Merge channels of NIfTI (.nii) images in python

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I am trying to superimpose a CT .nii image and its mask in another color (possibly red). This is easily achievable for example with imageJ, thanks to the "Merge Channels" functionality. What I would like to obtain looks like this:

this

given my original image:

original image

and its mask:

its mask

So basically I need to "convert to red" my mask and superimpose it on my grayscale image.

I've looked into SimpleITK (this is how I made the contour mask) but I can't proceed forward from here. Can anyone help?

nifti simpleitk mask python
1 Answers

Here's a SimpleITK script that overlays a mask on an image:

import SimpleITK as sitk

img = sitk.ReadImage("ct.jpg")
mask = sitk.ReadImage("mask.png")

# Extract one channel since the images are actually RGB
img = sitk.VectorIndexSelectionCast(img, 0)
mask = sitk.VectorIndexSelectionCast(mask, 0)

mask = mask>200

red = [255, 0, 0]

color_overlay = sitk.LabelMapOverlay( sitk.Cast(mask, sitk.sitkLabelUInt8),
    img, opacity=0.5, colormap=red )

sitk.WriteImage(color_overlay, "overlay.png")

And here's resulting output image: enter image description here

Note that the script first extracts one channel from image and mask to create grayscale images (since your examples were RGB). Also, it does a threshold on the mask to create a binary mask (0s and 1s).

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