Groupwise registration in SimpleITK or ITKElastix flipping images?

Beginner Questions
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1

Hello,

I am trying to run groupwise registrations in SimpleITK and ITKElastix, but with either the resulting images just seem to be flipped vertically. My original images are .tifs; I converted them to grayscale and then combined them into a .nii file before reading in. I am using code from tutorials for SimpleElastix in SimpleITK (Groupwise Registration — SimpleElastix 0.1 documentation) and for ITKElastix ( ITKElastix/examples/ITK_Example06_GroupwiseRegistration.ipynb at main · InsightSoftwareConsortium/ITKElastix · GitHub ). I have not altered the ITKElastix code; I only altered the SimpleITK code to read in a single .nii file rather than read in a folder and join the images together:

SimpleITK:

import SimpleITK as sitk

population = sitk.ReadImage("syngcleansizedgrey.nii")

vectorOfImages = sitk.VectorOfImage()

#for filename in population:
  #vectorOfImages.push_back(sitk.ReadImage(filename))

image = vectorOfImages

# Register
elastixImageFilter = sitk.ElastixImageFilter()
elastixImageFilter.SetFixedImage(population)
elastixImageFilter.SetMovingImage(population)
elastixImageFilter.SetParameterMap(sitk.GetDefaultParameterMap('groupwise'))
elastixImageFilter.Execute()

sitk.WriteImage(population, 'groupwise.tif')

ITKElastix:

import itk

# Load folder containing images.
images = itk.imread("syngcleansizedgrey.nii", itk.F) #", itk.F" loads images as floats

# Call registration function
# both fixed and moving image should be set with the vector_itk to prevent elastix from throwing errors

result_image, result_transform_parameters = itk.elastix_registration_method(
    images, images, parameter_object=parameter_object, log_to_console=True
)

# Call registration function
# both fixed and moving image should be set with the vector_itk to prevent elastix from throwing errors

result_image, result_transform_parameters = itk.elastix_registration_method(
    images, images, parameter_object=parameter_object, log_to_console=True
)

# Save image with itk
itk.imwrite(result_image, "exampleoutput/groupwise.tif")

With either, when I compare the output file to the original image, each image is simply vertically flipped. I would be very grateful for any insight on what I am doing wrong!

Thank you,

Rock

2

Hello @Rock,

The code looks correct. Can you post a sample input image and the vertically flipped image so that we can get a better understanding of your data and result?

In some cases the image may not be flipped, but the display method/program is flipping it. This likely isn’t your issue as I am assuming you are viewing the images using the same code or program, but just raising it as a possibility.

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