[Insight-users] Registration of one sub-brain to full-brain

[Erik Türke]

Am 21.10.2010 19:17, schrieb Torsten Rohlfing:
> Hi guys -
>
> This is more of a question than a suggestion: does ITK currently 
> support "pixel padding"? That is, can we currently define a value in 
> the image data that serves as a marker for pixels that aren't really 
> there? Think of it as a binary mask coded into the image itself.
>
> In my experience, when you register partial objects to complete 
> objects (also interesting to register skull-stripped brains to full 
> head images, for example), the key is to be able to exclude pixels 
> from the metric computation altogether, rather than just setting them 
> to zero.
>
> Alternatively, because we cannot always find a pixel value that isn't 
> actually used by the data already, one could implement this behaviour 
> by providing the registration framework with optional explicit binary 
> masks for fixed and moving images.
>
> Best,
>   Torsten
>
>> Hello Erik
>>
>> You may want to try changing the number of resolutions employed in the
>> multi-resolution pyramid used to perform the registration.   In
>> addition, you may want to try switching the role of the fixed/moving
>> image.  We are currently revising the registration framework so now is
>> a good time to bring these types of issues up and work with us on
>> improving registration performance.
>>
>> Brian
>>
>>
>> On Thu, Oct 21, 2010 at 4:35 AM, Erik Tuerke<tuerke at cbs.mpg.de  <http://www.itk.org/mailman/listinfo/insight-users>>  wrote:
>> >/  Hi!
>> />/
>> />/  I want to register one hemisphere (actually 30 slices of 0.75 mm) to a
>> />/  fullbrain scan (30 slices of 0.75mm, but shifted to superior for about 5 mm)
>> />/  . Currently i am using a MattesMutualInformationImageToImage metric, a
>> />/  RegularStepGradientDescentOptimizer and a VersorRigid3DTransform.
>> />/
>> />/  Prior to the registration the hemisphere is roughly aligned to the fullbrain
>> />/  (only needs translation of few mm and little rotation). If i start the
>> />/  registration the optimizer finishes with a rotation of about 90 deg x and y.
>> />/  I also tried a VersorRigid3DOptimizer and a NormalizedCorrelation with
>> />/  almost the same result.
>> />/
>> />/  The scalefactors of my optimizer are:
>> />/                 optimizerScaleRegularStepGradient[0] = 1.0;
>> />/                 optimizerScaleRegularStepGradient[1] = 1.0;
>> />/                 optimizerScaleRegularStepGradient[2] = 1.0;
>> />/                 optimizerScaleRegularStepGradient[3] = 1.0/1000.0;
>> />/                 optimizerScaleRegularStepGradient[4] = 1.0/1000.0;
>> />/                 optimizerScaleRegularStepGradient[5] = 1.0/1000.0;
>> />/
>> />/  I guess the itk examples are proposing the same values.
>> />/  Is there any trick to apply such a sub-brain registration to a full-brain
>> />/  registration. The worrying thing is that SPM gets it right :-(
>> />/
>> />/  Thanks and best regards!!
>> />/
>> />/  --
>> />/  Erik Tuerke
>> />/  Department of Neurophysics Max-Planck-Institute for Human Cognitive and
>> />/  Brain Sciences
>> />/  Stephanstrasse 1A
>> />/  04103 Leipzig
>> />/  Germany Tel: +49 341 99 40-2440
>> />/  Email:tuerke at cbs.mpg.de  <http://www.itk.org/mailman/listinfo/insight-users>
>> />/  www.cbs.mpg.de
>> />/
>> />/
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>>
>
> -- 
> Torsten Rohlfing, PhD          SRI International, Neuroscience Program
>   Senior Research Scientist      333 Ravenswood Ave, Menlo Park, CA 94025
>    Phone: ++1 (650) 859-3379      Fax: ++1 (650) 859-2743
>     torsten at synapse.sri.com         http://www.stanford.edu/~rohlfing/
>
>       "Though this be madness, yet there is a method in't"
>
>
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Hi!

Well i think extracting a region of interest which should be considered 
during the registration is possible by passing a mask to the image 
metric. So the challenge is to define this mask automatically. I am 
first thinking of an Otsu filter to define such a mask.
A second possibility would be to use the 
"SetUseFixedImageSamplesIntensityThreshold 
<http://www.itk.org/Doxygen318/html/classitk_1_1ImageToImageMetric.html#ae56734d7cc4bb45a6ba462e56f260546>" 
method or the "SetUseSequentialSampling" method  of the 
MattesMutualInformationImageToImageMetric. But since these both methods 
are only implemented in the review code i did not use one of them.

Best regards so far!

-- 
Erik Türke
Department of Neurophysics
Max-Planck-Institute for Human Cognitive and Brain Sciences
Stephanstrasse 1A
04103 Leipzig
Germany
Tel: +49 341 99 40-2440
Email: tuerke at cbs.mpg.de
www.cbs.mpg.de

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