questions > RE: Voxel values 500 times higher with dcm2niix
Feb 19, 2017  02:02 PM | Chris Rorden
RE: Voxel values 500 times higher with dcm2niix
To be clear, this is a problem with your vendor (Philips), not my software. They list the formula for precise scaling in the header of every PAR/REC file. Further, this precise "Float" value is often recommended over the "Display" value (see PMC3998685). Since Philips created this anomaly from the DICOM standard, they need to be consistent in how they support it. It clearly creates confusion is a user needs the display values for some situations and the precise float values for others. If Philips believes that the display value is the best solution, they only need to store SS as equal to RS. In cases where this is not happening, they are explicitly stating that the FP is a more precise answer than the DV. Having said this, I think in the real world this will matter very little. The raw data is identical, regardless of the scl_inter and scl_slope saved in the NIfTI header. Further, the raw MRI signal is relative, so the difference in scaling factors will not influence the results you get when deriving values from the raw data. I believe you will get much better derived values (FA, MD, ADC, etc) after pre-processing your raw data using TOPUP/EDDY rather than relying on the derived values generated by the scanner.

Regardless, to help users out, Github includes a new version of my software that allows the user to demand the DV scaling instead of the scaling FP. To do this, add the parameter "-p n" to disable precise scaling.
 ./dcm2niix -p n ~/tst_parrec
Further, I have updated the BIDS text file to report the Philips scaling parameters (SS, RS, RI) as well as whether the precise or display value was stored in the image. 

I really hate adding this option to my software, as I am sure many users will wonder when they should use this option. Again, for people processing their own data, this choice should not matter. Further, I wish to emphasize that the vendor really needs to clarify this, we are at the mercy of the images they generate.

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TitleAuthorDate
Pascal Pas Oct 23, 2016
RE: Voxel values 500 times higher with dcm2niix
Chris Rorden Feb 19, 2017
Chris Rorden Oct 26, 2016
Felix Navarro Guirado Feb 9, 2017
Chris Rorden Feb 9, 2017
Felix Navarro Guirado Feb 10, 2017
Pascal Pas Oct 26, 2016
Chris Rorden Oct 25, 2016
Pascal Pas Oct 25, 2016