[Insight-users] Registration of Slices
Shekhar Chandra
Shekhar.Chandra at monash.edu
Sun Sep 12 19:47:31 EDT 2010
Thanks Luis for your detailed answer. We appreciated it a lot! It will
allow us to move forward. :)
Will look into these points and post a guide on my blog when I get a chance.
Cheers
Shekhar
On 13/09/2010 4:49 AM, Luis Ibanez wrote:
> Hi Shekhar,
>
> Thanks for the detailed description of what you are doing.
>
> Please see comments below.
>
> -----------------------------------------------------------------------------------
> On Mon, Sep 6, 2010 at 10:36 PM, Shekhar Chandra
> <Shekhar.Chandra at monash.edu <mailto:Shekhar.Chandra at monash.edu>> wrote:
>
> Hi Everyone,
>
> I'm a VTK user who is new to ITK. In my current project I have to
> register a stack or series of Micro CT images, which will be used
> to reconstruct some biological samples.
>
> Via ITK I have worked out how to load the series (using the
> ImageSeries class, Multi-page TIFFs or MRC files). Traverse and
> filter (if necessary) the slices (using
> ImageSliceConstIteratorWithIndex and JoinSeriesImageFilter, as
> well as the itkSliceBySliceImageFilter). I put some of this on my
> blog for reference for those that are interested.
> <http://l3mmings.blogspot.com/2010/08/slices-stacks-and-itk.html>
>
>
>
> Thanks for posting the code in your blog.
> This is very helpful.
>
> The problem I have is that registering the slices give me barely
> adequate results. I went about it by using the Multi-res example
> and Software Guide.
>
>
> What is the size (in pixels) of these images ?
>
> Depending on the size, you may or may not need
> to do multi-resolution.
>
> I make the first slice the fixed image and treat the next slice as
> the moving image. I transform/resample the moving image after
> registering it and make it the next fixed image. The next slice is
> then the moving image. I realise that the error in registration
> propagates using this method. Is this the best way to register slices?
>
>
>
> This is a commonly used method.
> You are right in that the registration error will propagate,
> and that, therefore, a subsequent correction may be needed.
> We probably should go back to this point once we manage
> to register your slices (pair-wise).
>
> On one post, it was suggested that one could use a sliding window
> (e.g. register slice before and after with fixed slice), but it
> was not mentioned how to do this. Has someone solved this problem
> or encountered it?
>
> I know the parameters for registration are data dependent and have
> to be found. But when exploring a metric with a slice (as per
> Exploring a Metric example), it takes a while to compute even for
> -50 to 50 pixel translations for small images (300x300, few
> minutes for MeanSquares on a Core2duo with Optimised Registration
> methods). Is this normal?
>
>
> No way :-)
>
> The metric computation between two images of that size
> should be should be very fast. In my laptop (a dual core
> 2.8Ghz) it takes 7 milliseconds to evaluate the matrix with
> images of similar size.
>
> Doing this for a grid of 50x50 positions should take then
> about 20 seconds.
>
> Please make sure that you are compiling ITK for Release
> mode, and that both of your cores are being used at
> run time.
>
> BTW: What version of ITK are you using ?
>
> Finally, what is the best way to do very coarse alignment in ITK?
> Center of Gravity sounds good, but it has rotations (because of
> the CenteredRigid2DTransform) and I do not need rotations.
>
>
> You could use the CenteredTransformInitializer with
> a Translation 2D transform. Then use the resulting
> translation parameters to initialize the transform:
> CenteredRigid2DTransform that you are using.
>
>
> BTW: You should not use this transform.
> Instead, the Rigid2DTransform is a more
> modern way of performing this registration.
>
> The difference is that the CenteredRigid2DTransform
> attempts to fine tune the center of rotation at the
> same time that it optimizes the translation and rotation.
>
> The Rigid2DTransform, on the other hand, only
> optimizes the Translation and Rotation parameters.
>
>
> Searching the web has not yielded any further help. Any suggestion
> or advice would be greatly appreciated.
>
>
>
> The common suspects of registraiton failure are:
>
> 1) Poor initialization
> 2) Poor (or no) setting of the Optimizer Parameter Scale.
> 3) Poor settings of the optimizer step lenght
>
> ---
>
> The case (1) can be examined by running the
> registration for Zero iterations, or by simply
> taking the initialized transform and using it
> to resample the moving image, without running
> the registration at all.
>
> If the image looks roughly aligned, then you
> can exonerate (1).
>
> ----
>
> The case (2) is quite likely to blame here, since
> the Rigid2DTransform combines rotation and
> translation parameters.
>
> The scale for translation is in the range -100,100,
> while the scale of ration is in the range -0.5,0.5,
> (because the units are Radians).
>
> It is therefore, crucial to scale this parameters,
> as illustrated in many examples.
>
> Look for the line:
>
> optimizer->SetScales( optimizerScales );
>
> ----
>
> The case (3) can be examined by looking at the
> output of the array of parameters at every iteration.
> You must use a Observer in order to print out this
> values. Most of the registration examples show
> how to do this.
>
> If the values of the transform have dramatic
> changes between consecutive iterations,
> that will be an indication that the optimizer
> step length (or equivalent parameters) are
> too aggressive.
>
>
>
> Regards,
>
>
> Luis
>
>
> ------------------------------------------------------------------
>
> Cheers
> Shakes
>
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