# Nifti: ImageFileReader + ImageFileWriter changes orientation matrix

**URL:** https://discourse.itk.org/t/nifti-imagefilereader-imagefilewriter-changes-orientation-matrix/4064
**Category:** Beginner Questions
**Tags:** nifti
**Created:** [April 23, 2021, 11:25am UTC](https://discourse.itk.org/t/nifti-imagefilereader-imagefilewriter-changes-orientation-matrix/4064 "2021-04-23T11:25:26Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [April 23, 2021, 1:39pm UTC](https://discourse.itk.org/t/nifti-imagefilereader-imagefilewriter-changes-orientation-matrix/4064/2 "2021-04-23T13:39:04Z")

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Loss of precision. See these:

> [@Direction/Orientation matrix DICOM vs Nifti](https://discourse.itk.org/t/direction-orientation-matrix-dicom-vs-nifti/3289):
>
> Hi everyone, I’m having discrepancies between the orientation matrix read from DICOMs or from a Nifti generated from the same DICOM series. I’d like to understand what is going on. I have a DICOM series that I read in the normal way using the ImageSeriesReader: itkreader = sitk.ImageSeriesReader() dicom\_names = itkreader.GetGDCMSeriesFileNames(r"C:\tmp\DICOM\_series") itkreader.SetFileNames(dicom\_names) itkImage = itkreader.Execute() Then, I save this image as Nifti and MHD using a ImageFileW…

> <https://github.com/InsightSoftwareConsortium/ITK/issues/1042>
>
> \<!-- The text within this markup is a comment, and is intended to provide
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> 
> 
> \<!-- Before submitting an issue, please check that your issue has not been
> already filed. --\>
> 
> \### Description
> 
> Placeholder for possibly a longer bug report. But at least store the information for reproducing the issue.
> 
> \### Steps to Reproduce
> 
> So basically the steps are:
> 
> 1. cp gdcm/Testing/Data/\\\*SIEM\\\*FileSeq\* /tmp/dir/
> 2. gdcmanon --dumb --replace 0020,0037="0.9997586873\\0.02191020543\\0.001584328775\\0.02196741222\\\\-0.9971551496\\\\-0.0721043717" /tmp/dir /tmp/dir2
> 3. bin/DicomSeriesReadImageWrite2 /tmp/dir2 foo.nii
> 4. bin/ImageReadWrite foo.nii nii.dcm
> 
> \<!--
> 1. \[First Step\]
> 2. \[Second Step\]
> 3. \[and so on...\]
> 
> Provide a minimal, complete, compilable, and verifiable example (commonly
> abbreviated as MWE, Minimal Working Example, or sometimes referred to as SSEE,
> Short, Self Contained, Correct (Compilable) Example, SSCCE) or code snippet,
> either through a GitHub gist (https://gist.github.com/) or providing your own
> files (including your source code, \`CMakeLists.txt\` file if applicable, and your
> data) reproducing the issue or showing an incorrect result. --\>
> 
> \### Expected behavior
> 
> 
> Minimal approximation of the matrix orientation in between the different representations.
> 
> \`\`\`
> $ gdcmdump nii.dcm | grep Orie
> (0020,0037) ?? (DS) \[.999758687284262\\.021910205429893\\.001584328774992\\.021967412220091\\-.99715514960414\\-.07210437170029 \] # 102,6 Image Orientation (Patient)
> \`\`\`
> 
> This goal is achievable since the MetaImage seems to be giving proper results:
> 
> 1. bin/DicomSeriesReadImageWrite2 /tmp/dir2 foo.mha
> 2. bin/ImageReadWrite foo.mha mha.dcm
> 
> Leads to:
> 
> \`\`\`
> $ gdcmdump mha.dcm | grep Orie
> (0020,0037) ?? (DS) \[.999758687284262\\.021910205429893\\.001584328774992\\.021967412220091\\-.99715514960414\\-.07210437170029 \] # 102,6 Image Orientation (Patient)
> \`\`\`
> 
> \### Actual behavior
> 
> 
> Leads to:
> 
> \`\`\`
> $ gdcmdump nii.dcm | grep Orie
> (0020,0037) ?? (DS) \[.9997590014762\\.021938811333211\\7.921645009e-4\\.021938811254904\\-.99715514907211\\-.07211308646627 \] # 98,6 Image Orientation (Patient)
> \`\`\`
> 
> \### Reproducibility
> 
> 
> 
> \### Versions
> 
> \<!-- If a tagged version, you can get this information by inspecting the
> \`ITK\_VERSION\_MAJOR\` \`ITK\_VERSION\_MINOR\` and \`ITK\_VERSION\_PATCH\` variable
> values in the \`ITKConfig.cmake\` file.
> 
> If the commit number is required, run \`$ git rev-parse --short HEAD\`. --\>
> 
> \`\`\`
> $ git rev-parse --short=12 HEAD
> b089be7fdd16
> 
> \`\`\`
> 
> \### Environment
> 
> \<!-- Which your OS, CMake, and compiler versions are, or your Python and
> installed package versions are. --\>
> 
> Linux, but I am guessing this will be irrelevant.
> 
> \### Additional Information
> 
> \<!-- Any additional information, configuration or data that might be necessary
> to reproduce the issue. --\>
> 
> \`\`\`
> $ git diff
> diff --git a/Examples/IO/DicomSeriesReadImageWrite2.cxx b/Examples/IO/DicomSeriesReadImageWrite2.cxx
> index be15736..d435c10 100644
> \--- a/Examples/IO/DicomSeriesReadImageWrite2.cxx
> +++ b/Examples/IO/DicomSeriesReadImageWrite2.cxx
> @@ -74,7 +74,7 @@ int main( int argc, char\* argv\[\] )
> // Software Guide : EndLatex
>  
> // Software Guide : BeginCodeSnippet
> \- using PixelType = signed short;
> + using PixelType = unsigned short;
> constexpr unsigned int Dimension = 3;
>  
> using ImageType = itk::Image\< PixelType, Dimension \>;
> diff --git a/Examples/IO/ImageReadWrite.cxx b/Examples/IO/ImageReadWrite.cxx
> index 0ccc48a..1eb8e71 100644
> \--- a/Examples/IO/ImageReadWrite.cxx
> +++ b/Examples/IO/ImageReadWrite.cxx
> @@ -85,8 +85,8 @@ int main( int argc, char \*\* argv )
> // Software Guide : EndLatex
>  
> // Software Guide : BeginCodeSnippet
> \- using PixelType = short;
> \- constexpr unsigned int Dimension = 2;
> + using PixelType = unsigned short;
> + constexpr unsigned int Dimension = 3;
> using ImageType = itk::Image\< PixelType, Dimension \>;
> // Software Guide : EndCodeSnippet
>  
> \`\`\`
> 
> \<!-- \*\*Note\*\*: Use issues for their purpose; issues are not for code help. Need
> help? Ask your question at ITK discourse (https://discourse.itk.org/). --\>

> [@Saving non-orthogonal volume in Nifti format](https://discourse.itk.org/t/saving-non-orthogonal-volume-in-nifti-format/2760):
>
> When writing a Nifti image, NiftiImageIO seems to [silently orthogonalize the IJK to LPS matrix that is written to the file](https://github.com/InsightSoftwareConsortium/ITK/blob/0676d81d927036c3666fdd12b7196aad849a3781/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx#L1961-L1962). Is this normalization really necessary? Can nifti store images with non-orthogonal axes? (I’ve tried to decode this from nifti’s documentation, but I’ve found image orientation definition extremely complicated, with lots of ambiguities and redundancy. I hope that there is someone here who knows nifti format well.)

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