Add empty slice at the end of the CT image

Beginner Questions
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1

Hello,

I have a simple question. i need to resize CT scan saved in nifty file. I need to add one black slice at the end of the 3D image (in Z direction).
I would appreciate for any help/suggestion. How can I do that in simpleitk ?
Is there any simple way to modify that image ?

Best,
Agata

2

Hello @agatadefr,

“one black slice” - this is not well defined as black is a display color, not an intensity value. As you are working with CT, likely you want to add a slice with air, which has a HU value of -1000 (often people equate “black” with 0 intensity).

Images in ITK/SimpleITK are spatial objects, so padding an image involves modifications to the spatial information.

Code below does what you want (significantly simplified based on the feedback below from @blowekamp). It can be further simplified to a one liner if you know which side you want to pad, wasn’t clear to me so this is a flag:

import SimpleITK as sitk

file_name = 
image = sitk.ReadImage(file_name)


air_hu = -1000
# which end of the slice stack to pad front or back
front_end = True

if front_end:
  padded_image = sitk.ConstantPad(image, [0,0,1], [0,0,0], air_hu)
else:
    padded_image = sitk.ConstantPad(image, [0,0,0],[0,0,1], air_hu)
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3

It may be simpler to use the ConstantPadImageFilter.

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4

Thanks a lot @zivy ! It works so well. Thats exactly what I needed! I am so grateful for your help!

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