# Stacking Z dimension images using SimpleITK

**URL:** https://discourse.itk.org/t/stacking-z-dimension-images-using-simpleitk/6623
**Category:** Beginner Questions
**Tags:** python, simpleitk
**Created:** [May 9, 2024, 12:12pm UTC](https://discourse.itk.org/t/stacking-z-dimension-images-using-simpleitk/6623 "2024-05-09T12:12:00Z")
**Posts on this page:** 1
**Showing post:** 22

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### Author: ![sleepingcat4](https://discourse.itk.org/user_avatar/discourse.itk.org/sleepingcat4/32/4032_2.png) [@sleepingcat4](https://discourse.itk.org/u/sleepingcat4)
#### Post date: [May 10, 2024, 8:28pm UTC](https://discourse.itk.org/t/stacking-z-dimension-images-using-simpleitk/6623/22 "2024-05-10T20:28:48Z")

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I used a similar method like you suggested and it resulted in no improvement.

Code:

```auto
import SimpleITK as sitk #1

raw_img = "resampled_image.tif"

raw_img_sitk = sitk.ReadImage(raw_img, sitk.sitkFloat32) #2
raw_img_sitk_arr = sitk.GetArrayFromImage(raw_img_sitk) #3

transformed = sitk.RescaleIntensity(raw_img_sitk, 0, 255) #1
transformed = sitk.LiThreshold(transformed,0,1) #2
head_mask = transformed

shrinkFactor = 4 #1
inputImage = raw_img_sitk

inputImage = sitk.Shrink( raw_img_sitk, [shrinkFactor] * inputImage.GetDimension() ) #2
maskImage = sitk.Shrink( head_mask, [shrinkFactor] * inputImage.GetDimension() ) #3

bias_corrector = sitk.N4BiasFieldCorrectionImageFilter() #4

corrected = bias_corrector.Execute(inputImage, maskImage) #5

log_bias_field = bias_corrector.GetLogBiasFieldAsImage(raw_img_sitk) #1
corrected_image_full_resolution = raw_img_sitk / sitk.Exp( log_bias_field ) #2

out_path = "field_corrected_image.tif"

# Cast the pixel type to float
corrected_float = sitk.Cast(corrected_image_full_resolution, sitk.sitkFloat32)

out_path = "corrected_resampled_image.tif"
sitk.WriteImage(corrected_float, out_path)

```

![image](https://discourse.itk.org/uploads/default/original/2X/9/93e33e1c6056789590933b2a31cca9655a5823a2.jpeg)

I was reading through Optical flow to fix “artifacts” that comes-up after tile merging and it looked nice. You have any thoughts or other algorithms to point to? [Registration using optical flow — skimage 0.23.2 documentation](https://scikit-image.org/docs/stable/auto_examples/registration/plot_opticalflow.html) @dzenanz

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