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

Bill Lorensen bill.lorensen at gmail.com
Thu Oct 22 12:41:41 EDT 2009 

I meant the value of the parameters...

On Thu, Oct 22, 2009 at 11:56 AM, Manuel David Tabas Calle
<manueldavid.tabas at hotmail.es> wrote:
>
> Hi Bill,
>
> The optimum value for the metric that I spect is about 2000, and I normally
> get a metric of 4000.
>
> I will try just now to set:
>
> optimizer->SetMaximumStepLength( 0.1 );
>
> and I´ll let you know the results in a while.
>
> Thanks!
>
> Manuel.
>
>> Date: Thu, 22 Oct 2009 11:52:23 -0400
>> Subject: Re: [Insight-users] Problem with 2D Registration (local minima)
>> From: bill.lorensen at gmail.com
>> To: manueldavid.tabas at hotmail.es
>> CC: insight-users at itk.org
>>
>> The optimizer is stopping after reaching the maximum number of
>> iterations. This is normally not the best way to terminate an
>> optimization.
>>
>> What do you expect for the optimum value of the parameters?
>>
>> Perhaps you need a larger maximum step length? Or perhaps, as Luis
>> suggested, the starting point is too far from the optimum for this
>> optimizer.
>>
>> Bill
>>
>>
>> On Thu, Oct 22, 2009 at 10:09 AM, Manuel David Tabas Calle
>> <manueldavid.tabas at hotmail.es> wrote:
>> >
>> > 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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>> >> >
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