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function nii = nii2jnii(filename, format, varargin)
%
% nii=nii2jnii(niifile, format, options)
% or
% nii2jnii(niifile, jniifile, options)
% nii=nii2jnii(niifile)
%
% A fast and portable NIFTI-1/2 and Analyze7.5 file parser and converter
% to the text and binary JNIfTI formats defined in JNIfTI specification:
% https://github.com/NeuroJSON/jnifti
%
% This function is compatible with both MATLAB and GNU Octave.
% It accepts .nii, .nii.gz, .hdr/.img and .hdr.gz/.img.gz input files
%
% author: Qianqian Fang (q.fang <at> neu.edu)
%
% input:
% fname: the file name to the .nii, .nii.gz, .hdr/.img or .hdr.gz/.img.gz file
% format:'nii' for reading the NIfTI-1/2/Analyze files;
% 'jnii' to convert the nii data into an in-memory JNIfTI structure.
% 'niiheader' return only the nii header without the image data
%
% if format is not listed above and nii2jnii is called without
% an output, format must be a string specifying the output JNIfTI
% file name - *.jnii for text-based JNIfTI, or *.bnii for the
% binary version
% options: (optional) if saving to a .bnii file, please see the options for
% savebj.m (part of JSONLab); if saving to .jnii, please see the
% supported options for savejson.m (part of JSONLab).
%
% output:
% if the output is a JNIfTI data structure, it has the following subfield:
% nii.NIFTIHeader - a structure containing the 1-to-1 mapped NIFTI-1/2 header
% nii.NIFTIData - the main image data array
% nii.NIFTIExtension - a cell array contaiing the extension data buffers
%
% when calling as nii=nii2jnii(file,'nii'), the output is a NIFTI object containing
% nii.img: the data volume read from the nii file
% nii.datatype: the data type of the voxel, in matlab data type string
% nii.datalen: data count per voxel - for example RGB data has 3x
% uint8 per voxel, so datatype='uint8', datalen=3
% nii.voxelbyte: total number of bytes per voxel: for RGB data,
% voxelbyte=3; also voxelbyte=header.bitpix/8
% nii.hdr: file header info, a structure has the full nii header
% key subfileds include
%
% sizeof_hdr: must be 348 (for NIFTI-1) or 540 (for NIFTI-2)
% dim: short array, dim(2: dim(1)+1) defines the array size
% datatype: the type of data stored in each voxel
% bitpix: total bits per voxel
% magic: must be 'ni1\0' or 'n+1\0'
%
% For the detailed nii header, please see
% https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
%
% dependency:
% No external dependency if reading .nii/.hdr/.img files;
%
% To load gzipped input files (.nii.gz/.hdr.gz/.img.gz), one must
% install the ZMat Toolbox (http://github.com/NeuroJSON/zmat) and
% JSONLab Toolbox (http://github.com/NeuroJSON/jsonlab);
%
% To save files into the text/binary JNIfTI formatted files, one
% need to install JSONLab (http://github.com/NeuroJSON/jsonlab).
%
% this file was initially developed for the MCX project: https://github.com/fangq/mcx/blob/master/utils/mcxloadnii.m
%
% this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifti
%
% License: Apache 2.0, see https://github.com/NeuroJSON/jnifti for details
%
hdrfile = filename;
isnii = -1;
if (regexp(filename, '(\.[Hh][Dd][Rr](\.[Gg][Zz])*$|\.[Ii][Mm][Gg](\.[Gg][Zz])*$)'))
isnii = 0;
elseif (regexp(filename, '\.[Nn][Ii][Ii](\.[Gg][Zz])*$'))
isnii = 1;
end
if (isnii < 0)
error('file must be a NIfTI (.nii/.nii.gz) or Analyze 7.5 (.hdr/.img,.hdr.gz/.img.gz) data file');
end
if (regexp(filename, '\.[Ii][Mm][Gg](\.[Gg][Zz])*$'))
hdrfile = regexprep(filename, '\.[Ii][Mm][Gg](\.[Gg][Zz])*$', '.hdr$1');
end
niftiheader = niiformat('nifti1');
if (~isempty(regexp(hdrfile, '\.[Gg][Zz]$', 'once')) || (exist('OCTAVE_VERSION', 'builtin') ~= 0))
finput = fopen(hdrfile, 'rb');
input = fread(finput, inf, 'uint8=>uint8');
fclose(finput);
if (regexp(hdrfile, '\.[Gg][Zz]$'))
if (~exist('gzipdecode', 'file'))
error('To process zipped files, you must install gzipdecode.m from the JSONLab toolbox: http://github.com/NeuroJSON/jsonlab');
end
gzdata = gzipdecode(input);
else
gzdata = input;
end
clear input;
nii.hdr = memmapstream(gzdata, niftiheader);
else
fileinfo = dir(hdrfile);
if (isempty(fileinfo))
error('specified file does not exist');
end
header = memmapfile(hdrfile, ...
'Offset', 0, ...
'Writable', false, ...
'Format', niftiheader(1:end - (fileinfo.bytes < 352), :));
nii.hdr = header.Data(1);
end
[os, maxelem, dataendian] = computer;
if (nii.hdr.sizeof_hdr ~= 348 && nii.hdr.sizeof_hdr ~= 540)
nii.hdr.sizeof_hdr = swapbytes(nii.hdr.sizeof_hdr);
end
if (nii.hdr.sizeof_hdr == 540) % NIFTI-2 format
niftiheader = niiformat('nifti2');
if (exist('gzdata', 'var'))
nii.hdr = memmapstream(gzdata, niftiheader);
else
header = memmapfile(hdrfile, ...
'Offset', 0, ...
'Writable', false, ...
'Format', niftiheader(1:end - (fileinfo.bytes < 352), :));
nii.hdr = header.Data(1);
end
end
if (nii.hdr.dim(1) > 7)
names = fieldnames(nii.hdr);
for i = 1:length(names)
nii.hdr.(names{i}) = swapbytes(nii.hdr.(names{i}));
end
if (nii.hdr.sizeof_hdr > 540)
nii.hdr.sizeof_hdr = swapbytes(nii.hdr.sizeof_hdr);
end
if (dataendian == 'B')
dataendian = 'little';
else
dataendian = 'big';
end
end
type2byte = [
0 0 % unknown %
1 0 % binary (1 bit/voxel) %
2 1 % unsigned char (8 bits/voxel) %
4 2 % signed short (16 bits/voxel) %
8 4 % signed int (32 bits/voxel) %
16 4 % float (32 bits/voxel) %
32 8 % complex (64 bits/voxel) %
64 8 % double (64 bits/voxel) %
128 3 % RGB triple (24 bits/voxel) %
255 0 % not very useful (?) %
256 1 % signed char (8 bits) %
512 2 % unsigned short (16 bits) %
768 4 % unsigned int (32 bits) %
1024 8 % long long (64 bits) %
1280 8 % unsigned long long (64 bits) %
1536 16 % long double (128 bits) %
1792 16 % double pair (128 bits) %
2048 32 % long double pair (256 bits) %
2304 4 % 4 byte RGBA (32 bits/voxel) %
];
type2str = {
'uint8' 0 % unknown %
'uint8' 0 % binary (1 bit/voxel) %
'uint8' 1 % unsigned char (8 bits/voxel) %
'uint16' 1 % signed short (16 bits/voxel) %
'int32' 1 % signed int (32 bits/voxel) %
'single' 1 % float (32 bits/voxel) %
'single' 2 % complex (64 bits/voxel) %
'double' 1 % double (64 bits/voxel) %
'uint8' 3 % RGB triple (24 bits/voxel) %
'uint8' 0 % not very useful (?) %
'int8' 1 % signed char (8 bits) %
'uint16' 1 % unsigned short (16 bits) %
'uint32' 1 % unsigned int (32 bits) %
'int64' 1 % long long (64 bits) %
'uint64' 1 % unsigned long long (64 bits) %
'uint8' 16 % long double (128 bits) %
'uint8' 16 % double pair (128 bits) %
'uint8' 32 % long double pair (256 bits) %
'uint8' 4 % 4 byte RGBA (32 bits/voxel) %
};
typeidx = find(type2byte(:, 1) == nii.hdr.datatype);
nii.datatype = type2str{typeidx, 1};
nii.datalen = type2str{typeidx, 2};
nii.voxelbyte = type2byte(typeidx, 2);
nii.endian = dataendian;
if (type2byte(typeidx, 2) == 0)
nii.img = [];
return
end
if (type2str{typeidx, 2} > 1)
nii.hdr.dim = [nii.hdr.dim(1) + 1 uint16(nii.datalen) nii.hdr.dim(2:end)];
end
if (nargin > 1 && strcmp(format, 'niiheader'))
return
end
if (regexp(filename, '\.[Hh][Dd][Rr](\.[Gg][Zz])*$'))
filename = regexprep(filename, '\.[Hh][Dd][Rr](\.[Gg][Zz])*$', '.img$1');
end
imgbytenum = prod(double(nii.hdr.dim(2:nii.hdr.dim(1) + 1))) * nii.voxelbyte;
if (isnii == 0 && ~isempty(regexp(filename, '\.[Gg][Zz]$', 'once')))
finput = fopen(filename, 'rb');
input = fread(finput, inf, 'uint8=>uint8');
fclose(finput);
gzdata = gzipdecode(input);
nii.img = typecast(gzdata(1:imgbytenum), nii.datatype);
else
if (~exist('gzdata', 'var'))
fid = fopen(filename, 'rb');
if (isnii)
fseek(fid, nii.hdr.vox_offset, 'bof');
end
nii.img = fread(fid, imgbytenum, [nii.datatype '=>' nii.datatype]);
fclose(fid);
else
nii.img = typecast(gzdata(nii.hdr.vox_offset + 1:nii.hdr.vox_offset + imgbytenum), nii.datatype);
end
end
nii.img = reshape(nii.img, nii.hdr.dim(2:nii.hdr.dim(1) + 1));
if (nargin > 1 && strcmp(format, 'nii'))
return
end
nii0 = nii;
nii = niiheader2jnii(nii0);
nii.NIFTIData = nii0.img;
if (isfield(nii0.hdr, 'extension') && nii0.hdr.extension(1) > 0)
if (exist('gzdata', 'var'))
nii.NIFTIExtension = cell(1);
count = 1;
bufpos = nii0.hdr.sizeof_hdr + 4;
while (bufpos < nii0.hdr.vox_offset)
nii.NIFTIExtension{count}.Size = typecast(gzdata(bufpos + 1:bufpos + 4), 'int32') - 8;
nii.NIFTIExtension{count}.Type = typecast(gzdata(bufpos + 5:bufpos + 8), 'int32');
bufpos = bufpos + 8;
if (strcmp(dataendian, 'big'))
nii.NIFTIExtension{count}.Size = swapbytes(nii.NIFTIExtension{count}.Size);
nii.NIFTIExtension{count}.Type = swapbytes(nii.NIFTIExtension{count}.Type);
end
if (bufpos + nii.NIFTIExtension{count}.Size <= nii0.hdr.vox_offset)
nii.NIFTIExtension{count}.x0x5F_ByteStream_ = gzdata(bufpos + 1:bufpos + nii.NIFTIExtension{count}.Size);
end
bufpos = bufpos + bufpos + nii.NIFTIExtension{count}.Size;
count = count + 1;
end
else
fid = fopen(filename, 'rb');
fseek(fid, nii0.hdr.sizeof_hdr + 4, 'bof');
nii.NIFTIExtension = cell(1);
count = 1;
while (ftell(fid) < nii0.hdr.vox_offset)
nii.NIFTIExtension{count}.Size = fread(fid, 1, 'int32=>int32') - 8;
nii.NIFTIExtension{count}.Type = fread(fid, 1, 'int32=>int32');
if (strcmp(dataendian, 'big'))
nii.NIFTIExtension{count}.Size = swapbytes(nii.NIFTIExtension{count}.Size);
nii.NIFTIExtension{count}.Type = swapbytes(nii.NIFTIExtension{count}.Type);
end
if (ftell(fid) + nii.NIFTIExtension{count}.Size < nii0.hdr.vox_offset)
nii.NIFTIExtension{count}.x0x5F_ByteStream_ = fread(fid, nii.NIFTIExtension{count}.Size, 'uint8=>uint8');
end
count = count + 1;
end
fclose(fid);
end
end
if (nargout == 0 && strcmp(format, 'nii') == 0 && strcmp(format, 'jnii') == 0)
if (~exist('savejson', 'file'))
error('you must first install JSONLab from http://github.com/NeuroJSON/jsonlab/');
end
if (regexp(format, '\.jnii$'))
savejson('', nii, 'FileName', format, varargin{:});
elseif (regexp(format, '\.bnii$'))
savebj('', nii, 'FileName', format, varargin{:});
else
error('file suffix must be .jnii for text JNIfTI or .bnii for binary JNIfTI');
end
end
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