[Insight-users] SetFixedImageRegion

[Luis Ibanez]

Hi Mark,

There is not a direct way to specify a region of interest to the
Demons Deformable registration filter. However, you can easily
obtain the equivalent effect by extracting a region of interest
from the input images using one of the following filters


    --- ExtractImageFilter
http://www.itk.org/Insight/Doxygen/html/classitk_1_1ExtractImageFilter.html


    --- RegionOfInterestImageFilter
http://www.itk.org/Insight/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html



"Consensus" is unfortunately a very uncommon word in medical image
processing. Our field is still in the pre-adolescent stage where
everybody wants to demonstrate that their method is better than the
others. We are still caring more for our reputation than for the
well-being of patients, so unfortunately the answer to your question
will be different depending on who you ask.

What I will suggest you is to use a "Masked" registration. That should
matter more than the selection of one transform over another. You may
want to setup a registration in which the region that will intake the
contrast agent will *not* participate in the metric computation of
the registration process.

The Demons method may work fine if you apply enough smoothing, but
there is a tradeof between how much you want to smooth...

What anatomical structure are you working on ?

If it is the brain, you probably want to stay with a rigid registration
and verify how many image features are remaining in the difference
image after registration.


Please let us know if you have further questions.


    Thanks


      Luis



----------------------------
Mark Wyszomierski wrote:

> Hi Luis,
> 
> That was it and it worked great, thanks! Is there a way to hand a
> region of interest to the demons deformable registration method? I am
> basically using the example in the itk example folder, 
> (DeformableRegistration2).
> 
> Also, is there some consensus on which registration method is best for
> an MR dataset using contrast agents? The rigid registration seems to
> work fairly well, the demons deformable has worked wonders though in
> other registration problems I have handed it. But by the nature of the
> demons registration (intensity matching) this is probably not feasible
> for MR contrast enhanced datasets). Any info would be appreciated,
> thank you very much Luis,
> 
> Regards,
> Mark
> 
> 
> On Fri, 24 Sep 2004 13:55:36 -0400, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> 
>>Hi Mark,
>>
>>You can define your region of interest using
>>lines like the following (assuming 3D...):
>>
>>ImageType::IndexType start;
>>start[0] = 144;
>>start[1] = 123;
>>start[2] = 223;
>>
>>ImaggeType::SizeType size;
>>size[0] = 400;
>>size[1] = 400;
>>size[2] = 400;
>>
>>ImageType::RegionType region;
>>
>>region.SetIndex(start);
>>region.SetSize(size);
>>
>>registration->SetFixedImageRegion( region );
>>
>>It will be up to you to define the actual values
>>to put in "start" and "size" in order to define
>>the region of interest. They should probably be
>>taken from a GUI interace by letting the user do
>>mouse clicks....
>>
>>Just make sure that the region is entirely contained
>>inside the BufferedRegion, otherwise the Metric will
>>throw an exception.
>>
>>  Regards,
>>
>>     Luis
>>
>>-----------------------
>>Mark Wyszomierski wrote:
>>
>>
>>>Hello All,
>>>
>>>I have been using motion registration and it is great. A quick question -
>>>
>>>Currently I am considering the whole image for registration, when
>>>using only a region of interest would be preferable. Currently I am
>>>using this method to set the considered region:
>>>
>>>registration->SetFixedImageRegion(
>>>fixedItkBuffer->GetOutput()->GetBufferedRegion() );
>>>
>>>fixedItkBuffer is a buffer containing the pixel data for a reference
>>>image. registration is my registration type pointer.
>>>
>>>How then can I specify a simple rectanglar region of interest to be
>>>considered instead of the entire buffer?
>>>
>>>Thanks!
>>>_______________________________________________
>>>Insight-users mailing list
>>>Insight-users at itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
>>>
>>
>>
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