional]
% image.mrtrix_version: a character array [optional]
% image.transform: a 4x4 matrix [optional]
% image.dw_scheme: a NDWx4 matrix of gradient directions [optional]
% helper function: acts as ternary conditional operator
choose = @(varargin)varargin{end-varargin{1}};
fid = fopen (filename, 'w');
assert(fid ~= -1, 'error opening %s', filename);
fprintf (fid, 'mrtrix image\ndim: ');
if isstruct(image)
dim = size(image.data);
else
dim = size(image);
end
while prod(size(dim)) < 3
dim(end+1) = 1;
end
fprintf (fid, '%d', dim(1));
fprintf (fid, ',%d', dim(2:end));
fprintf (fid, '\nvox: ');
if isstruct (image) && isfield (image, 'vox')
fprintf (fid, '%.15f', image.vox(1));
fprintf (fid, ',%.15f', image.vox(2:end));
else
fprintf(fid, '2');
fprintf(fid, ',%d', 2*ones(1,size(dim,2)-1));
end
fprintf (fid, '\nlayout: +0');
fprintf (fid, ',+%d', 1:(size(dim,2)-1));
[computerType, maxSize, endian] = computer;
if isstruct (image) && isfield (image, 'datatype')
datatype = lower(image.datatype);
switch datatype(end-1:end)
case 'le', precision = datatype(1:end-2); byteorder = 'l';
case 'be', precision = datatype(1:end-2); byteorder = 'b';
otherwise
switch datatype
case 'bit', precision = 'bit1'; byteorder = 'n';
case { 'int8', 'uint8' }, precision = datatype; byteorder = 'n';
otherwise,
precision = datatype;
datatype = [ datatype choose(endian=='L','le','be') ];
byteorder = choose (endian=='L', 'l', 'b');
end
end
else
datatype = [ 'float32' choose(endian=='L','le','be') ];
precision = 'float32';
byteorder = choose (endian=='L', 'l', 'b');
end
fprintf (fid, [ '\ndatatype: ' datatype ]);
fprintf (fid, '\nmrtrix_version: %s', 'matlab');
if isstruct (image) && isfield (image, 'transform')
fprintf (fid, '\ntransform: %.15f', image.transform(1,1));
fprintf (fid, ',%.15f', image.transform(1,2:4));
fprintf (fid, '\ntransform: %.15f', image.transform(2,1));
fprintf (fid, ',%.15f', image.transform(2,2:4));
fprintf (fid, '\ntransform: %.15f', image.transform(3,1));
fprintf (fid, ',%.15f', image.transform(3,2:4));
end
if isstruct (image) && isfield (image, 'dw_scheme')
for i=1:size(image.dw_scheme,1)
fprintf (fid, '\ndw_scheme: %.15f', image.dw_scheme(i,1));
fprintf (fid, ',%.15f', image.dw_scheme(i,2:4));
end
end
% write out any other fields:
if isstruct (image)
f = fieldnames(image);
% don't worry about fields that have already been dealt with:
f(strcmp(f,'dim')) = [];
f(strcmp(f,'vox')) = [];
f(strcmp(f,'layout')) = [];
f(strcmp(f,'datatype')) = [];
f(strcmp(f,'transform')) = [];
f(strcmp(f,'dw_scheme')) = [];
f(strcmp(f,'data')) = [];
% write out contents of the remainging fields:
for n = 1:numel(f)
val = getfield (image, f{n});
if iscell (val)
for i=1:numel(val)
fprintf (fid, '\n%s: %s', f{n}, val{i});
end
else
fprintf (fid, '\n%s: %s', f{n}, val);
end
end
end
fprintf (fid, '\nfile: ');
[filepath,basename,ext] = fileparts(filename);
if strcmp(ext, '.mif')
dataoffset = ftell (fid) + 18;
dataoffset = dataoffset + mod((4 - mod(dataoffset, 4)), 4);
s = sprintf ('. %d\nEND\n ', dataoffset);
s = s(1:(dataoffset-ftell(fid)));
fprintf (fid, s);
fclose (fid);
fid = fopen (filename, 'a+', byteorder);
elseif strcmp(ext, '.mih')
datafile = fullfile(filepath, strcat(basename,'.dat'));
fprintf (fid, '%s 0\nEND\n', datafile);
fclose(fid);
fid = fopen (datafile, 'w', byteorder);
else
fclose(fid);
error('unknown file suffix "%s" - aborting', ext);
end
if isstruct(image)
fwrite (fid, image.data, precision);
else
fwrite (fid, image, precision);
end
fclose (fid);
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