[Insight-developers] Fwd: nifti direction cosines; bug?

[Stefan Klein]

Hi all,
Could anybody of NiftiImageIO-developers confirm that the behaviour 
described below is indeed a bug, and was not intentional?
Kind regards,
Stefan

-------- Original Message --------
Subject: 	[Insight-developers] nifti direction cosines; bug?
Date: 	Fri, 10 Feb 2012 19:44:54 +0100
From: 	Stefan Klein <s.klein at erasmusmc.nl>
To: 	Insight Developers <insight-developers at itk.org>



Hi developers,

In case of an Analyze75 file, loaded by NiftiImageIO, the Direction
Cosines are not stored in the m_Direction variable. Consequently, all
Analyze files get an identity direction matrix.

The error occurs in the SetImageIOOrientationFromNifTI function. The
code first reads the orientation correctly and stores it in a local
variable called 'dir', but this variable is never stored in the member
variable m_Direction.

Here is the relevant code (ITK v4.1rc01):

void
NiftiImageIO::SetImageIOOrientationFromNIfTI(unsigned short int dims)
{
  typedef SpatialOrientationAdapter OrientAdapterType;

   //
   // in the case of an Analyze75 file, use old analyze orient method.
   if ( this->m_NiftiImage->qform_code == 0
&&  this->m_NiftiImage->sform_code == 0 )
     {
     SpatialOrientationAdapter::DirectionType   dir;
     SpatialOrientationAdapter::OrientationType orient;
     switch ( this->m_NiftiImage->analyze75_orient )
       {
       case a75_transverse_unflipped:
         orient = SpatialOrientation::ITK_COORDINATE_ORIENTATION_RPI;
         break;
       case a75_sagittal_unflipped:
         orient = SpatialOrientation::ITK_COORDINATE_ORIENTATION_PIR;
         break;
       // according to analyze documents, you don't see flipped
       // orientation in the wild
       case a75_transverse_flipped:
       case a75_coronal_flipped:
       case a75_sagittal_flipped:
       case a75_orient_unknown:
       case a75_coronal_unflipped:
         orient = SpatialOrientation::ITK_COORDINATE_ORIENTATION_RIP;
         break;
       }
     dir =  OrientAdapterType().ToDirectionCosines(orient);
     m_Origin[0] = 0;
     if ( dims>  1 )
       {
       m_Origin[1] = 0;
       }
     if ( dims>  2 )
       {
       m_Origin[2] = 0;
       }
     return;
     }


  ...  // implementation for non-Analyze files.

}


I'm aware that Analyze75 is deprecated, and that I could use the
Deprecated/itkAnalyzeImageIO.h class, but this looks to me like a bug.

Kind regards,
Stefan

-- 
Stefan Klein
+31 10 7043049
http://www.bigr.nl/people/StefanKlein

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