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help > RE: Range (i.e. Darkest and Brightest values) are not correct when loading a .nii file
Oct 7, 2020 12:10 PM | Chris Rorden
RE: Range (i.e. Darkest and Brightest values) are not correct when loading a .nii file
This is a feature. MRIcroGL will clip values below the "Darkest"
value and above the "Brightest" value, and linearly scale the
intensity between these two values. This like adjusting the
contrast and brightness of an image, or in radiological terms the
"Window Center" and "Window Width". Setting the minimum for the
darkest value in the image and the maximum to the brightest value
in the image is typically a bad choice, as it it wildly impacted by
outliers. The initial values are set to the "robust intensity
range", which minimizes the impact of outliers. This provides much
better contrast, brightness for typical images. If you want to
override this behavior to use any arbitrary value, simply set the
cal_min and cal_max values of your NIfTI header to the values you
prefer.
As an aside, on Linux and MacOS if you launch MRIcroGL from the command line, it will report both the full image intensity range and the robust image intensity range to the terminal. For example, with the spmMotor image that comes with the software, the full range is -6.86..+12.1, but the robust range is -1.58..2.976:
int16 range -6.8623576164245605...12.15650463104248
int16 window -1.5804531574249268...2.9761490821838379
As an aside, on Linux and MacOS if you launch MRIcroGL from the command line, it will report both the full image intensity range and the robust image intensity range to the terminal. For example, with the spmMotor image that comes with the software, the full range is -6.86..+12.1, but the robust range is -1.58..2.976:
int16 range -6.8623576164245605...12.15650463104248
int16 window -1.5804531574249268...2.9761490821838379
Threaded View
Title | Author | Date |
---|---|---|
makis | Oct 6, 2020 | |
Chris Rorden | Oct 7, 2020 | |
makis | Oct 7, 2020 | |
Chris Rorden | Oct 7, 2020 | |