Nifti: ImageFileReader + ImageFileWriter changes orientation matrix

dzenanz · April 23, 2021, 1:39pm

Loss of precision. See these:

github.com/InsightSoftwareConsortium/ITK

NiftiImageIO: Round Trip issue with Image Orientation (Patient)

opened 07:55AM - 27 Jun 19 UTC

type:Bug status:Backlog area:IO

### 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  ### 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  ``` $ git rev-parse --short=12 HEAD b089be7fdd16 ``` ### Environment  Linux, but I am guessing this will be irrelevant. ### Additional Information  ``` $ 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 ```