[Insight-users] Inconsistencies in Image Orientation

[nadan zhu]

Sorry for not relevant to your issues. But i found inconsistency in
itkPhilipsRECImageIO.cxx line 766

     // Sagittal - the REC data appears to be stored as anterior-posterior,
      // superior-inferior, and right-left.
///////////////////////////////////////////////////should be left-right ?
      // Verified using marker on right side of brain.
      coord_orient = SpatialOrientation::ITK_COORDINATE_ORIENTATION_ASL;



nadan

On Thu, Dec 2, 2010 at 2:06 PM, Don Bigler <dcb210 at psu.edu> wrote:

> 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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