Hi @Dre,
Welcome to ITK!
Moreover, the output image seems to have some noise.
It looks like the original image has a higher dynamic range than supported by the unsigned char pixel type used to read the image, so we are seeing more variations over this small range and wrap-around when the values exceed the 0-255 range. One option is to read in the image with a different pixel type with a larger range, like short, or to rescale the intensity to 0-255 with an itk.RescaleIntensityImageFilter.
However, I am unable to customize the color of the masks
The itk.LabelMapOverlayImageFilter does not support custom colors, but we may be able to add them with other classes. Can you share your input images to create an example?
Thanks,
Matt