[Insight-users] Changing itk.Examples.Registration.Translation1.cs to work with 3d images

Wed Apr 7 11:22:24 EDT 2010

Hi Luis,

thanks for getting back to me. Do you mean this?

START: [007.00, 012.00, 000.00]
000:   [005.10, 009.41, -002.39]
001:   [003.95, 006.69, 000.30]
002:   [001.88, 004.75, -002.52]
003:   [-000.29, 002.16, -000.38]
004:   [-002.46, -000.96, 000.86]
005:   [-003.21, -002.80, -002.61]
006:   [-003.55, -004.41, -001.47]
007:   [-004.40, -004.95, 000.26]
008:   [-004.78, -005.75, -000.19]
009:   [-005.28, -006.60, -000.02]
010:   [-005.41, -007.59, -000.06]
011:   [-005.49, -008.59, -000.01]
012:   [-005.53, -009.59, -000.02]
013:   [-006.09, -010.41, -000.02]
014:   [-006.97, -010.89, -000.05]
015:   [-007.02, -011.89, 000.02]
016:   [-006.82, -012.83, -000.23]
017:   [-006.96, -012.46, 000.07]
018:   [-007.02, -012.01, -000.14]
019:   [-007.00, -012.01, 000.11]
020:   [-007.00, -012.01, -000.01]
021:   [-007.00, -012.00, 000.05]
022:   [-007.00, -012.00, 000.02]
023:   [-007.00, -012.00, -000.02]
024:   [-007.00, -012.00, 000.00]
END:   [-007.00, -012.00, 000.00]

Actually, after further investigation it looks as though there's some confusion over the raw data format. I changed the DimSize in the mhd from
  DimSize = 128 128 128
to
  DimSize = 256 256 128

and the code *seems* to work correctly, although it does generate the message:
  MetaImage: M_ReadElements: data not read completely
     ideal = 8388608 : actual = 4194304

also, after applyiing the found parameters the resulting image seems pixelated (see attached png).

Is there something wrong with the Read method? Is the image type incorrect? Or could it be the header file? (ImageJ reads the raw file correctly with 128, 128, 128.)

Regards,

Carl

>>> Luis Ibanez <luis.ibanez at kitware.com> 07/04/2010 14:43 >>>
Hi Carl,

Thanks for the detailed description of what you are doing.

You changes to the code look reasonable.

The fact that the fixed image has a different number of
slices than the moving image shouldn't be a problem,
*as long as* both images have the correct values of
pixel spacing.

I would have expected the "registered" image to have the
same image grid as the "fixed" image, since it is usually
generated by mapping the intensity values of the moving
image into the image grid of the fixed image.

How does the current setup behaves when you run the
registration ?

Can you please post to the list the values of the Metric,
and the transform parameters at every iteration of the
registration process ?

    Thanks

         Luis

------------------------------------------------------------
On Tue, Apr 6, 2010 at 12:34 PM, Carl Bateman <Carl.Bateman at icr.ac.uk> wrote:
> I'm trying to change itk.Examples.Registration.Translation1.cs to work with 3d images.
>
> I've changed the existing using statements to:
>  using ImageType = itk.itkImage_UC3;
>  using InterpolatorType = itk.itkLinearInterpolateImageFunction_IUC3D;
>  using TransformType = itk.itkTranslationTransform_D3;
>  using ResampleType = itk.itkResampleImageFilter_IUC3IUC3;
>  using MetricType = itk.itkMeanSquaresImageToImageMetric_IUC3IUC3;
>  using OptimizerType = itk.itkRegularStepGradientDescentOptimizer;
>  using RegistrationType = itk.itkImageRegistrationMethod_IUC3IUC3;
>
> and the transform.Translate lines to:
>  transform.Translate(new itkVector(7.0, 12.0, 0.0));
> and
>  transform.Translate(new itkVector(0.0, 0.0, 0.0));
>
>
> I'm using a raw image with a mhd header as input.
>
> The original image has 128 slices, but the "_FIXED", "_MOVING" and "_REGISTERED" images only have 64 slices.
>
> Additionally, the "_MOVING" and "_REGISTERED" images have a white cross through them (see attached png).
>
> I suspect that the problem lies in the transformation, as
>  transform.Translate(new itkVector(7.0, 0.0, 0.0));
> gives a horizontal line, while
>  transform.Translate(new itkVector(0.0, 12.0, 0.0));
> gives a vertical line.
>
>
> Is it the transformation? And if so how should it be used correctly?
>
> Any help appreciated.
>
> Carl Bateman
>
>
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