Editing Scanco User Instructions (section)

==Import foreign data with calibration information for BMD mg HA/ccm or Hounsfield Units==

Data can be converted from any other source (e.g. mha, nii, png, bmp, dicom, etc) into an AIM format using the BoneLab GitHub repository, which includes <code>blImageConvert</code>. However, those data should be represented as 'short' (2 byte) integers. Obviously that data cannot be used directly to measure BMD without conversion. Normally, an AIM file will contain the following information in the extended header (use aix -l to read the AIM header). 

 !-------------------------------------------------------------------------------
 Patient Name                  PATIENT_001                                         
 Index Patient                                      28
 Index Measurement                                 641
 !-------------------------------------------------------------------------------
 Site                                               39
 Scanner ID                                       3418
 Scanner type                                        9
 Position Slice 1 [um]                          163359
 No. samples                                      2304
 No. projections per 180                           900
 Scan Distance [um]                             139852
 Integration time [us]                           43000
 Reference line [um]                            141359
 Reconstruction-Alg.                                 3
 Energy [V]                                      68000
 Intensity [uA]                                   1470
 Angle-Offset [mdeg]                                 0
 Default-Eval                                        3
 !-------------------------------------------------------------------------------
 Mu_Scaling                                       8192
 Calibration Data              68 kVp, BH: 200 mg HA/ccm, Scaling 8192           
 Calib. default unit type      2 (Density)                                       
 Density: unit                 mg HA/ccm                                         
 Density: slope                         1.55715601e+03
 Density: intercept                    -3.82782013e+02
 HU: mu water                                  0.24220
 !-------------------------------------------------------------------------------

The slope and intercept is the calibration data that came from the scanner. Normally, when creating an AIM from an ISQ, the calibration data will come from the ISQ, which in turn came from the database of the scanner. 
When an evaluation of BMD is made in IPL, the calibration data is taken from the extended header.

Since the imported data converted to an AIM does not have calibration data in the header, you must use the following options in IPL. When you read in the AIM into IPL using <code>/import_freeformat</code> it assumes
the data to be µ values with scaling 1. You can then use <code>/header_log_set</code> to change the µ scaling. If you do not follow this procedure (i.e., no calibration data) then the IPL output for BMD will be in the units of your input (i.e., 2-byte short).

More information about the calibration information and µ scaling is found in the Scanco FAQ. Some key parts are copied to here:

A physical CT image contains the values for the Linear Attenuation Coefficients at each voxel. These are floating point values, typically between 0.0 and about 4.0 for bone (at our energies). To store them in our files, we scale these numbers with typically 4096 (XtremeCT: 8192) to a short integer value to be able to save a 2-byte number (-32768 to 32767, negative values not physically meaningful, but exist because of detector noise) instead of a 4-byte float.

BMD (mg HA/ccm):
 For the bone density measure, the µ-values are converted to mg HA/ccm units by 'Density: slope and intercept'. This conversion is linear, so slope and y-intercept defines the equation:
 mg HA/ccm = µ-value * slope + intercept

Hounsfield units:

SCANCO data files do not directly contain the image values in Hounsfield Units, but they contain scaled µ-values. To get Hounsfield Units, the µ-value of water is needed, and then the conversion formula is this: 
 HU(pixel) = -1000 + µ(pixel)*1000/µ(water)
 where the µ-values are the native image values divided by the above mentioned µ-scaling 4096 or 8192.
 An approximation for the µ of water can be found in the AIM or ISQ header, if (and only if) the scan was performed with the bone density calibration turned on.

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