Map image into matrix in R to 3d Print

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We have an image like this: enter image description here

Where I have a skull, and the raw counts of how many bones were broken in each area of the skull.

I also have a 3d printer and can make things like this:

enter image description here

Which was made in R using a matrix and the r2stl package.

What I want to do is map the x's and y's of that skull into certain locations of a matrix so that I could add the raw counts to those cells and 3d print that skull in a way where each portion of the skull would be higher based on how many fractures were in that location. Thoughts? It didn't seem like an example where an example dataset would be useful, I apologize if I should have included that.

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