Editing Opportunistic CT (section)

==Calibration==
To ensure accurate material properties and comparability across clinical sites and scanners during quantitative analysis derived from clinical CT scans, the native in-scan Hounsfield Units (HUs) must be converted to their corresponding bone equivalent densities. 

There are three main types of calibration for CT scans. All of these methods are available in our GitHub repository called [https://github.com/Bonelab/Ogo Ogo].

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===Phantom calibration===

Phantom calibration is the current imaging gold standard for converting HUs to bone densities. Phantom calibration involves placing a calibration phantom with known density values of either solid CHA or liquid K<sub>2</sub>HPO<sub>4</sub> under the patient in the scan field of view, as seen here: 

[[Image:phantom_rods_noseg.png|600px]]

The solid CHA or liquid  K<sub>2</sub>HPO<sub>4</sub> found in the phantom acts as the bone equivalent reference standard. Phantom calibration requires sampling the in-scan HUs of the bone equivalent reference rods (from the calibration phantom) and comparing those values to the known reference values. A simple linear regression between the known values within the calibration phantom rods and the in-scan HUs can be created to convert the HUs to bone equivalent density (BMD). 

The calibration curve takes the form of
 BMD = (HU⋅a) + b

where a is the slope of the resulting calibration curve and b is the intercept. This calibration curve is applied to specific bone compartments in the image or to the entire image, creating a bone-equivalent density image. The values of a and b  depend on many factors, such as the composition of the X-ray spectrum emitted by the X-ray tube, tube current, reconstruction kernel or table height, and as a result are scanner and image protocol dependent. 

To run phantom calibration in Ogo, you will need two things: 
<ol> 
  <li>The raw CT scan (.nii or .nii.gz)</li>
<li>A segmentation mask of the phantom rods</li> 
</ol>

Typically, this is done using ITKSnap or some other automated method [TBD], and you segment the inside of the rods, making sure to stop before reaching the edge of the rod to avoid partial volume effects.

An example of the phantom rods segmented: 

[[Image:phantom_rods_seg.png|600px]]

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===Asynchronous calibration===

This also uses a phantom, but not at the same time as the scan of the patient. Sometimes it can be months or even years away. (This is an ongoing edited section...)

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===Internal calibration===

This doesn't use a phantom, but instead uses the internal tissues as referents.

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