/
make_nii.m
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make_nii.m
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% Make NIfTI structure specified by an N-D matrix. Usually, N is 3 for
% 3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the NIfTI structure is made, it can be saved into NIfTI file
% using "save_nii" command (for more detail, type: help save_nii).
%
% Usage: nii = make_nii(img, [voxel_size], [origin], [datatype], [description])
%
% Where:
%
% img: Usually, img is a 3D matrix [x y z], or a 4D
% matrix with time series [x y z t]. However,
% NIfTI allows a maximum of 7D matrix. When the
% image is in RGB format, make sure that the size
% of 4th dimension is always 3 (i.e. [R G B]). In
% that case, make sure that you must specify RGB
% datatype, which is either 128 or 511.
%
% voxel_size (optional): Voxel size in millimeter for each
% dimension. Default is [1 1 1].
%
% origin (optional): The AC origin. Default is [0 0 0].
%
% datatype (optional): Storage data type:
% 2 - uint8, 4 - int16, 8 - int32, 16 - float32,
% 32 - complex64, 64 - float64, 128 - RGB24,
% 256 - int8, 511 - RGB96, 512 - uint16,
% 768 - uint32, 1792 - complex128
% Default will use the data type of 'img' matrix
% For RGB image, you must specify it to either 128
% or 511.
%
% description (optional): Description of data. Default is ''.
%
% e.g.:
% origin = [33 44 13]; datatype = 64;
% nii = make_nii(img, [], origin, datatype); % default voxel_size
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function nii = make_nii(varargin)
nii.img = varargin{1};
dims = size(nii.img);
dims = [length(dims) dims ones(1,8)];
dims = dims(1:8);
voxel_size = [0 ones(1,7)];
origin = zeros(1,5);
descrip = '';
switch class(nii.img)
case 'uint8'
datatype = 2;
case 'int16'
datatype = 4;
case 'int32'
datatype = 8;
case 'single'
if isreal(nii.img)
datatype = 16;
else
datatype = 32;
end
case 'double'
if isreal(nii.img)
datatype = 64;
else
datatype = 1792;
end
case 'int8'
datatype = 256;
case 'uint16'
datatype = 512;
case 'uint32'
datatype = 768;
otherwise
error('Datatype is not supported by make_nii.');
end
if nargin > 1 & ~isempty(varargin{2})
voxel_size(2:4) = double(varargin{2});
end
if nargin > 2 & ~isempty(varargin{3})
origin(1:3) = double(varargin{3});
end
if nargin > 3 & ~isempty(varargin{4})
datatype = double(varargin{4});
if datatype == 128 | datatype == 511
dims(5) = [];
dims(1) = dims(1) - 1;
dims = [dims 1];
end
end
if nargin > 4 & ~isempty(varargin{5})
descrip = varargin{5};
end
if ndims(nii.img) > 7
error('NIfTI only allows a maximum of 7 Dimension matrix.');
end
maxval = round(double(max(nii.img(:))));
minval = round(double(min(nii.img(:))));
nii.hdr = make_header(dims, voxel_size, origin, datatype, ...
descrip, maxval, minval);
switch nii.hdr.dime.datatype
case 2
nii.img = uint8(nii.img);
case 4
nii.img = int16(nii.img);
case 8
nii.img = int32(nii.img);
case 16
nii.img = single(nii.img);
case 32
nii.img = single(nii.img);
case 64
nii.img = double(nii.img);
case 128
nii.img = uint8(nii.img);
case 256
nii.img = int8(nii.img);
case 511
img = double(nii.img(:));
img = single((img - min(img))/(max(img) - min(img)));
nii.img = reshape(img, size(nii.img));
nii.hdr.dime.glmax = double(max(img));
nii.hdr.dime.glmin = double(min(img));
case 512
nii.img = uint16(nii.img);
case 768
nii.img = uint32(nii.img);
case 1792
nii.img = double(nii.img);
otherwise
error('Datatype is not supported by make_nii.');
end
return; % make_nii
%---------------------------------------------------------------------
function hdr = make_header(dims, voxel_size, origin, datatype, ...
descrip, maxval, minval)
hdr.hk = header_key;
hdr.dime = image_dimension(dims, voxel_size, datatype, maxval, minval);
hdr.hist = data_history(origin, descrip);
return; % make_header
%---------------------------------------------------------------------
function hk = header_key
hk.sizeof_hdr = 348; % must be 348!
hk.data_type = '';
hk.db_name = '';
hk.extents = 0;
hk.session_error = 0;
hk.regular = 'r';
hk.dim_info = 0;
return; % header_key
%---------------------------------------------------------------------
function dime = image_dimension(dims, voxel_size, datatype, maxval, minval)
dime.dim = dims;
dime.intent_p1 = 0;
dime.intent_p2 = 0;
dime.intent_p3 = 0;
dime.intent_code = 0;
dime.datatype = datatype;
switch dime.datatype
case 2,
dime.bitpix = 8; precision = 'uint8';
case 4,
dime.bitpix = 16; precision = 'int16';
case 8,
dime.bitpix = 32; precision = 'int32';
case 16,
dime.bitpix = 32; precision = 'float32';
case 32,
dime.bitpix = 64; precision = 'float32';
case 64,
dime.bitpix = 64; precision = 'float64';
case 128
dime.bitpix = 24; precision = 'uint8';
case 256
dime.bitpix = 8; precision = 'int8';
case 511
dime.bitpix = 96; precision = 'float32';
case 512
dime.bitpix = 16; precision = 'uint16';
case 768
dime.bitpix = 32; precision = 'uint32';
case 1792,
dime.bitpix = 128; precision = 'float64';
otherwise
error('Datatype is not supported by make_nii.');
end
dime.slice_start = 0;
dime.pixdim = voxel_size;
dime.vox_offset = 0;
dime.scl_slope = 0;
dime.scl_inter = 0;
dime.slice_end = 0;
dime.slice_code = 0;
dime.xyzt_units = 0;
dime.cal_max = 0;
dime.cal_min = 0;
dime.slice_duration = 0;
dime.toffset = 0;
dime.glmax = maxval;
dime.glmin = minval;
return; % image_dimension
%---------------------------------------------------------------------
function hist = data_history(origin, descrip)
hist.descrip = descrip;
hist.aux_file = 'none';
hist.qform_code = 0;
hist.sform_code = 0;
hist.quatern_b = 0;
hist.quatern_c = 0;
hist.quatern_d = 0;
hist.qoffset_x = 0;
hist.qoffset_y = 0;
hist.qoffset_z = 0;
hist.srow_x = zeros(1,4);
hist.srow_y = zeros(1,4);
hist.srow_z = zeros(1,4);
hist.intent_name = '';
hist.magic = '';
hist.originator = origin;
return; % data_history