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

Sat Dec 7 10:48:33 EST 2013

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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