Tamir,

If you are using dcm2nnix then scale-slope should be implemented correctly, I cannot speak for other conversions. It is a relatively simple transformation - the equation for it was in the text you originally posted. If you look at the values in the DICOM images and then see how they translate into the Nifit images I think you should be able to check whether the rescaling is being applied (note that the conversion normally takes integer values in the DICOM into floating point).

You could try a value of 10 for calibration gain, this would certainly be consistent with other ASL implementations I have seen and is implied by the text you posted.

Michael



On 20 May 2019, at 12:50, Tamir Eisenstein <[log in to unmask]> wrote:

Hi Michael,

How do I ensure that the scale-slope is being correctly implemented in the conversion from DICOM to Nifti? just by examining the intensity values of the nifti files?
In the DICOM images it is stated that the rescale slope of the M0 is 0.16, while the rescale slope in the label/control raw images is 0.05 - is it something I need to take into account?

In the calibration gain option I should enter a value of 10?

Thanks!
Tamir






I think that this implies that in terms of the raw data there might be a factor of 10 scaling difference between the M0 images and the raw ASL volumes (something that can be handled in BASIL using the calibration gain option). You need to ensure that the scale-slope is being correctly implemented on your conversion from DICOM to Nifti (as you want both the ASL volumes and M0 image to be on the same scale after conversion), this should be handled correctly if you are using dcm2niix.
The other information here relates to the scaling that is being done to produce the derivative maps such as the PWI image and CBF image.

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Michael Chappell MEng DPhil
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Associate Professor, Institute of Biomedical Engineering, University of Oxford.
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