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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.
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.
Threaded View
Title | Author | Date |
---|---|---|
Pascal Pas | Oct 23, 2016 | |
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 | |