How can I find coordinates of a point after resampling?

Beginner Questions
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1

Suppose I apply a resampling operation to my image as below:

    resampler = sitk.ResampleImageFilter()
    resampler.SetSize(target_size)
    resampler.SetOutputSpacing(target_spacing)
    resampler.SetOutputOrigin(original_origin) 
    resampler.SetOutputDirection(image.GetDirection())
    resampled_image = resampler.Execute(image)

Now suppose that in the original image, there is a voxel at point (x,y,z). I now want to calculate/find the coordinates of this point in the new image space.

I tried using

transform = resampler.GetTransform()
new_coordinates = transform.TransformPoint((x,y,z))

but that does not seem to work since GetTransform() returns an identity transformation. Any help would be greatly appreciated. Thanks!

2

Hello @Eloy_Schultz,

In the code you provided, the transformation is the identity so the index of a point changes in the resampled_image, but its physical coordinates do not. The various options of moving between physical coordinates and indexes are illustrated below:

original_index = [x, y, z] 
original_physical_coords = image.TransformIndexToPhysicalPoint(original_index) 
# If you have a continuous value for the index, sub pixel use TransformContinuousIndexToPhysicalPoint

# Obtain the corresponding index in the resampled image, either continuous or discrete 
new_index_continous = resampled_image.TransformPhysicalPointToContinuousIndex(original_physical_coords)
new_index = resampled_image.TransformPhysicalPointToIndex(original_physical_coords)
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3

Great thanks! That is exactly what I was looking for. Also thanks for pointing out the difference between physicial space (coordinates) and image space (indices), this cleared it up for me. Thanks again

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