[Insight-users] Problem with 2D Registration (local minima)

Thu Oct 22 10:09:01 EDT 2009

Hi Luis,

Thank you for answering me.

1) As you said, my images are from Microscopy and the spacing is about 2.85 micrometres/pixel. The images are in a raw format and I used the following .mhd file for reading it:

    NDims = 2

    DimSize = 2000 2000

    ElementType = MET_UCHAR

    ElementSpacing = 1.0 1.0

    Offset = 0.0 0.0

    ElementByteOrderMSB = False

    ElementDataFile = fixed.raw

I also tried to as ElementSpacing 2.83 and 0.00283 (just in case...) but the results weren´t good either.

2) I also try to put a relaxation factor of 0.9 as you said and I couldn´t see any improvement.

3)  I´m attaching three .txt files with some results obtained. 

The results1.txt file shows the output of the program as you can find it on ITK/Examples/Registration/. 

The results2.txt file shows the output of the program with a predifined center in the position 1000x1000. The results3.txt file shows the output of the program with a predifined center in the position 1000x1000, a predefined angle of 0.9 radians and a predefined traslation of -340 in the X axis and 800 in the Y axis (that are the values for an optimal registration).

I hope you can help me to fix my problem with that information... an be free to ask anything else :P.

Thank you really much.

Manuel.

> Date: Wed, 21 Oct 2009 17:29:08 -0400
> Subject: Re: [Insight-users] Problem with 2D Registration (local minima)
> From: luis.ibanez at kitware.com
> To: manueldavid.tabas at hotmail.es
> CC: insight-users at itk.org
> 
> Hi Manuel,
> 
> Thanks for the detailed description of your problem.
> 
> A couple of questions:
> 
> 
> 1) What is the pixel spacing of your image ?
> 
> The typical proportion of :
> 
> > const double translationScale = 1.0 / 1000.0;
> 
> is set up for images whose physical extent in
> the units used by the spacing is in the range
> of hundreds.
> 
> For example, a typical CT scan will have 512x512
> pixels with a spacing close to 1mm / pixel.
> 
> Your images are probably from Microscopy or
> from a Satellite, so I'm wondering about the units
> that you use (microns or kilometers) and the
> exact numeric values of the spacing.
> 
> 
> 2) Could you post to the list the output of the
> command observer that tracks the values of
> the metric and the transform at every iteration ?
> 
> 
> Something that happens often when using the
> RegularStepGradientDescentOptimizer is that,
> if the registration process have a couple of
> bounces of direction in the parametric space,
> the step length may be reduced too fast, and
> not give the optimizer the oportunity to walk
> far enough to get to the solution.
> 
> 
> You may want to try using the method:
> 
> optimizer->SetRelaxationFactor( 0.9 );
> 
> 
> This method defines the factor by which the
> step length is reduced at every time that the
> parametric space step changes direction.
> This may prevent the premature shrinkage
> of the step length (assuming that this is the
> real problem).
> 
> 
> Anothe typical issue: It may simply be that you
> need a better initialization for your images.
> 
> 
> Note that the Transform initializer in the example:
> 
> ImageRegistration6.cxx
> 
> is using the methods MomentsOn().
> 
> This may or may not be the right method to use,
> depending on the content of your images.
> 
> For example: If the two images have different
> modalities, or if the main features of one image
> may not overlap to the one in the other image.
> 
> If you could post a screenshot of both images
> we could avoid all this speculation... :-)
> 
> Or...
> If you can share your images in a public web
> site, that will be even better.
> 
> 
> 
> Thanks
> 
> 
> Luis
> 
> 
> ----------------------------------------------------------------
> On Wed, Oct 21, 2009 at 11:56 AM, Manuel David Tabas Calle
> <manueldavid.tabas at hotmail.es> wrote:
> > Hello ITK,
> >
> > I´m working with ITK to do registration of 2D images and I think I reach a
> > local minima that makes a poor registration.
> >
> > I´m using 2D images 2000x2000 pixels in what the moving image needs a
> > rotation and a translation. So I reproduced the ImageRegistration6.cxx to do
> > that. But the result I got is not good enough so I think that the
> > MeanSquares metric reaches a local minima. The value of the metric is about
> > 4000 (aprox.), and I run a test using as input parameters the optimal ones
> > (that is, the result I think i should obtain) and the metric returns a value
> > of 2500 (aprox.).
> >
> > The framework I use is:
> >
> >    itkImageRegistrationMethod
> >    itkMeanSquaresImageToImageMetric
> >    itkLinearInterpolateImageFunction
> >    itkRegularStepGradientDescentOptimizer
> >    itkCenteredRigid2DTransform
> >
> > And the parameters of my registration are:
> >
> > const double translationScale = 1.0 / 1000.0;
> > optimizerScales[0] = 1.0;
> > optimizerScales[1] = translationScale;
> > optimizerScales[2] = translationScale;
> > optimizerScales[3] = translationScale;
> > optimizerScales[4] = translationScale;
> >
> > optimizer->SetMaximumStepLength( 0.1 );
> > optimizer->SetMinimumStepLength( 0.001 );
> > optimizer->SetNumberOfIterations( 200 );
> >
> >
> > The scales are well defined and I tried to vary the parameters of the
> > optimizer but the results were similar, so I don´t know what to do next. Any
> > idea??
> >
> > Thank you in advance, I hope you can have more ideas to try.
> >
> >
> >
> > Manuel.
> >
> >
> >
> >
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