[Insight-users] Clarification on itkOrientImageFilter orientationcodes

[Mark Wyszomierski]

Would it be possible to have the fixes CVS'd? Or is there any expected
date for Bill's new implementation? Or is there a different filter
that can do this?

Thanks for all your help,
Mark

On 4/21/05, Miller, James V (Research) <millerjv at crd.ge.com> wrote:
> Bill recently found a problem with some of the orientation codes
> in the OrientImageFilter.  The problems arose on some cases where
> two permutations were required.  He discovered if he changed the
> order of the permutations (in these case), he got the
> the answer he was expecting.
> 
> Unfortunately, these fixes have not been committed back into the
> repository.
> 
> In the interum, you could edit OrientImageFilter and experiment
> with changing the order of permutations for the cases giving
> you problems.
> 
> Jim
> 
> 
> -----Original Message-----
> From: Mark Wyszomierski [mailto:markww at gmail.com]
> Sent: Thursday, April 21, 2005 1:18 PM
> To: Miller, James V (Research)
> Cc: insight-users at itk.org
> Subject: Re: [Insight-users] Clarification on itkOrientImageFilter
> orientationcodes
> 
> I'm experiencing some problems in with image orientation translations
> for axial images;
> 
> When translating a coronal image to sagittal, everything works as expected:
> start w/: RSA
> ask for:  ASL
> get:       ASL
> 
> However, when translating an axial image to sagittal, I'm ending up
> with a coronal image instead:
> start w/: RAI (or LAS)
> ask for:  ASL
> get:       IRA (or SLA)
> 
> This result is confusing.  Essentially, the RSA=>ASL translation
> requires a 90 degree turn clockwise along the y-axis, which itk does
> correctly.  Meanwhile, the RAI=>ASL translation requires a 90 degree
> turn clockwise around both the x-axis and y-axis.  But it seems for
> RAI=>ASL, itk is instead rotating 90 degrees clockwise along the x-
> and *z-axis* which results in a coronal image of IRA rather than a
> sagittal of ASL...   any idea why this is happening?
> 
> In attempting to work around the problem, I pretended that my axial
> image (RAI) was instead a coronal image (RSA).  I instructed itk to
> translate the image to ARS (an unorthodox axial image) which
> essentially is asking itk to rotate the image 90 degrees clockwise
> around the x-axis and y-axis; the same as an RAI=>ASL translation
> would ask.  This translation did indeed result in the expected output
> of an ASL image.
> 
> Can anyone shed light onto the problems w/ translating axial to
> sagittal?  thanks,
> 
> Mark
> 
> On 4/21/05, Miller, James V (Research) <millerjv at crd.ge.com> wrote:
> > For DICOM files, you would need to calculate codes from the
> > ImageOrientationPatient and not the ImagePositionPatient.
> >
> > The codes in the OrientImageFilter label the "start" of the
> > row, column, slices.  So in that nomenclature, your Desired
> > orientation would probably be ASL.
> >
> > Bill Lorensen has been working on some changes to the OrientImageFilter
> > so that it will automatically set the Given orientation from the
> > direction cosines of the image (ImageOrientationPatient), so the user
> > would only have to specify the Desired orientation.  He is also
> > adding convenience methods so that the user can simply request
> > Axials, Coronals, or Sagittals instead of having to specify
> > the codes.
> >
> > It doesn't look as though his changes to the OrientImageFilter
> > have been checked in yet.  But he is close to having it ready
> > for committing to the repository.
> >
> > Jim
> >
> >
> > -----Original Message-----
> > From: insight-users-bounces at itk.org
> > [mailto:insight-users-bounces at itk.org]On Behalf Of Mark Wyszomierski
> > Sent: Thursday, April 21, 2005 9:45 AM
> > To: insight-users at itk.org
> > Subject: [Insight-users] Clarification on itkOrientImageFilter
> > orientationcodes
> >
> > Hello all,
> >
> > I implemented the itkOrientImageFilter so I can snap all my volumes to
> > a particular orientation.The input/output is working, I am just unsure
> > of what the orientation codes mean. For instance, I would like all my
> > images to have their rows going towards the Posterior, columns going
> > towards the Feet, and the Z (slice direction) going towards the Right
> > side of the patient. How do I translate that into the codes provided
> > by the filter?
> >
> > Also, since my input are DICOM files, can I translate the
> > ImagePositionPatient tag directly to one of the filter codes?
> >
> > Thanks for any clues,
> > Mark
> > _______________________________________________
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> >
>