Promoting the use of R in the NHS

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This post was originally published on this site

(This article was first published on R-Bloggers – Learning Machines, and kindly contributed to R-bloggers)

Noseman is having a headache and as an old-school hypochondriac he goes to see his doctor. His doctor is quite worried and makes an appointment with a radiologist for Noseman to get a CT scan.

Because Noseman always wants to know how things work he asks the radiologist about the inner workings of a CT scanner.

The basic idea is that X-rays are fired from one side of the scanner to the other. Because different sorts of tissue (like bones, brain cells, cartilage etc.) block different amounts of the X-rays the intensity measured on the other side varies accordingly.

The problem is of course that a single picture cannot give the full details of what is inside the body because it is a combination of different sorts of tissue in the way of the respective X-rays. The solution is to rotate the scanner and combine the different slices.

How, you ask? Good old linear algebra to the rescue!

We start with the initial position and fire X-rays with an intensity of 30 (just a number for illustrative purposes) through the body:

As can be seen in the picture the upper ray goes through areas 1, 2 and 3 and let’s say that the intensity value of 12 is measured on the other side of the scanner:

or

The rest of the formula is found accordingly:

We then rotate the scanner for the first time…

…which gives the following formula:

And a second rotation…

…yields the following formula:

Now we are combining all three systems of equations:

or written out in full:

Here is the data of the matrix for you to download: ct-scan.txt).

We now have 9 equations with 9 unknown variables… which should easily be solvable by R, which can also depict the solution as a gray-scaled image… the actual CT-scan!

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CT of NosemanThe radiologist looks at the picture… and has good news for Noseman: everything is how it should be! Noseman is relieved and his headache is much better now…
Real CT scans make use of the same basic principles (of course with a lot of additional engineering and maths magic  )
Here are real images of CT scans of a human brain…
Source: Wikimedia… which can be combined into a 3D-animation:
Source: WikimediaIsn’t it fascinating how a little bit of maths can save lives!