neurolabusc
commented
3 years ago @drmclem I propose changing the Image Scaling section of the Philips conversion notes. The new text is now explicit that precedence is given to the real world scaling. Further, the alternative scaling factors are available in the BIDS sidecar. The variation described by the user appears to describe differences in image export between Classic and Enhanced DICOM data. As you are one of the experts in this topic, I would be grateful if you could proof the text below and suggest edits.
Image Scaling
dcm2niix losslessy copies the raw data from DICOM to NIfTI format. These values are typically stored as 16-bit integers in the range -32768..32767. Both the DICOM and NIfTI formats describe how scaling intercept and slope values can be used to convert these raw values into calibrated values. For example, with an intercept of 0 and slope of 0.01 the raw value of 50 would be converted to 0.5.
The NIfTI header provides the scl_slope and scl_inter fields so each voxel value in the dataset is scaled as:
I = scl_slope * R + scl_interwhere R is the voxel value stored and I is the "true" transformed voxel intensity.
For all manufacturers except Philips, the scl_slope and scl_inter correspond to the DICOM tags 0028,1053 and 0028,1052, respectively.
Philips has three possible intensity transforms for their DICOM images (world (W), display (D), precise (P)). All of these transforms might be provided in a single DICOM image, while the NIfTI standard only designates a single scl_slope and scl_inter for each image. dcm2niix will retain the raw value (R) and sets the NIfTI scl_inter and scl_slope values for the desired intensity transform. dcm2niix will use W if possible. If this is not possible it will use P unless the user specifies -p n to disable the precise calculation resulting in D.
The formulas are provided below. The DICOM tags are in brackets (e.g. (0040,9225)) and the BIDS tag is in double quotes (e.g. "PhilipsRWVSlope"). Since all the scaling values are stored in the BIDS sidecar, you can always use these to generate your preferred intensity transform.
Inputs:
R = raw stored value of voxel in DICOM without scaling
WS = RealWorldValue slope (0040,9225) "PhilipsRWVSlope"
WI = RealWorldValue intercept (0040,9224) "PhilipsRWVIntercept"
RS = rescale slope (0028,1053) "PhilipsRescaleSlope"
RI = rescale intercept (0028,1052) "PhilipsRescaleIntercept"
SS = scale slope (2005,100E) "PhilipsScaleSlope"
Outputs:
W = real world value
P = precise value
D = displayed value
Formulas:
W = R * WS + WI
D = R * RS + RI
P = D / (RS * SS)
drmclem
I have had a query from one of our users - It looks as if there is a problem with the scaling logic when the real world tags are present for the rescale slope and rescale intercept. For the "precise" conversion (FP in Philips terminology) the scale slope needs to also be taken into consideration but I think even though displayed in the logs only the RS and RI are being used leading to a conversion to the displayed value (matching the scanner console display) rather than the FP value.
Using RWVSlope:RWVIntercept = 0.596581:0 Philips Scaling Values RS:RI:SS = 0.596581:0:1.6765 (see PMC3998685) Convert 20 DICOM as DICOM\DICOM_pCASL_rest_20210309125250_201a (128x128x20x1)
To Reproduce Compare the nii output from data with and without the real world scaling tags but with identical conventional rescale tags - the scaling is different
Expected behavior For FP output the results should be the same.
Chris Rorden's dcm2niiX version v1.0.20190902 (JP2:OpenJPEG) (JP-LS:CharLS) MSC1900 (64-bit Windows) Found 4 DICOM file(s) Philips Scaling Values RS:RI:SS = 0.596581:0:1.6765 (see PMC3998685) Convert 1 DICOM as Z:\mjf_head\PCASL_ENHANCED_DICOM\DICOM\20210309125250_pCASL_rest_201_real (128x128x20x1)
Further info - It looks like for this system that the real-world tags are present when the export is in classic dicom but are not present when the export is enhanced (no idea why this decision was made) but the conventional rescale tags are present in both versions.
Matthew