AW: [Insight-users] image orientation and registration, current
status? : STATUS UPDATE
Luis Ibanez
luis.ibanez at kitware.com
Sun Feb 3 17:25:10 EST 2008
Hi Sebastien,
You should only be concerned about this new flag
if you are using the Derivative computation helpers
classes directly.
As indicated in the Wiki:
http://www.itk.org/Wiki/Proposals:Oriented_Image_Registration
These classes are:
http://www.itk.org/Wiki/Proposals:Oriented_Image_Registration#Adding_Boolean_flags_to_Image_Gradient_computation_classes
* Code/BasicFilters/itkGradientRecursiveGaussianImageFilter
* Code/Common/itkCentralDifferenceImageFunction
* Code/BasicFilters/itkGradientImageFilter
* Insight/Code/BasicFilters/itkBSplineInterpolateImageFunction
If you are using the Image Registration framework, this boolean
flag is set to ON for you by the ImageToImage Metric classes,
as soon as you turn the following CMake option ON:
ITK_USE_ORIENTED_IMAGE_DIRECTION
See for example lines 54-56 of
itkMutualInformationImageToImageMetric.txx
and
lines 172-174 of
itkImageToImageMetric.txx
To summarize:
The only two things that you have to do in order to properly perform
image registration with images whose direction cosines are not an
identity are:
1) Use itkOrientedImage instead of itkImage
2) Set ITK_USE_ORIENTED_IMAGE_DIRECTION to ON in CMake.
Please let us know if you have any other questions,
Thanks
Luis
------------------------
Thees, Sebastian wrote:
> Hello Luis,
>
> regarding point 3): on which object of the regeistration framework do I have to set the ->UseImageDirectionOn() flag ?
>
> I tried the optimizer (VersorRigid3DTransform), the orientedImages, the metric (MattesMutualInformationImageToImageMetric) and the registration (MultiResolutionImageRegistrationMethod) but none of them offerd a ->UseImageDirectionOn() member function.
>
> My system config is:
> winXP SP2, visual studio 2006, itk cvs-ceckout (3 Feb 2008) and cmake 2.4 patch 7.
> In the cmake config the ITK_USE_ORIENTED_IMAGE_DIRECTION option is set to ON by default.
>
> perfoming a grep for "UseImageDirection" on the source directory gives me:
> itkBSplineInterpolateImageFunction.h
> itkGradientImageFilter.h
> itkGradientRecursiveGaussianImageFilter.h
> itkOrientImageFilter.h
> itkCentralDifferenceImageFunction.h
> itkOptBSplineInterpolateImageFunction.h
>
> so I guess the use of image directions is configured, however I dont know how to set the flag within the registration framework - can you give me another hint ?
>
> best regards and thanks in advance
> Sebastian
>
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: insight-users-bounces+sebastian.thees=medizin.uni-leipzig.de at itk.org im Auftrag von Luis Ibanez
> Gesendet: Fr 01.02.2008 21:31
> An: rbrooks at cyberus.ca
> Cc: insight-users at itk.org
> Betreff: Re: [Insight-users] image orientation and registration, current status? : STATUS UPDATE
>
>
>
> 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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