[Insight-users] Clarification on itkOrientImageFilterorientationcodes

[Miller, James V (Research)]

Bill is anxious to get his changes checked in.  He is just trying to 
verify all the orientations.  We're trying to get a phantom scanned
in all (orthogonal) directions to use for verification.  With this 
phantom data, we'll be to read all the different scan orientations 
and request all axials or all coronals and the data from the various 
orientation scans should all line up.

Bill is out of the office today.  Perhaps he can clean that part of the 
code up and check it in tomorrow.

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 3:05 PM
To: Miller, James V (Research)
Cc: insight-users at itk.org; wlorens1 at nycap.rr.com
Subject: Re: [Insight-users] Clarification on
itkOrientImageFilterorientationcodes


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
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
> >
>
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