niftiread niftiwrite cycle inappropriately changes image orientation

Hello, 

I have neuroimaging files which I have exported from Slicer as NIFTI files.

The following code snippet should produce outputImage.nii as an exact copy of inputImage.nii, but it does not.

filename = 'inputImage.nii'
im = niftiread(filename);
info = niftiinfo(filename);
niftiwrite(im,'outputImage.nii',info)

When I load outputImage.nii in Slicer, it is shown in a different orientation and location as inputImage.nii. I have found Slicer to be extraordinarily reliable for importing and exporting medical imaging data properly, so I do not think there is any error in Slicer. Even if there were, MATLAB should not have introduced any changes between inputImage.nii and outputImage.nii, so there is still evidence of a problem in MATLAB's functions even if there were a problem with Slicer.

Answer 1

[Devineni Aslesha]

Hi Randolph,

I have heard that the issue with niftiwrite function is known and the concerned parties may be investigating further.

[Ignacio]

Hi Devineni, has there been an update on this?

[Devineni Aslesha]

Hi Ignacio,

niftiwrite orientation issue might be solved in MATLAB R2020b.

Answer 2

[Rafael]

Hi,

I was also facing this problem when writing a NIfTI file using the niftiwrite function together with a header obtained from niftiinfo in MATLAB R2024b. The issue appears to be that the info.raw substructure (which contains vox_offset and other parameters) is not fully written to the new file.

A simple workaround is to edit the niftiwrite.m script (...\MATLAB\R2024b\toolbox\images\iptformats\niftiwrite.m) and add the following line of code at line 97:

params.Info = varargin{1}.raw;

However, I cannot guarantee that this solution will work for every NIfTI file. Please make backups of your files before modifying the MATLAB source code. Good luck! :)

Below is the complete updated version of niftiwrite.m:

++++++++++++++++++++++++++++++++++++

++++++++++++++++++++++++++++++++++++

function niftiwrite(V, filename, varargin)

%NIFTIWRITE Write images as NIfTI files.

% NIFTIWRITE(V, FILENAME) writes a '.nii' file using the image data from

% V. By default, NIFTIWRITE creates a 'combined' NIfTI file that contains

% both metadata and volumetric data, giving it the '.nii' file extension.

% NIFTIWRITE populates the file metadata using appropriate default values

% and volume properties like size and data type.

%

% NIFTIWRITE(V, FILENAME, METADATA) writes a '.nii' file using the image

% data from V and metadata from METADATA. NIFTIWRITE creates a 'combined'

% NIFTI file, giving it the file extension '.nii'. If the metadata does

% not match the image contents and size, NIFTIWRITE returns an error.

%

% NIFTIWRITE(____, Name, Value) writes a '.nii' file using options

% specified in the Name Value pairs, described below.

%

% Optional Name-Value parameters include:

%

% 'Combined' - true (default) or false. If true, NIFTIWRITE

% creates one file with the file extension '.nii'.

% If false, NIFTIWRITE creates two files. One file

% contains metadata and has the file extension

% '.hdr'. The other files contains the volumetric

% data and has the file extension '.img'.

% NIFTIWRITE uses the file name you specified in

% FILENAME for both files.

%

% 'Compressed' - false(default) or true. If true, NIFTIWRITE

% compresses the generated file (or files) using

% gzip encoding, giving the file the .gz file

% extension as well as the NIFTI file extension.

%

% 'Endian' - 'little' (default) or 'big'.

% Controls the endianness of the data NIFTIWRITE

% writes to the file.

%

% 'Version' - 'NIfTI1' or 'NIfTI2'. Specifies the NIfTI format

% the data is to be written in. Default value

% depends on the maximum value of the dimensions

% of the volumetric data. The default value is

% 'NIfTI1' unless the maximum size in any

% dimension is more than 32767.

%

% References:

% -----------

% [1] Cox, R.W., Ashburner, J., Breman, H., Fissell, K., Haselgrove, C.,

% Holmes, C.J., Lancaster, J.L., Rex, D.E., Smith, S.M., Woodward, J.B.

% and Strother, S.C., 2004. A (sort of) new image data format standard:

% Nifti-1. Neuroimage, 22, p.e1440.

%

% Example 1

% ---------

% % This example illustrates writing a median filtered volume to a .nii

% % file.

%

% % Load a NIfTI image using its .nii file name.

% V = niftiread('brain.nii');

%

% % Filter the image in 3D using a 3-by-3-by-3 median filter.

% V = medfilt3(V);

%

% % Visualize the volume

% volshow(V)

%

% % Write the image to a .nii file. This uses default header values.

% niftiwrite(V, 'outbrain.nii');

%

% Example 2

% ---------

% % This example illustrates modifying the header structure and re-saving

% % a .nii file.

%

% % Load a NIfTI image using its .nii file name.

% info = niftiinfo('brain.nii');

% V = niftiread(info);

%

% % Edit the description of the file.

% info.Description = 'Modified using MATLAB R2017b';

%

% % Write the image to a .nii file.

% niftiwrite(V, 'outbrain.nii', info);

%

% See also NIFTIINFO, NIFTIREAD.

% Copyright 2016-2023 The MathWorks, Inc.

matlab.images.internal.errorIfgpuArray(V, filename, varargin{:});

[V, path, filename, params, isCompressed] = parseInputs(V, filename, varargin{:});

if strcmp(params.Endian, 'little')

machineFmt = 'ieee-le';

else

machineFmt = 'ieee-be';

end

params.Info = varargin{1}.raw; % Here is the change

headerStruct = params.Info;

% Convert strings to chars for low-level write

for f=fieldnames(headerStruct)'

if isstring(headerStruct.(f{1}))

headerStruct.(f{1}) = convertStringsToChars(headerStruct.(f{1}));

end

end

if params.Combined

NV = images.internal.nifti.niftiImage(headerStruct);

fid = fopen([filename '.nii'], 'w', machineFmt);

% write header.

[fid, headerBytes] = NV.writeHeader(fid, machineFmt);

assert(headerBytes == 348||headerBytes == 540);

% Write empty data until vox_offset

skipBytes = double(headerStruct.vox_offset) - headerBytes;

fwrite(fid, zeros(1,skipBytes), 'uint8');

% write image data.

fid = NV.writeImage(V, fid, machineFmt);

fclose(fid);

if params.Compressed || isCompressed

gzip([filename '.nii'], path);

delete([filename '.nii']);

end

else

%headerStruct.vox_offset = 0; % pixels start from first byte.

NV = images.internal.nifti.niftiImage(headerStruct);

headerfid = fopen([filename '.hdr'], 'w', machineFmt);

% write header.

[headerfid, headerBytes] = NV.writeHeader(headerfid, machineFmt);

assert(headerBytes == 348||headerBytes == 540);

fclose(headerfid);

% write image data.

imagefid = fopen([filename '.img'], 'w', machineFmt);

imagefid = NV.writeImage(V, imagefid, machineFmt);

fclose(imagefid);

if params.Compressed

gzip([filename '.hdr'], path);

gzip([filename '.img'], path);

delete([filename '.hdr']);

delete([filename '.img']);

end

end

end

%--------------------------------------------------------------------------

% Input Parsing

%--------------------------------------------------------------------------

function [V, fPath, fName, params, isCompressed] = parseInputs(V, fName, varargin)

varargin = matlab.images.internal.stringToChar(varargin);

% V has to be numeric, and of specific data types.

if ~isnumeric(V)

error(message('images:nifti:volumeMustBeNumeric'))

end

% filename needs to be a string or a character vector.

fName = matlab.images.internal.stringToChar(fName);

if ~ischar(fName)

error(message('images:nifti:filenameMustBeStringOrChar'))

end

[fPath, filenameOnly, ext] = fileparts(fName);

if isequal(lower(ext), ".gz")

isCompressed = true;

[~,tmp, ext] = fileparts(filenameOnly);

if isequal(lower(ext), ".nii")

filenameOnly = tmp;

end

else

isCompressed = false;

end

fName = fullfile(fPath, filenameOnly);

% Parse the PV pairs

parser = inputParser;

parser.addParameter('Combined', true, @(x)canBeLogical(x));

parser.addParameter('Compressed', false, @(x)canBeLogical(x));

parser.addParameter('Endian', 'little', @(x)ischar(x));

parser.addParameter('Version', 'NIfTI1', @(x)validateVersion(x));

parser.addOptional('Info', [], @(x)validateHeader(V,x));

parser.parse(varargin{:});

params.Combined = parser.Results.Combined ~= 0;

params.Compressed = parser.Results.Compressed ~= 0;

params.Endian = validatestring(parser.Results.Endian, {'little', 'big'});

params.Version = validatestring(parser.Results.Version, {'NIfTI1', 'NIfTI2'});

% If Version is not specified but Info is present

if any(strcmp(parser.UsingDefaults,'Version'))&&~isempty(parser.Results.Info)

params.Version = parser.Results.Info.Version;

end

%Default value of Version for size greater than 32767 is 'NIfTI2'

if any(strcmp(parser.UsingDefaults,'Version'))

if any(size(V)>32767)

params.Version = 'NIfTI2';

end

end

if strcmp(params.Version,'NIfTI1')

if any(size(V)>32767)

error(message('images:nifti:sizeTooBigNIfTI1'));

end

end

if isempty(parser.Results.Info)

params.Info = images.internal.nifti.niftiImage.niftiDefaultHeader(...

V, params.Combined, params.Version);

else

params.Info = images.internal.nifti.niftiImage.toRawStruct(...

parser.Results.Info, params.Combined, params.Version);

end

end

function T = validateVersion(version)

if ~ischar(version)

error(message('images:nifti:invalidVersion'));

else

T = true;

end

end

function TF = canBeLogical(input)

if isnumeric(input) || islogical(input)

TF = true;

else

TF = false;

end

end

function isHeader = validateHeader(V, simpleStruct)

if isstruct(simpleStruct)

if ~(isequal(simpleStruct.Datatype, class(V)))

error(message('images:nifti:volumeClassMustMatchHeader'))

end

% Allow trailing singleton dimensions in info.

dimsWithSingletonExpansion = max(ndims(V), numel(simpleStruct.ImageSize));

if ~(isequal(simpleStruct.ImageSize, size(V, 1:dimsWithSingletonExpansion)))

error(message('images:nifti:volumeSizeMustMatchHeader'))

end

if ~(length(simpleStruct.Description) <= 80)

error(message('images:nifti:descriptionLessThan80'))

end

if isfield(simpleStruct, 'AuxiliaryFile') && ...

~(length(simpleStruct.AuxiliaryFile) <= 24)

error(message('images:nifti:auxiliaryFileLessThan24'))

end

if isfield(simpleStruct, 'IntentDescription') && ...

~(length(simpleStruct.IntentDescription) <= 16)

error(message('images:nifti:intentMustBeLessThan16'))

end

isHeader = true;

else

isHeader = false;

end

end