SetSigma in sitk.SmoothingRecursiveGaussianImageFilter()

Algorithms
1

According to the documentation SetSigma is measured in the units of image spacing. If I have 3D image with spacing = [0.5, 0.5, 3] (mm) and sigma is set to 3, does this mean that I am smoothing 3mm isotropically? Or does this mean that sigma is 3 x [0.5, 0.5, 3] = [1.5, 1.5, 9] (mm)?

2

I found this in the source code:

image
image.png1768Ă—508 72.5 KB

Does this mean that the parameter sigma is divided by the spacing of the image to calculate how many pixels on each direction the filter smooths over?

suggestion: the documentation could be clearer about the sigma parameter. If it said that sigma is measured in real world units I think it would be helpful. Thanks.

3

Hello,

Thank you for you suggestion and discussion. But technically it is not in “Physical Coordinates” ( common ITK term) because it does not take into consideration the direction cosine matrix. For that reason I think the existing wording is more accurate than your proposed wording. Though the original could be clearer… So further suggestions are quite welcomed!

1 Like
4

Thanks for the reply Bradley,

I just checked the ITK doxygen and it says now “world coordinates”. :+1: thanks for that.

As a user of the library I needed to know If sigma was in index space (voxels) or world space (mm in my case)

Thanks,

Diego