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[jnifty] import NIfTI/JNIfTI writers from jnifty (savenifti, jnii2nii, etc.)
1 parent 85ee54b commit 19728df

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‎Contents.m‎

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Original file line numberDiff line numberDiff line change
@@ -57,6 +57,13 @@
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% loadjnifti - jnii=loadjnifti(inputfile)
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% loadnifti - jnii=loadnifti(inputfile)
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% nii2jnii - jnii=nii2jnii(niifile)
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% jnii2nii - nii=jnii2nii(jnii)
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% niicodemap - newval=niicodemap(name, value)
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% niiformat - niiheader=niiformat(format)
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% niiheader2jnii - nii = niiheader2jnii(nii0)
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% nifticreate - header=nifticreate(img)
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% jnifticreate - jnii=jnifticreate(img,'header1',value1,...)
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% savenifti - savenifti(img, filename)
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% savejnifti - savejnifti(jnii, outputfile)
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% savejnii - savejnii(jniidata, jniifile)
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% savebnii - savebnii(jniidata, bniifile)

‎INDEX‎

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Original file line numberDiff line numberDiff line change
@@ -57,9 +57,16 @@ JNIfTI file parser
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loadjnifti
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loadnifti
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nii2jnii
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jnii2nii
6061
niicodemap
6162
niiformat
6263
niiheader2jnii
64+
nifticreate
65+
jnifticreate
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savenifti
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savejnifti
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savejnii
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savebnii
6370
Helper Functions
6471
decodevarname
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encodevarname

‎jnifticreate.m‎

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function jnii = jnifticreate(varargin)
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%
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% jnii=jnifticreate
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% or
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% jnii=jnifticreate('header1', value1, 'header2', value2, ...)
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% jnii=jnifticreate(img, 'header1', value1, ...)
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%
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% Create a default JNIfTI structure with default header and image volume
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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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% img: set the jnii.NIFTIData section
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% 'header_i': the header subfield name defined in the JNIfTI
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% specification, see https://github.com/NeuroJSON/jnifty
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% value_i: set the value for the specified JNIfTI header field
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%
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% output:
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% jnii: without any input, jnii gives the default jnii header
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% if img is given, jnii also includes the NIFTIData field
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%
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%
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% this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifty
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%
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% License: Apache 2.0, see https://github.com/NeuroJSON/jnifty for details
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%
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jnii = struct(encodevarname('_DataInfo_'), struct(), 'NIFTIHeader', struct(), 'NIFTIData', []);
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% jnii.NIFTIHeader.NIIHeaderSize= 0;
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% jnii.NIFTIHeader.A75DataTypeName= 'uint8';
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% jnii.NIFTIHeader.A75DBName= '';
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% jnii.NIFTIHeader.A75Extends= 0;
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% jnii.NIFTIHeader.A75SessionError='';
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% jnii.NIFTIHeader.A75Regular= 0;
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jnii.NIFTIHeader.DimInfo.Freq = 0;
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jnii.NIFTIHeader.DimInfo.Phase = 0;
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jnii.NIFTIHeader.DimInfo.Slice = 0;
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jnii.NIFTIHeader.Dim = [];
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jnii.NIFTIHeader.Param1 = 0;
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jnii.NIFTIHeader.Param2 = 0;
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jnii.NIFTIHeader.Param3 = 0;
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jnii.NIFTIHeader.Intent = '';
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jnii.NIFTIHeader.DataType = 'uint8';
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jnii.NIFTIHeader.BitDepth = 8;
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jnii.NIFTIHeader.FirstSliceID = 1;
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jnii.NIFTIHeader.VoxelSize = [1, 1, 1, 1];
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jnii.NIFTIHeader.Orientation = struct('x', 'r', 'y', 'a', 'z', 's');
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% jnii.NIFTIHeader.NIIByteOffset= 0;
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jnii.NIFTIHeader.ScaleSlope = 0;
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jnii.NIFTIHeader.ScaleOffset = 0;
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jnii.NIFTIHeader.LastSliceID = 1;
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jnii.NIFTIHeader.SliceType = '';
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jnii.NIFTIHeader.Unit = struct('L', 'mm', 'T', 's');
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jnii.NIFTIHeader.MaxIntensity = 255;
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jnii.NIFTIHeader.MinIntensity = 0;
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jnii.NIFTIHeader.SliceTime = 1;
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jnii.NIFTIHeader.TimeOffset = 0;
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% jnii.NIFTIHeader.A75GlobalMax= 255;
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% jnii.NIFTIHeader.A75GlobalMin= 0;
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jnii.NIFTIHeader.Description = '';
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% jnii.NIFTIHeader.AuxFile= '';
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jnii.NIFTIHeader.QForm = '';
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jnii.NIFTIHeader.SForm = 'scanner_anat';
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jnii.NIFTIHeader.Quatern.b = 0;
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jnii.NIFTIHeader.Quatern.c = 0;
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jnii.NIFTIHeader.Quatern.d = 0;
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jnii.NIFTIHeader.QuaternOffset.x = 0;
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jnii.NIFTIHeader.QuaternOffset.y = 0;
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jnii.NIFTIHeader.QuaternOffset.z = 0;
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jnii.NIFTIHeader.Affine(1, :) = [1 0 0 0];
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jnii.NIFTIHeader.Affine(2, :) = [0 1 0 0];
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jnii.NIFTIHeader.Affine(3, :) = [0 0 1 0];
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jnii.NIFTIHeader.Name = 'default';
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jnii.NIFTIHeader.NIIFormat = 'jnifti';
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% jnii.NIFTIHeader.NIIExtender= [0,0,0,0];
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datainfo.JNIFTIVersion = '0.5';
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datainfo.Comment = 'Created by JNIFTY Toolbox (https://github.com/NeuroJSON/jnifty)';
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datainfo.AnnotationFormat = 'https://neurojson.org/jnifti/draft2';
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datainfo.SerialFormat = 'https://json.org';
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datainfo.Parser = struct('Python', [], ...
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'MATLAB', [], ...
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'JavaScript', 'https://github.com/NeuroJSON/jsdata', ...
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'CPP', 'https://github.com/NeuroJSON/json', ...
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'C', 'https://github.com/NeuroJSON/ubj');
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datainfo.Parser.Python = {'https://pypi.org/project/jdata', 'https://pypi.org/project/bjdata'};
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datainfo.Parser.MATLAB = {'https://github.com/NeuroJSON/jnifty', 'https://github.com/NeuroJSON/jsonlab'};
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jnii.(encodevarname('_DataInfo_')) = datainfo;
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if (nargin == 0)
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return
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end
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img = [];
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pid = 1;
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if (~ischar(varargin{1}))
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img = varargin{1};
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pid = 2;
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end
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if (~isempty(varargin))
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for i = pid:2:length(varargin)
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jnii.NIFTIHeader.(varargin{i}) = varargin{i + 1};
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end
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end
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if (~isnumeric(img) && ~islogical(img))
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error('img input must be a numerical or logical array');
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end
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jnii.NIFTIHeader.Dim = size(img);
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jnii.NIFTIHeader.DataType = class(img);
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info = whos('img');
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jnii.NIFTIHeader.BitDepth = info.bytes / numel(img) * 8;
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jnii.NIFTIHeader.MinIntensity = min(img(:));
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jnii.NIFTIHeader.MaxIntensity = max(img(:));
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jnii.NIFTIData = img;

‎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 (https://github.com/NeuroJSON/zmat) and
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% JSONLab Toolbox (https://github.com/NeuroJSON/jsonlab);
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%
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% this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifty
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%
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% License: Apache 2.0, see https://github.com/NeuroJSON/jnifty 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 (isfield(jnii.NIFTIHeader, 'Intent') && 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 (isfield(jnii.NIFTIHeader, 'DataType') && 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 (isfield(jnii.NIFTIHeader, 'SliceType') && 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 (isfield(jnii.NIFTIHeader, 'Unit') && isfield(jnii.NIFTIHeader.Unit, 'L') && 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 (isfield(jnii.NIFTIHeader, 'Unit') && isfield(jnii.NIFTIHeader.Unit, 'T') && ischar(jnii.NIFTIHeader.Unit.T))
125+
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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if (isfield(jnii.NIFTIHeader, 'QForm') && ischar(jnii.NIFTIHeader.QForm))
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jnii.NIFTIHeader.QForm = niicodemap('qform_code', jnii.NIFTIHeader.QForm);
145+
end
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if (isfield(jnii.NIFTIHeader, 'SForm') && ischar(jnii.NIFTIHeader.SForm))
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jnii.NIFTIHeader.SForm = niicodemap('sform_code', jnii.NIFTIHeader.SForm);
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end
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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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if (isfield(jnii.NIFTIHeader, 'NIIExtender'))
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nii.hdr.extension = bytematch(jnii.NIFTIHeader, 'NIIExtender', nii.hdr.extension);
167+
end
168+
if (isfield(jnii.NIFTIHeader, 'NIIQfac_'))
169+
nii.hdr.pixdim(1) = bytematch(jnii.NIFTIHeader, 'NIIQfac_', nii.hdr.pixdim(1));
170+
end
171+
if (isfield(jnii.NIFTIHeader, 'NIIUnused_'))
172+
nii.hdr.reserved = bytematch(jnii.NIFTIHeader, 'NIIUnused_', nii.hdr.reserved);
173+
end
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175+
if (isfield(jnii, 'NIFTIExtension') && iscell(jnii.NIFTIExtension))
176+
nii.extension = jnii.NIFTIExtension;
177+
if (nii.hdr.extension(1) ~= length(jnii.NIFTIExtension))
178+
nii.hdr.extension(1) = length(jnii.NIFTIExtension);
179+
warning('header extension count does not match the extension data, force update');
180+
end
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end
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183+
if (nargin >= 2 && ischar(varargin{1}))
184+
savenifti(nii.img, varargin{1}, nii.hdr);
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end
186+
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% ---------------------------------------------------------------------------
188+
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function dat = bytematch(jobj, key, orig)
190+
dtype = class(orig);
191+
if (isfield(jobj, key))
192+
dat = cast(jobj.(key), dtype);
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else
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dat = cast(0, dtype);
195+
end
196+
if (length(dat) < length(orig))
197+
dat(length(orig)) = cast(0, dtype);
198+
end
199+
dat = dat(1:length(orig));

‎jsonlab.prj‎

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@@ -158,9 +158,16 @@ Please note that data files produced by `saveubjson` may utilize a special "opti
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<file>${PROJECT_ROOT}/loadnifti.m</file>
159159
<file>${PROJECT_ROOT}/memmapstream.m</file>
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<file>${PROJECT_ROOT}/nii2jnii.m</file>
161+
<file>${PROJECT_ROOT}/jnii2nii.m</file>
161162
<file>${PROJECT_ROOT}/niicodemap.m</file>
162163
<file>${PROJECT_ROOT}/niiformat.m</file>
163164
<file>${PROJECT_ROOT}/niiheader2jnii.m</file>
165+
<file>${PROJECT_ROOT}/nifticreate.m</file>
166+
<file>${PROJECT_ROOT}/jnifticreate.m</file>
167+
<file>${PROJECT_ROOT}/savenifti.m</file>
168+
<file>${PROJECT_ROOT}/savejnifti.m</file>
169+
<file>${PROJECT_ROOT}/savejnii.m</file>
170+
<file>${PROJECT_ROOT}/savebnii.m</file>
164171
<file>${PROJECT_ROOT}/regrouph5.m</file>
165172
<file>${PROJECT_ROOT}/transposemat.m</file>
166173
</fileset.rootfiles>

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