[Insight-users] how to set the initial parameter for a rigid registration manually?

[Luis Ibanez]

Hi Michiel,

Thanks for sending the image data.

1) Given that the direction cosines of your Fixed image
    are an identity matrix, the geometrical center of your
    Fixed image is:

              Origin +  Spacing * Size / 2

    That is:

     X: 44.0625 + 0.3125 *  215 / 2  =  77.65625
     Y:   0.0       + 0.3125 *  172 / 2  =  26.875
     Z:   0.0       + 1.9808 *    48 / 2  =  47.53919


1) Given that the direction cosines of your Moving image
    are an identity matrix, the geometrical center of your
    Moving image is:

              Origin +  Spacing * Size / 2

    That is:

     X:   0.0  + 0.3125 *  512 / 2  =  80.0
     Y:   0.0  + 0.3125 *  512 / 2  =  80.0
     Z:   0.0  + 1.9291 *    52 / 2  =  50.15


3) The relative position between the geometrical
     centers of the Moving image and Fixed image

          X:    80.0   - 77.65625   =     2.34375
          Y:    80.0   - 26.875       =   53.125
          Z:    50.15 - 47.53919   =     2.610

      that is consistent with the translation that
      the Transform initializer is reporting:

             [0, 0, 0, 2.34375, 53.125, 2.64351]



So, the TransformInitializer is doing the right thing.
Something else is wrong in the setup of your
registration process.


Questions:

A) Do you get the Exception message at the
     first iteration of the optimizer ?

B)  If you get the Exception message after
      several iterations of the optimizer, could
      you please post to the list:

        1) Type of the optimizer that you are using
        2) Full list of optimizer numerical parameters
        3) Scaling array that you are passing to the
            optimizer.



     Thanks


          Luis


-------------------------------------------------------------------------
On Tue, Mar 2, 2010 at 4:19 AM, michiel mentink
<michael.mentink at st-hughs.ox.ac.uk> wrote:
> hi Luis,
>
> fixed image size:      [215, 172, 48]
> fixed image origin:    [44.0625, 0, 0]
> fixed image spacing:   [0.3125, 0.3125, 1.9808]
> fixed image direction:
> 1 0 0
> 0 1 0
> 0 0 1
>
> moving image size:      [512, 512, 52]
> moving image origin:    [0, 0, 0]
> moving image spacing:   [0.3125, 0.3125, 1.92911]
> moving image direction:
> 1 0 0
> 0 1 0
> 0 0 1
>
> image mask size:      [215, 172, 48]
> image mask origin:    [44.0625, 0, 0]
> image mask spacing:   [0.3125, 0.3125, 1.9808]
> image mask direction:
> 1 0 0
> 0 1 0
> 0 0 1
>
> when GeometryOn() is used:  Initial Transform Parameters: [0, 0, 0, 2.34375,
> 53.125, 2.64351]
>
>
> When MomentsOn() is used:  Initial Transform Parameters: [0, 0, 0, 7.70064,
> 49.5835, -0.0834114]
>
>
>
> cheers,
>
> Michael
>
>
> On Mon, Mar 1, 2010 at 11:11 PM, Luis Ibanez <luis.ibanez at kitware.com>
> wrote:
>>
>> Hi Michiel,
>>
>> It is very unlikely that the CenteredTransformInitializer
>> will fail to overlap the two images.
>>
>>
>> DO NOT assign any value manually to the Transform.
>> That's what the Initializer is for.
>>
>>
>> Please do the following:
>>
>>   1) Set the initializer to use GeometryOn();
>>
>>   2) Run the code again and
>>       post to this mailing list the following information:
>>
>>        a) The Transform just as it is initialized by the
>>             initializer ( no need to run registration iterations).
>>
>>        b) Origin, Spacing, Orientation and number of pixels
>>             of both the Fixed Image and Moving Images.
>>
>>
>>  Thanks
>>
>>
>>       Luis
>>
>>
>>
>> ----------------------------------------------------
>> On Mon, Mar 1, 2010 at 11:40 AM, michiel mentink
>> <michael.mentink at st-hughs.ox.ac.uk> wrote:
>> > spoke too soon :(
>> >
>> > Now the moving image dimensions are zeroed too.
>> >
>> > help?
>> >
>> > On Mon, Mar 1, 2010 at 4:30 PM, michiel mentink
>> > <michael.mentink at st-hughs.ox.ac.uk> wrote:
>> >>
>> >> ah solved it.
>> >>
>> >> For any that are interested:
>> >>
>> >>  TransformType::OutputVectorType translation_vector;
>> >>   translation_vector[0] = 0.0;
>> >>   translation_vector[1] = 0.0;
>> >>   translation_vector[2] = 0.0;
>> >>   transform->SetTranslation(translation_vector);
>> >>
>> >> and then comment out
>> >>   initializer->InitializeTransform();
>> >>
>> >> Still doesn't solve my problem though.
>> >>
>> >> cheers, Michael
>> >>
>> >>
>> >> On Mon, Mar 1, 2010 at 3:39 PM, michiel mentink
>> >> <michael.mentink at st-hughs.ox.ac.uk> wrote:
>> >>>
>> >>> Dear all,
>> >>>
>> >>> is there anyway of setting the initial iteration of the
>> >>> CentredTransformInitializer manually?
>> >>>
>> >>> The CentredTransformInitializer uses either GeometryOn() or
>> >>> momentsOn()
>> >>> that calculates
>> >>> the center of the image, but that produces an initial parameter that
>> >>> fails the registration even
>> >>> before it starts, because its errors:
>> >>> Description: itk::ERROR: MeanSquaresImageToImageMetric(0x9dfa3f0): All
>> >>> the points mapped to outside of the moving image
>> >>>
>> >>> Alternatively, can I just overwrite the parameters that are produced
>> >>> by
>> >>> the centredTransformInitializer? How?
>> >>>
>> >>> I'm using the VersorRigid3DTransform.
>> >>>
>> >>> cheers, Michael
>> >>>
>> >>
>> >
>> >
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