Convert Transform parameter file to transform matrix

[XXZhou25]

Hi,

I was trying to convert a euler 3D transform parameter file to a transform matrix to manually compute deformation field, by SimpleITK Euler3DTransform. I also used elastix command line to generate a deformation field. However, my manually computed results were always a little bit different from elastix generated. I was wondering if you would know the possible reasons? I thought for Euler transform, it only transforms the coordinates by the transform matrix, and no interpolation or other operations is needed, do I understand correctly?

My code and result:

image_origin = np.array([0, -239, 0]) theta_x = -0.094891 theta_y = 0.006870 theta_z = 0.031377 translation = np.array([-9.053901, -23.358420, -8.338770]) rotation_center = np.array([119.5, -119.5, 77]) rigid_euler = sitk.Euler3DTransform(rotation_center, theta_x, theta_y, theta_z, translation) A1 = np.asarray(rigid_euler.GetMatrix()).reshape(3,3) c1 = np.asarray(rigid_euler.GetCenter()) t1 = np.asarray(rigid_euler.GetTranslation())

p = np.array([100, 200, 200]) truec = rotation_center - image_origin p_transform = np.dot(A1, p - truec) + t1 + truec p_displacement = p_transform - p

result: p_displacement = array([-11.0793279 , -12.68448335, -16.38891453]) p_displacement_byelastix = DVF[100, 200, 200] = array([-11.518286, -19.103964, -16.620592], dtype=float32)

their difference is: array([-0.43895785, -6.4194805 , -0.23167759])

The transform file: (Transform "EulerTransform") (NumberOfParameters 6) (TransformParameters -0.094891 0.006870 0.031377 -9.053901 -23.358420 -8.338770) (InitialTransformParametersFileName "NoInitialTransform") (UseBinaryFormatForTransformationParameters "false") (HowToCombineTransforms "Compose")

// Image specific (FixedImageDimension 3) (MovingImageDimension 3) (FixedInternalImagePixelType "float") (MovingInternalImagePixelType "float") (Size 240 240 155) (Index 0 0 0) (Spacing 1.0000000000 1.0000000000 1.0000000000) (Origin 0.0000000000 -239.0000000000 0.0000000000) (Direction 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000) (UseDirectionCosines "true")

// EulerTransform specific (CenterOfRotationPoint 119.5000000000 -119.5000000000 77.0000000000) (ComputeZYX "false")

// ResampleInterpolator specific (ResampleInterpolator "FinalBSplineInterpolator") (FinalBSplineInterpolationOrder 3)

// Resampler specific (Resampler "DefaultResampler") (DefaultPixelValue 0.000000) (ResultImageFormat "nii.gz") (ResultImagePixelType "short") (CompressResultImage "false")

I will appreciate any of your ideas! Thank you so much!

[wu-yi-hong]

Excuse me, how can I obtain the matrix of the transformation

[wu-yi-hong]

你好，我最近也想在TransformParameters.0.txt 这个文件中找到变换矩阵，但是我并没有发现有类似的参数，请问你有什么建议吗？谢谢