DeformationFields from BSplineStackTransform

[BailiangJ]

Hi,

I have done a groupwise registration with

vectorOfImages = sitk.VectorOfImage()

for filename in population:
  vectorOfImages.push_back(sitk.ReadImage(filename))

image = sitk.JoinSeries(vectorOfImages)

# Register
elastixImageFilter = sitk.ElastixImageFilter()
elastixImageFilter.SetFixedImage(image)
elastixImageFilter.SetMovingImage(image)
elastixImageFilter.SetParameterMap(sitk.GetDefaultParameterMap('groupwise'))
elastixImageFilter.Execute()

and after that I want to get the result deformation fields by

transformixFilter.SetTransformParameterMap(elastixImageFilter.GetTransformParameterMap())
transformixFilter.ComputeDeformationFieldOn()
transformixFilter.SetMovingImage(image)
transformixFilter.LogToConsoleOn()
transformixFilter.Execute()
# transformixFilter.GetDeformationField()

However, it raised error sitk::ERROR: TransformixImageFilter does not support the combination of image type float and dimension 4. This a serious error.

and according to @kaspermarstal 's solution, it can enable the TransformixImageFilter support for 4D.

Would it still be possible for the current version of SimpleITK-Elastix? If yes, where should I add it to?

Or is there any other way ways to obtain the deformation field from a BSplineStackTransform?

Thanks a lot.

[BailiangJ]

Or is there some ways to use the command transformix from elastix to obtain the separate deformation fields (independent subtransforms) mapping each images of the group to the template space from the 'BSplineStackTransform'?

Thanks a lot.

[BailiangJ]

Hi,

I have tried elastix command transformix -out ./ tp BSplineStackTransformParameterMap.txt -in img0.nii.gz and it seems warping the first image img0.nii.gz correctly.

But when I tried with the second/third image of the group transformix -out ./ tp BSplineStackTransformParameterMap.txt -in img1.nii.gz, the results images are not the same with elastixImageFilter.GetResultImage().

This means transformix is only taking the first subtransform, '(NumberOfSubTransforms 5)', there are 5 images so 5 subtransforms in my BSplineStackTransform.

Could anybody give me a hand? @N-Dekker @ntatsisk @mstaring Thanks a lot!

[BailiangJ]

Hi, I managed to get the separate BSpline Transform by doing another registration between the original image and the warped image with a same BSplineTransform setting (grid spacing etc).