[ITK Community] [Insight-users] Making a deformation field denser in order to deform points

Sat Dec 7 12:23:25 EST 2013

Hi Yago,

An Image that defines the displacement field vectors can be set on a
DisplacementFieldTransfrom with SetDisplacementFieldTransform [1].  It
is also possible to save the displacement field as a transform
directly, instead of an image, with the TransformFileWriter [2].

Hope this helps,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1DisplacementFieldTransform.html#ab0b5ac8b6792ed0acddbd0a6666b39d2
[2] http://www.itk.org/Doxygen/html/classitk_1_1TransformFileWriterTemplate.html

On Sat, Dec 7, 2013 at 10:48 AM, Yago Diez <yagodiezdonoso at gmail.com> wrote:
> First of all, thanks a lot for your answer and sorry I couldn't solve the
> problem on my own. I have been fighting for a while with this but so far I
> have not had much success. At least I am now a bit more aware of how many
> things I don't know.
>
> First of all, I realise what I want to do boils down to :
>
> typename CompositeTransformType::Pointer compositeTransform =
> CompositeTransformType::New();
> compositeTransform->AddTransform( deffield);
> compositeTransform->TransformPoint( p0 );
>
> The problem now is that my deformation field is not recognised as a valid
> transformation.
>
> My deformation field which is the output of demons registration and it is
> stored in a file in mha format. I read it like this (as a vector image as
> used to be done in itk3):
>
>>  typedef float      PixelType;
>>  typedef   float VectorComponentType;
>>
>>   const   unsigned int        Dimension = 3;
>>
>>  typedef itk::Vector< PixelType, Dimension  > VectorPixelType;
>>  typedef itk::Image< VectorPixelType, Dimension > DeformationFieldType;
>>  typedef itk::ImageFileReader< DeformationFieldType > ReaderType;
>>
>>  ReaderType::Pointer reader = ReaderType::New();
>>  reader->SetFileName(argv[1]);
>>  reader->Update();
>>  DeformationFieldType::Pointer deffield = reader->GetOutput();
>
>
>
> When I try to add it to the composite transform, however, I get the error:
>
> /media/disc4/code/newTransformPoints.cxx:112:47: error: no matching function
> for call to ‘itk::CompositeTransform<float,
> 3u>::AddTransform(itk::Image<itk::Vector<float, 3u>, 3u>::Pointer&)’
> /media/disc4/code/newTransformPoints.cxx:112:47: note: candidate is:
> /usr/local/include/ITK-4.4/itkMultiTransform.h:145:16: note: void
> itk::MultiTransform<TScalar, NDimensions,
> NSubDimensions>::AddTransform(itk::MultiTransform<TScalar, NDimensions,
> NSubDimensions>::TransformType*) [with TScalar = float, unsigned int
> NDimensions = 3u, unsigned int NSubDimensions = 3u,
> itk::MultiTransform<TScalar, NDimensions, NSubDimensions>::TransformType =
> itk::Transform<float, 3u, 3u>]
> /usr/local/include/ITK-4.4/itkMultiTransform.h:145:16: note:   no known
> conversion for argument 1 from ‘itk::Image<itk::Vector<float, 3u>,
> 3u>::Pointer {aka itk::SmartPointer<itk::Image<itk::Vector<float, 3u>, 3u>
>>}’ to ‘itk::MultiTransform<float, 3u, 3u>::TransformType* {aka
> itk::Transform<float, 3u, 3u>*}’
>
>
> From what I understand, instead of reading my deformation field as a vector
> image, I should probably be using the itk4 "displacementfieldtransform".
>
>> typedef itk::DisplacementFieldTransform<VectorComponentType, 3>
>> DeformationFieldTransformType;
>
>
> My main problem now is that I cannot seem to "connect" my mha file
> containing the deformation field with the displacementFieldTransformType. I
> probably need some type of basic "read DisplacementFieldTransform from file"
> function, but so far I have not been able to make one.
>
> Any ideas that might help? I realise that the bigger problem here is my own
> lack of knowledge on the details of itk4, so please do not hesitate to point
> me to as basic a source as necessary.
> Gratefully
> Yago Diez Donoso
>
>
>
> Yago Diez Donoso (PhD)
> Computer Vision and Robotics Group http://vicorob.udg.es/
> E-mail: yago at eia.udg.es; yagodiezdonoso at gmail.com
> Phone: (int. code) 34 972418013
> University of Girona
>
>
> On Wed, Dec 4, 2013 at 8:48 PM, brian avants <stnava at gmail.com> wrote:
>>
>> see line 142 here:
>>
>>
>> https://github.com/stnava/ANTs/blob/d99d9c9e23ae17c116377a248cd370ddbd8c2599/Examples/antsApplyTransformsToPoints.cxx
>>
>> you can do the same thing in your application but note that the
>> deformation field , when applied to a point , should be the inverse of the
>> deformation field applied to an image
>>
>> see my previous email regarding SyN and inverse warps.
>>
>>
>> brian
>>
>>
>>
>>
>> On Wed, Dec 4, 2013 at 2:33 PM, Yago Diez <yagodiezdonoso at gmail.com>
>> wrote:
>>>
>>> Hi everyone,
>>>
>>> I have a problem regarding itk deformation fields:
>>>
>>> Specifically, I want to know where a particular point ends up after
>>> registration. Said registration has produced a deformation field. I have
>>> already used this deformation field to deform the source image and produce
>>> the output image for registration (this was done using itkWarpImageFilter).
>>>
>>> My problem is that at this moment I only want to transform one point. The
>>> obvious solution was to read the corresponding voxel in the deformation
>>> field and add it to the point, but the problem is that the deformation field
>>> is not "dense enough", so in most cases, the read deformation for a point
>>> ends up being zero (see attached image for a screen capture of a 2D slice of
>>> my 3D deformation field).
>>>
>>>  I have noticed how when I deform an image with itkWarpImageFilter, there
>>> is an "extra" interpolation step which would avoid the problem I am having,
>>> but so far I have not been able to interpolate a deformation field. Any
>>> ideas on how to do that?
>>>
>>> Thank you
>>>
>>>
>>>
>>>
>>> Yago Diez Donoso (PhD)
>>> Computer Vision and Robotics Group http://vicorob.udg.es/
>>> E-mail: yago at eia.udg.es; yagodiezdonoso at gmail.com
>>> Phone: (int. code) 34 972418013
>>> University of Girona
>>>
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>>
>
>
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