open-discussion > MIRcroGL Absolute Intensity Calculation?
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Oct 14, 2016  09:10 AM | Mo Ben
MIRcroGL Absolute Intensity Calculation?
Hello All,

I'm working on a virtual reality NIfTI viewer and I'm using some of the color scheme look up tables from this project as reference.

The LUT files in the source use an absolute value for min and max intensity, matching the values displayed in the top left corner of the MIRcroGL viewer. For example, CT_Lungs uses the following values:

    [FLT]
    min=-902
    max=-305

I'm not sure how these values are calculated, or how the NIfTI files are mapped to this scale. I did some analyzing of the header file and data. It seems they are encoded from [0,255] and the header files' glmin and glmax values match those values. Meanwhile cl_min and cl_max are unused.

How are these absolute values calculated? Am I missing something obvious here?
Oct 14, 2016  09:10 AM | Mo Ben
RE: MIRcroGL Absolute Intensity Calculation?
Did some more digging and figured it out. Using the scl_slop and scl_inter values you can find the scaled values.
Oct 16, 2016  12:10 AM | Mo Ben
RE: MIRcroGL Absolute Intensity Calculation?
Ok, opening this back up.

Some of the .clut (Color scheme source look up tables) files have min and max set to 0. I expected those color schemes to use the lowest and highest intensity for each file they were used on, but it turns out it is determining a seemingly arbitrary range of intensity, which is different for each file.

Does anyone know how the minimum and maximum intensity for those color schemes is calculated? For example the default grayscale when used on the ch256.nii file uses a minimum of 40 and maximum of 120, even though the intensity can go down to 0.