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add jnii2nii to convert jnii back to nii for compatibility
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‎gzipdecode.m‎

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function varargout = gzipdecode(varargin)
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%
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% output = gzipdecode(input)
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% or
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% output = gzipdecode(input,info)
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%
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% Decompressing a GZIP-compressed byte-stream to recover the original data
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% This function depends on JVM in MATLAB or, can optionally use the ZMat
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% toolbox (http://github.com/fangq/zmat)
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%
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% Copyright (c) 2012, Kota Yamaguchi
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% URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
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%
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% Modified by: Qianqian Fang (q.fang <at> neu.edu)
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%
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% input:
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% input: a string, int8/uint8 vector or numerical array to store the GZIP-compressed data
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% info (optional): a struct produced by the zmat/lz4hcencode function during
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% compression; if not given, the inputs/outputs will be treated as a
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% 1-D vector
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%
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% output:
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% output: the decompressed byte stream stored in a uint8 vector; if info is
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% given, output will restore the original data's type and dimensions
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%
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% examples:
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% [bytes, info]=gzipencode(eye(10));
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% orig=gzipdecode(bytes,info);
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%
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% license:
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% BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details
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%
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% -- this function is part of JSONLab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
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%
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if(nargin==0)
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error('you must provide at least 1 input');
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end
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if(exist('zmat','file')==2 || exist('zmat','file')==3)
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if(nargin>1)
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[varargout{1:nargout}]=zmat(varargin{1},varargin{2:end});
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else
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[varargout{1:nargout}]=zmat(varargin{1},0,'gzip',varargin{2:end});
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end
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return;
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elseif(isoctavemesh)
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error('You must install the ZMat toolbox (http://github.com/fangq/zmat) to use this function in Octave');
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end
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error(javachk('jvm'));
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if(ischar(varargin{1}))
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varargin{1}=uint8(varargin{1});
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end
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input=typecast(varargin{1}(:)','uint8');
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gzip = java.util.zip.GZIPInputStream(java.io.ByteArrayInputStream(input));
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buffer = java.io.ByteArrayOutputStream();
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org.apache.commons.io.IOUtils.copy(gzip, buffer);
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gzip.close();
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if(nargout>0)
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varargout{1} = typecast(buffer.toByteArray(), 'uint8')';
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if(nargin>1 && isstruct(varargin{2}) && isfield(varargin{2},'type'))
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inputinfo=varargin{2};
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varargout{1}=typecast(varargout{1},inputinfo.type);
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varargout{1}=reshape(varargout{1},inputinfo.size);
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end
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end

‎gzipencode.m‎

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function varargout = gzipencode(varargin)
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%
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% output = gzipencode(input)
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% or
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% [output, info] = gzipencode(input)
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%
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% Compress a string or numerical array using the GZIP-compression
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%
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% This function depends on JVM in MATLAB or, can optionally use the ZMat
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% toolbox (http://github.com/fangq/zmat)
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%
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% Copyright (c) 2012, Kota Yamaguchi
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% URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
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%
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% Modified by: Qianqian Fang (q.fang <at> neu.edu)
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%
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% input:
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% input: the original data, can be a string, a numerical vector or array
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%
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% output:
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% output: the decompressed byte stream stored in a uint8 vector; if info is
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% given, output will restore the original data's type and dimensions
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%
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% examples:
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% [bytes, info]=gzipencode(eye(10));
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% orig=gzipdecode(bytes,info);
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%
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% license:
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% BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details
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%
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% -- this function is part of JSONLab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
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%
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if(nargin==0)
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error('you must provide at least 1 input');
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end
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if(exist('zmat','file')==2 || exist('zmat','file')==3)
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[varargout{1:nargout}]=zmat(varargin{1},1,'gzip');
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return;
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elseif(isoctavemesh)
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error('You must install the ZMat toolbox (http://github.com/fangq/zmat) to use this function in Octave');
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end
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error(javachk('jvm'));
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if(ischar(varargin{1}))
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varargin{1}=uint8(varargin{1});
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end
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input=typecast(varargin{1}(:)','uint8');
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buffer = java.io.ByteArrayOutputStream();
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gzip = java.util.zip.GZIPOutputStream(buffer);
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gzip.write(input, 0, numel(input));
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gzip.close();
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varargout{1} = typecast(buffer.toByteArray(), 'uint8')';
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if(nargout>1)
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varargout{2}=struct('type',class(varargin{1}),'size',size(varargin{1}),'method','gzip','status',0);
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end

‎jnii2nii.m‎

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function nii=jnii2nii(jnii, varargin)
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%
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% nii=jnii2nii(jnii)
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% or
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% nii=jnii2nii(jniifile)
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% jnii2nii(jniifile, niifile)
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%
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% Covert a JNIfTI file or data structure to a NIfTI-1/2 structure or file
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%
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% This function is compatible with both MATLAB and GNU Octave.
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% It accepts .jnii and .bnii input files
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%
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% author: Qianqian Fang (q.fang <at> neu.edu)
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%
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% input:
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% jnii: a JNIfTI data structure (a struct with NIFTIHeader and NIFTIData fields);
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% if jnii is a string, it represents a JNIfTI file (.jnii/.bnii)
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% niifile: if the 2nd parameter is given as a file name, the converted nifti data
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% will be save as a nii file with filename specified by niifile.
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% if the filename in niifile contains .gz, the file will be compressed using
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% the zmat toolbox.
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%
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% output:
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% nii: is the converted nifti-1/2 data structure, it contains the below subfields
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% nii.img: the data volume read from the nii file
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% nii.hdr: extended raw file header, a structure that is byte-wise compatible with a
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% nifti-1 - in this case, typecast(nii.hdr,'uint8') must be 348+4=352 bytes,
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% including the raw nifti-1 hdr header (348 bytes) plus the 4-byte
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% extension flags), or
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% nifti-2 - in this case, typecast(nii.hdr,'uint8') must be 540+4=544 bytes,
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% including the raw nifti-2 hdr header (540 bytes) plus the 4-byte
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% extension flags)
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% if one run nii.hdr.extension=[]; the resulting struct is 348/540-byte in length
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% nii.hdr key subfileds include
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%
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% sizeof_hdr: must be 348 (for NIFTI-1) or 540 (for NIFTI-2)
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% dim: short array, dim(2: dim(1)+1) defines the array size
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% datatype: the type of data stored in each voxel
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% bitpix: total bits per voxel
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% magic: must be 'ni1\0' or 'n+1\0' for NIFTI-1 data, and 'ni2\0' or 'n+2\0' for NIFTI-2 data
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%
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% For the detailed nii header, please see
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% https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
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%
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% dependency:
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%
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% To load a JNIfTI file with compression or niifile ends with (.nii.gz/.hdr.gz/.img.gz),
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% one must install the ZMat Toolbox (http://github.com/fangq/zmat) and
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% JSONLab Toolbox (http://github.com/fangq/jsonlab);
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%
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% this file is part of JNIfTI specification: https://github.com/fangq/jnifti
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%
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% License: Apache 2.0, see https://github.com/fangq/jnifti for details
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%
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if(nargin<=0)
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help jnii2nii
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return;
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end
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if(~isstruct(jnii))
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jnii=loadjnifti(jnii);
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end
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if(~(isfield(jnii,'NIFTIHeader') && isfield(jnii,'NIFTIData')))
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error('input must be a valid JNIfTI structure (needs both NIFTIHeader and NIFTIData subfields)');
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end
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niiformat='nifti1';
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if((isfield(jnii.NIFTIHeader,'NIIFormat') && ismember(jnii.NIFTIHeader.NIIFormat(1:3),{'ni2','n+2'})) || max(jnii.NIFTIHeader.Dim)>=2^32)
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niiformat='nifti2';
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end
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nii.hdr=nifticreate(jnii.NIFTIData, niiformat);
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nii.img=jnii.NIFTIData;
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if(isfield(jnii.NIFTIHeader,'NIIHeaderSize'))
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nii.hdr.sizeof_hdr =bytematch(jnii.NIFTIHeader, 'NIIHeaderSize', nii.hdr.sizeof_hdr);
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end
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if(isfield(nii.hdr,'data_type'))
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nii.hdr.data_type =bytematch(jnii.NIFTIHeader, 'A75DataTypeName', nii.hdr.data_type);
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nii.hdr.db_name =bytematch(jnii.NIFTIHeader, 'A75DBName', nii.hdr.db_name);
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nii.hdr.extents =bytematch(jnii.NIFTIHeader, 'A75Extends', nii.hdr.extents);
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nii.hdr.session_error =bytematch(jnii.NIFTIHeader, 'A75SessionError', nii.hdr.session_error);
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nii.hdr.regular =bytematch(jnii.NIFTIHeader, 'A75Regular', nii.hdr.regular);
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end
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dim_info=bitor(uint8(jnii.NIFTIHeader.DimInfo.Freq),bitshift(uint8(jnii.NIFTIHeader.DimInfo.Phase),3));
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dim_info=bitor(dim_info,bitshift(uint8(jnii.NIFTIHeader.DimInfo.Slice),6));
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nii.hdr.dim_info=cast(dim_info, class(nii.hdr.dim_info));
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nii.hdr.dim(1)=cast(length(jnii.NIFTIHeader.Dim),class(nii.hdr.dim));
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nii.hdr.dim(2:1+length(jnii.NIFTIHeader.Dim)) =bytematch(jnii.NIFTIHeader, 'Dim', nii.hdr.dim(2:1+length(jnii.NIFTIHeader.Dim)));
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nii.hdr.intent_p1 =bytematch(jnii.NIFTIHeader, 'Param1', nii.hdr.intent_p1);
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nii.hdr.intent_p2 =bytematch(jnii.NIFTIHeader, 'Param2', nii.hdr.intent_p2);
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nii.hdr.intent_p3 =bytematch(jnii.NIFTIHeader, 'Param3', nii.hdr.intent_p3);
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if(ischar(jnii.NIFTIHeader.Intent))
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jnii.NIFTIHeader.Intent=niicodemap('intent',jnii.NIFTIHeader.Intent);
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end
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nii.hdr.intent_code =bytematch(jnii.NIFTIHeader, 'Intent', nii.hdr.intent_code);
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if(ischar(jnii.NIFTIHeader.DataType))
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jnii.NIFTIHeader.DataType=niicodemap('datatype',jnii.NIFTIHeader.DataType);
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end
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nii.hdr.datatype =bytematch(jnii.NIFTIHeader, 'DataType', nii.hdr.datatype);
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nii.hdr.bitpix =bytematch(jnii.NIFTIHeader, 'BitDepth', nii.hdr.bitpix);
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nii.hdr.slice_start =bytematch(jnii.NIFTIHeader, 'FirstSliceID', nii.hdr.slice_start);
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nii.hdr.pixdim(1)=cast(length(jnii.NIFTIHeader.VoxelSize),class(nii.hdr.pixdim));
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nii.hdr.pixdim(2:2+nii.hdr.dim(1)-1) =bytematch(jnii.NIFTIHeader, 'VoxelSize', nii.hdr.pixdim(2:2+nii.hdr.dim(1)-1));
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nii.hdr.vox_offset =bytematch(jnii.NIFTIHeader, 'NIIByteOffset', nii.hdr.vox_offset);
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nii.hdr.scl_slope =bytematch(jnii.NIFTIHeader, 'ScaleSlope', nii.hdr.scl_slope);
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nii.hdr.scl_inter =bytematch(jnii.NIFTIHeader, 'ScaleOffset', nii.hdr.scl_inter);
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nii.hdr.slice_end =bytematch(jnii.NIFTIHeader, 'LastSliceID', nii.hdr.slice_end);
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if(ischar(jnii.NIFTIHeader.SliceType))
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jnii.NIFTIHeader.SliceType=niicodemap('slicetype',jnii.NIFTIHeader.SliceType);
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end
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nii.hdr.slice_code =bytematch(jnii.NIFTIHeader, 'SliceType', nii.hdr.slice_code);
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if(ischar(jnii.NIFTIHeader.Unit.L))
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jnii.NIFTIHeader.Unit.L=niicodemap('unit',jnii.NIFTIHeader.Unit.L);
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end
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if(ischar(jnii.NIFTIHeader.Unit.T))
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jnii.NIFTIHeader.Unit.T=niicodemap('unit',jnii.NIFTIHeader.Unit.T);
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end
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xyzt_units=bitor(uint8(jnii.NIFTIHeader.Unit.L),uint8(jnii.NIFTIHeader.Unit.T));
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nii.hdr.xyzt_units=cast(xyzt_units, class(nii.hdr.xyzt_units));
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nii.hdr.cal_max =bytematch(jnii.NIFTIHeader, 'MaxIntensity', nii.hdr.cal_max);
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nii.hdr.cal_min =bytematch(jnii.NIFTIHeader, 'MinIntensity', nii.hdr.cal_min);
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nii.hdr.slice_duration =bytematch(jnii.NIFTIHeader, 'SliceTime', nii.hdr.slice_duration);
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nii.hdr.toffset =bytematch(jnii.NIFTIHeader, 'TimeOffset', nii.hdr.toffset);
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if(isfield(nii.hdr,'glmax'))
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nii.hdr.glmax =bytematch(jnii.NIFTIHeader, 'A75GlobalMax', nii.hdr.glmax);
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nii.hdr.glmin =bytematch(jnii.NIFTIHeader, 'A75GlobalMin', nii.hdr.glmin);
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end
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nii.hdr.descrip =bytematch(jnii.NIFTIHeader, 'Description', nii.hdr.descrip);
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nii.hdr.aux_file =bytematch(jnii.NIFTIHeader, 'AuxFile', nii.hdr.aux_file);
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nii.hdr.qform_code =bytematch(jnii.NIFTIHeader, 'QForm', nii.hdr.qform_code);
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nii.hdr.sform_code =bytematch(jnii.NIFTIHeader, 'SForm', nii.hdr.sform_code);
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nii.hdr.quatern_b =bytematch(jnii.NIFTIHeader, 'Quatern.b', nii.hdr.quatern_b);
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nii.hdr.quatern_c =bytematch(jnii.NIFTIHeader, 'Quatern.c', nii.hdr.quatern_c);
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nii.hdr.quatern_d =bytematch(jnii.NIFTIHeader, 'Quatern.d', nii.hdr.quatern_d);
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nii.hdr.qoffset_x =bytematch(jnii.NIFTIHeader, 'QuaternOffset.x', nii.hdr.qoffset_x);
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nii.hdr.qoffset_y =bytematch(jnii.NIFTIHeader, 'QuaternOffset.y', nii.hdr.qoffset_y);
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nii.hdr.qoffset_z =bytematch(jnii.NIFTIHeader, 'QuaternOffset.z', nii.hdr.qoffset_z);
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nii.hdr.srow_x =cast(jnii.NIFTIHeader.Affine(1,:), class(nii.hdr.srow_x));
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nii.hdr.srow_y =cast(jnii.NIFTIHeader.Affine(2,:), class(nii.hdr.srow_y));
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nii.hdr.srow_z =cast(jnii.NIFTIHeader.Affine(3,:), class(nii.hdr.srow_z));
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nii.hdr.intent_name =bytematch(jnii.NIFTIHeader, 'Name', nii.hdr.intent_name);
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%nii.hdr.magic =bytematch(jnii.NIFTIHeader, 'NIIFormat', nii.hdr.magic);
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158+
if(isfield(jnii.NIFTIHeader,'NIIExtender'))
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nii.hdr.extension =bytematch(jnii.NIFTIHeader, 'NIIExtender', nii.hdr.extension);
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end
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if(isfield(jnii.NIFTIHeader,'NIIQfac_'))
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nii.hdr.pixdim(1) =bytematch(jnii.NIFTIHeader, 'NIIQfac_', nii.hdr.pixdim(1));
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end
164+
if(isfield(jnii.NIFTIHeader,'NIIUnused_'))
165+
nii.hdr.reserved =bytematch(jnii.NIFTIHeader, 'NIIUnused_', nii.hdr.reserved);
166+
end
167+
168+
if(isfield(jnii,'NIFTIExtension') && iscell(jnii.NIFTIExtension))
169+
nii.extension=jnii.NIFTIExtension;
170+
if(nii.hdr.extension(1)~=length(jnii.NIFTIExtension))
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nii.hdr.extension(1)=length(jnii.NIFTIExtension);
172+
warning('header extension count does not match the extension data, force update');
173+
end
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end
175+
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if(nargin>=2 && ischar(varargin{1}))
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savenifti(nii.img, varargin{1}, nii.hdr);
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end
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%---------------------------------------------------------------------------
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function dat=bytematch(jobj, key, orig)
183+
dtype=class(orig);
184+
dat=orig;
185+
if(isfield(jobj,key))
186+
dat=cast(jobj.(key),dtype);
187+
else
188+
dat=cast(0,dtype);
189+
end
190+
if(length(dat)<length(orig))
191+
dat(length(orig))=cast(0,dtype);
192+
end
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dat=dat(1:length(orig));

‎nifticreate.m‎

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@@ -35,6 +35,7 @@
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header=memmapstream(uint8(zeros(1,headerlen+4)),niiformat(format));
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header.sizeof_hdr=cast(headerlen, class(header.sizeof_hdr));
3737
header.datatype=cast(datatype.(class(img)), class(header.datatype));
38+
header.dim(1:end)=cast(1,class(header.dim));
3839
header.dim(1:ndims(img)+1)=cast([ndims(img),size(img)], class(header.dim));
3940
header.pixdim(1:ndims(img)+1)=cast(1, class(header.pixdim));
4041
header.vox_offset=cast(headerlen+4, class(header.vox_offset));

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