[Insight-users] Inconsistencies in Image Orientation

[Don Bigler]

All,
	When I wrote itkPhilipsRECImageIO I correctly identified the image storage orientation as R-L, A-P, I-S (RAI) for axial images, ASL for sagittal, and RSA for coronal using a marker on the right side of a brain image.  Currently, the reader sets the direction cosines using the SpatialOrientation class.  However, the reader does not currently (ITK 3.20) set the correct origin or modify the direction cosines according to rotations specified in the PAR header.  I'm in the process of implementing these features using itkNiftiImageIO as an example and I'm discovering some apparent inconsistencies/problems in itkNiftiImageIO.  
1. First, I noticed that qform_xorient, qform_yorient, and qform_zorient don't appear to used anywhere in the reader to determine the storage orientation of the NIFTI image.  Unless nifticlib uses these values internally, this would appear to be a bug.  
2. Second, the origin and direction cosines are automatically negated for the first two dimensions (indexes 0 and 1).  Why?  I found a previous posting  mentioning that NIFTI images are stored RAS and ITK uses LPS.  However, as I already mentioned this may not be the case if qform_xorient, qform_yorient, and qform_zorient are not set to RAS.  I may be missing something from a previous posting, but there appears to be an inconsistency.  
	Having said all this, how should I set the direction cosines and origins for itkPhilipsRECImageIO?
-Don
 
Don Bigler, Ph.D.
Postdoctoral Scholar
Center for Emerging Neurotechnology and Imaging
Penn State University College of Medicine
500 University Dr.
Psychiatry, C5518
Hershey, PA 17033 
Phone: (717) 531-7963
Fax: (717) 531-6491

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