Meta data conversion to density

[wallematthias]

I have a problem converting loaded AIMs to density

after reading an aim file (XCT 1), the image data is in hounsfield units. I seem to be missing the density intercept and density slope. Is there any way these can be added to the meta data? Thank you for your help!

{'CalibrationData': '60kVp, BH: 200 mg HA/ccm, Scaling 8192',
 'CreationDate': 'XXXXXX', #blinded
 'DataRange': (-1314.0, 10451.0),
 'Energy': 59.4,
 'Intensity': 0.9,
 'MeasurementIndex': 0000, #blinded
 'ModificationDate': 'XXXXX', #blinded
 'MuScaling': 8192.0,
 'MuWater': 0.2415,
 'NumberOfProjections': 750,
 'NumberOfSamples': 1536,
 'PatientIndex': 0000, #blinded
 'PatientName': 'XXXXXX', #blinded
 'ReconstructionAlg': 3,
 'ReferenceLine': 0.0,
 'RescaleIntercept': -1000.0,
 'RescaleSlope': 0.505467132505176,
 'RescaleType': 2,
 'RescaleUnits': 'mg HA/ccm',
 'SampleTime': 100.0,
 'ScanDistance': 125.952,
 'ScannerID': 3330,
 'ScannerType': 9,
 'Site': 20,
 'SliceIncrement': 0.0820000022649765,
 'SliceThickness': 0.0820000022649765,
 'Version': 'AIMDATA_V020   ',
 'origin': array([ 0.        , 51.65999985, 46.49399948]),
 'spacing': array([0.082, 0.082, 0.082]),
 'direction': array([[1., 0., 0.],
        [0., 1., 0.],
        [0., 0., 1.]])}

[dzenanz]

Already in metadata?

'RescaleIntercept': -1000.0,
'RescaleSlope': 0.505467132505176,

[wallematthias]

These seem to be the conversions from raw scanner to hounsfield units, for the density separate conversion factors are required. I am looking for slope and intercept for calibrated mg HA/ccm

[dzenanz]

@mkuczyns do you have some suggestion?

[wallematthias]

In /src/itkScancoImageIO.cxx it looks like density slope and intercept are being pulled

ITKIOScanco/src/itkScancoImageIO.cxx

Lines 949 to 955 in c7352ec

	else if (skey == "Density: slope")
	{
	this->m_RescaleSlope = strtod(value, nullptr);
	}
	else if (skey == "Density: intercept")
	{
	this->m_RescaleIntercept = strtod(value, nullptr);

but then again overwritten later on when the image is read

ITKIOScanco/src/itkScancoImageIO.cxx

Lines 1021 to 1029 in c7352ec

	// This code causes rescaling to Hounsfield units
	if (this->m_MuScaling > 1.0 && this->m_MuWater > 0)
	{
	// mu(voxel) = intensity(voxel) / m_MuScaling
	// HU(voxel) = mu(voxel) * 1000/m_MuWater - 1000
	// Or, HU(voxel) = intensity(voxel) * (1000 / m_MuWater * m_MuScaling) - 1000
	this->m_RescaleSlope = 1000.0 / (this->m_MuWater * this->m_MuScaling);
	this->m_RescaleIntercept = -1000.0;
	}

[dzenanz]

Then we should introduce new metadata members to hold DensitySlope and DensityIntercept? Could you propose a PR?