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I'm using ITK-SNAP to compare the intensities of several Regions of Interest between several conditions.

For some subjects, I need to realign one image to another by using the Registration tool.

However, I noticed that the intensity values of a specific segmentation that I drew on the reference image doesn't change no matter how I register.

The value will be different between the two images, but even if I manually register the second image to something completely off, it will stay the same.

Is it possible to get the actual mean intensity of my segmentation depending on where it is on the registered image ?

Pollux
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2 Answers2

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Segmentation menu, option "Volumes and Statistics..." should show you what you are looking for.

Dženan
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  • It's what I am using to get my values, even after changing registration and updating this window it doesn't change. – Pollux May 04 '17 at 13:22
  • This looks like a bug. It looks like you have posted the question to the right mailing list (https://groups.google.com/forum/#!topic/itksnap-users/MuwjYOPf5TQ). Paul or somebody else will probably answer it. – Dženan May 04 '17 at 13:32
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Registration does not impact the intensity. Depending on how you transform your image, it affects the location and coordination of your voxels! It does not play with the intensities! It may reform, or reshape, rotate, or translate the image. If you expect different intensities after registration, you need to apply some other techniques rather than registration! because all the transformation matrix are applied on the coordination and location. You should play with the other features of your data! There are some registration methods which influence the intensities but they are not used in ITKSNAP for example. You should look for its special package.

For example this paper is on:

Intensity based image registration by minimizing the complexity of weighted subtraction under illumination changes

Which is specifically playing with the intensities for fusion. https://www.sciencedirect.com/science/article/abs/pii/S1746809415001755

Other example is this matlab script for Intensity based automatic registration, The process begins with the transform type you specify and an internally determined transformation matrix. Together, they determine the specific image transformation that is applied to the moving image with bilinear interpolation.

https://www.sciencedirect.com/science/article/abs/pii/S1746809415001755

fati
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