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/fangq/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
% saveubjson.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/fangq/zmat) and
% JSONLab Toolbox (http://github.com/fangq/jsonlab);
%
% To save files into the text/binary JNIfTI formatted files, one
% need to install JSONLab (http://github.com/fangq/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/fangq/jnifti
%
% License: Apache 2.0, see https://github.com/fangq/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/fangq/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);
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$1');
end
imgbytenum=prod(nii.hdr.dim(2:nii.hdr.dim(1)+1))*nii.voxelbyte;
if(isnii==0 && ~isempty(regexp(filename,'\.[Gg][Zz]$', '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=struct();
nii.NIFTIHeader.NIIHeaderSize= nii0.hdr.sizeof_hdr;
if(isfield(nii0.hdr,'data_type'))
nii.NIFTIHeader.A75DataTypeName=deblank(char(nii0.hdr.data_type));
nii.NIFTIHeader.A75DBName= deblank(char(nii0.hdr.db_name));
nii.NIFTIHeader.A75Extends= nii0.hdr.extents;
nii.NIFTIHeader.A75SessionError=nii0.hdr.session_error;
nii.NIFTIHeader.A75Regular= nii0.hdr.regular;
end
nii.NIFTIHeader.DimInfo.Freq= bitand(nii0.hdr.dim_info,7);
nii.NIFTIHeader.DimInfo.Phase= bitand(bitshift(nii0.hdr.dim_info,-3),7);
nii.NIFTIHeader.DimInfo.Slice= bitand(bitshift(nii0.hdr.dim_info,-6),7);
nii.NIFTIHeader.Dim= nii0.hdr.dim(2:2+nii0.hdr.dim(1)-1);
nii.NIFTIHeader.Param1= nii0.hdr.intent_p1;
nii.NIFTIHeader.Param2= nii0.hdr.intent_p2;
nii.NIFTIHeader.Param3= nii0.hdr.intent_p3;
nii.NIFTIHeader.Intent= niicodemap('intent',nii0.hdr.intent_code);
nii.NIFTIHeader.DataType= niicodemap('datatype',nii0.hdr.datatype);
nii.NIFTIHeader.BitDepth= nii0.hdr.bitpix;
nii.NIFTIHeader.FirstSliceID= nii0.hdr.slice_start;
nii.NIFTIHeader.VoxelSize= nii0.hdr.pixdim(2:2+nii0.hdr.dim(1)-1);
nii.NIFTIHeader.Orientation= struct('x','r','y','a','z','s');
if(nii0.hdr.pixdim(1)<0)
nii.NIFTIHeader.Orientation= struct('x','l','y','a','z','s');
end
nii.NIFTIHeader.NIIByteOffset= nii0.hdr.vox_offset;
nii.NIFTIHeader.ScaleSlope= nii0.hdr.scl_slope;
nii.NIFTIHeader.ScaleOffset= nii0.hdr.scl_inter;
nii.NIFTIHeader.LastSliceID= nii0.hdr.slice_end;
nii.NIFTIHeader.SliceType= niicodemap('slicetype',nii0.hdr.slice_code);
nii.NIFTIHeader.Unit.L= niicodemap('unit',bitand(nii0.hdr.xyzt_units, 7));
nii.NIFTIHeader.Unit.T= niicodemap('unit',bitand(nii0.hdr.xyzt_units, 56));
nii.NIFTIHeader.MaxIntensity= nii0.hdr.cal_max;
nii.NIFTIHeader.MinIntensity= nii0.hdr.cal_min;
nii.NIFTIHeader.SliceTime= nii0.hdr.slice_duration;
nii.NIFTIHeader.TimeOffset= nii0.hdr.toffset;
if(isfield(nii0.hdr,'glmax'))
nii.NIFTIHeader.A75GlobalMax= nii0.hdr.glmax;
nii.NIFTIHeader.A75GlobalMin= nii0.hdr.glmin;
end
nii.NIFTIHeader.Description= deblank(char(nii0.hdr.descrip));
nii.NIFTIHeader.AuxFile= deblank(char(nii0.hdr.aux_file));
nii.NIFTIHeader.QForm= nii0.hdr.qform_code;
nii.NIFTIHeader.SForm= nii0.hdr.sform_code;
nii.NIFTIHeader.Quatern.b= nii0.hdr.quatern_b;
nii.NIFTIHeader.Quatern.c= nii0.hdr.quatern_c;
nii.NIFTIHeader.Quatern.d= nii0.hdr.quatern_d;
nii.NIFTIHeader.QuaternOffset.x=nii0.hdr.qoffset_x;
nii.NIFTIHeader.QuaternOffset.y=nii0.hdr.qoffset_y;
nii.NIFTIHeader.QuaternOffset.z=nii0.hdr.qoffset_z;
nii.NIFTIHeader.Affine(1,:)= nii0.hdr.srow_x;
nii.NIFTIHeader.Affine(2,:)= nii0.hdr.srow_y;
nii.NIFTIHeader.Affine(3,:)= nii0.hdr.srow_z;
nii.NIFTIHeader.Name= deblank(char(nii0.hdr.intent_name));
nii.NIFTIHeader.NIIFormat= deblank(char(nii0.hdr.magic));
if(isfield(nii0.hdr,'extension'))
nii.NIFTIHeader.NIIExtender= nii0.hdr.extension;
end
nii.NIFTIHeader.NIIQfac_= nii0.hdr.pixdim(1);
nii.NIFTIHeader.NIIEndian_= dataendian;
if(isfield(nii0.hdr,'reserved'))
nii.NIFTIHeader.NIIUnused_= nii0.hdr.reserved;
end
nii.NIFTIData=nii0.img;
if(isfield(nii0.hdr,'extension') && nii0.hdr.extension(1)>0)
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');
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
nii.NIFTIExtension{count}.x0x5F_ByteStream_=fread(fid,nii.NIFTIExtension{count}.Size-8,'uint8=>uint8');
count=count+1;
end
fclose(fid);
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/fangq/jsonlab/');
end
if(regexp(format,'\.jnii$'))
savejson('',nii,'FileName',format,varargin{:});
elseif(regexp(format,'\.bnii$'))
saveubjson('',nii,'FileName',format,varargin{:});
else
error('file suffix must be .jnii for text JNIfTI or .bnii for binary JNIfTI');
end
end
