[Insight-users] image orientation and registration, current status ? : STATUS UPDATE

[Bill Lorensen]

Luis,

Thanks for the great summary. I agree with everything except point 8. I am
confident we can come to a solution in the future that will have the correct
behaviour but maintain backward compatibility. Realistically, the results of
registration may change, but not dramatically I think.

Bill

On Fri, Feb 1, 2008 at 3:31 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:

>
>
> Just to clarify on the status of this problem:
>
>
> 1) Today: itkImage accepts, and carries Direction
>    but *does not* take it into account when
>    converting between indexes and physical points.
>
>
> 2) Today: itkOrientedImage accepts, and carries
>    Direction *and* takes it into account when
>    converting between indexes and physical points.
>
>
> 3) Today: Computation of derivatives *by default*
>    do not take image direction into account. BUT,
>    if you turn the following CMake option ON:
>
>        ITK_USE_ORIENTED_IMAGE_DIRECTION
>
>    Then they will offer the option of
>
>          UseImageDirectionOn / Off
>
>    *and* if you use them on itkOrientedImages
>    then they will compute the derivatives by
>    taking orientation into account.
>
>
> 4) The comments regarding the inconsistency of
>    the API are justified, and we can simply say
>    "shame on use" because we failed to retain
>    image direction into the image when we removed
>    the default affine transform that was originally
>    mapping from indexes to points in the very early
>    stage of the project.
>
>
> 5) Image registration of oriented images can be done
>    correctly today in ITK by doing:
>
>     A) Turn  "ITK_USE_ORIENTED_IMAGE_DIRECTION"   ON
>     B) Using itkOrientedImage instead of itkImage
>
>             ...It is not ideal...
>             ...It is not pretty...
>
>    But it is the compromise we reached when trying to
>    fix the bug and at the same time maintain backward
>    compatibility.
>
>
> 6) Registration of oriented images is tested Nightly
>    in all machines that have the above CMake flag
>    turned on. (e.g. Zion, Redwall).
>
>
>
> 7) This is the behavior that we are planning to
>    ship with ITK 3.6.
>
>
> 8) If there is enough support from the users community,
>    it will be great to fix this the right way in ITK 4.0.
>
>    [That means that some level of backward compatibility
>     may need to be sacrificed in the interest of removing
>     the current misleading/inconsistent API]
>
>
>
>
>   Regards,
>
>
>       Luis
>
>
>
> --------------------
> Rupert Brooks wrote:
> > Yes the OrientedImage derivative problem is troublesome.
> >
> > If your images are small enough, and your transformation is simple
> > enough, the easiest way around it is to use an optimizer that does not
> > need derivatives.  Powell's would probably be my choice.  This
> > approach gets slow for any sort of complex problem, unfortunately.
> >
> > I wrote an Insight Journal paper on the topic that may interest you,
> > with some code.  I use the classes in it on a daily basis, so i am
> > quite confident in them.  However, you would have to modify the code
> > of your metrics.
> > http://insight-journal.org/midas/handle.php?handle=1926/1293
> >
> > I've also been poring over the code for the multithreaded/optimized
> > metrics (it is now in the Review directory in CVS)  It seems to have a
> > general gradient method where the problem probably COULD be corrected.
> > (http://hdl.handle.net/1926/566)
> >
> > Please understand, i am just reading, not developing those
> > multithreaded metrics, so I cannot say for sure if they correct this
> > problem or not. Perhaps someone working on that project can advise.
> >
> > Cheers,
> > Rupert B.
> >
> >
> >
> >
> >
> >>Date: Fri, 1 Feb 2008 08:17:34 -0500
> >>From: "Bill Lorensen" <bill.lorensen at gmail.com>
> >>Subject: Re: [Insight-users] image orientation and registration,
> >>       current status ?
> >>To: "Stefan Klein" <stefan at isi.uu.nl>
> >>Cc: insight-users at itk.org
> >>Message-ID:
> >>       <4db4735c0802010517pc6f45bdw7506c29200b1d64d at mail.gmail.com>
> >>Content-Type: text/plain; charset="iso-8859-1"
> >>
> >>The gradient problem is being corrected for itkOrientedImage. See:
> >>http://public.kitware.com/Bug/view.php?id=5081
> >>
> >>If you need to take into account orientation, you should use
> >>itkOrientedImage. Another option is to use itkImage and reorient the
> series
> >>with itkOrientImageFilter so that both series have the same orientation.
> >>
> >>Bill
> >
> >
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>
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