Output image post-Feldkamp reformat


Volume flip


The reconstructed volume can be flipped relatively any axis (X,Y or Z) to meet requirements regarding accurate object orientation.


Conversion to Hounsfield units 


Cobra incorporates an option to convert output images to Hounsfield units (HU). By definition, HU is the scale where water has a density 0 and air gets a density –1000 so if the scanner is accurately calibrated to get accurate object densities in mg/cm3 then HU scaling is just offset values by -1000. A user also has an option to apply arbitrary offset value.


Thresholding  signal to keep it above zero


Some 3D viewer software packages or/and applications require output image densities positive (the most common case is requirement of 12-bit dynamic range between –1024 and +3071 HU). Cobra supports an option to cut off a signal below 0 mg/cm3 (-1000 HU)


Non-linear scaling


There is an option to apply an additional gain (scale) factor to output image values higher than 2000 (mg/cm3). It allows boosting a bone contrast in cases when such a contrast is substantially lower than should be comparing to real physical density  values.

 
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Description of the reconstruction task

Within the COBRA reconstruction package, all input, output and intermediate data are kept on the hard disk. The user defines and controls the reconstruction task through a parameter file, a text file with extension .xxm. This file contains tags and assigned values, and describes the scanner hardware setup, input and output data characteristics and representation, and the chosen reconstruction method. Some of the reconstruction options are only accessible through SDK API’s. These are related to synchronization and control of in-line reconstruction (recon concurrent with acquisition), and the setup of COBRA’s working folders.
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Tags defining output image reformat

OPTTAG_GAMMASLICESCALE

OPTTAG_GAMMASLICESCALE

is used to correct for nonlinearity resulting from beam hardening and scattering according to the following formula
Cube(x,y,z) =  Cube(x,y,z)  |  Cube(x,y,z)<1300
Cube(x,y,z) =  1300 + {Cube(x,y,z)-1300}*Gamma  |  Cube(x,y,z)<1300
Value type: float
Default value: 1.0

PARTAG_MINUS1000

PARTAG_MINUS1000

Converting reconstructed volume values from density units (mg/cm3) to Hounsfield units if set to 1
Value type: integer (0 or 1)
Default value: 0
PARTAG_SLICEOFFSETVALUE

PARTAG_SLICEOFFSETVALUE

Numerical offset of reconstructed volume values. It overrides PARTAG_MINUS1000. It is typically used to increase a contrast keeping air level below –1000 Hounsfield units
Value type: integer
Default value: 0
PARTAG_NEGATIVE_DENIED

PARTAG_NEGATIVE_DENIED

If set to 1 then negative densities below 0 mg/cm3 in the reconstructed volume values are converted to 0
Value type: integer
Default value: 0
PARTAG_SLICEFLIPX

PARTAG_SLICEFLIPX

Flips the cube about X-axis at output if set to 1
Value type: integer (0 or 1)
Default value: 0
PARTAG_SLICEFLIPY

PARTAG_SLICEFLIPY

Flips the cube abpout Y-axis at output if set to 1
Value type: integer (0 or 1)
Default value: 0
PARTAG_SLICEFLIPZ

PARTAG_SLICEFLIPZ

Flips the cube about Z-axis at output if set to 1
Value type: integer (0 or 1)
Default value: 0
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