help > RE: datasets generated with AFNI
Aug 13, 2020  08:08 AM | Chris Rorden
RE: datasets generated with AFNI
If you want to independently control the negative values and the positive values for a single overlay, you should just load the image twice. You can then set the positive and negative intensities independently. You can use the same principle for MRIcron or MRIcroGL. Since MRIcroGL allows full scripting, I prefer it for exposition. Here is the sample script you see if you choose the Scripting/Templates/Basic. Note it loads the same overlay "spmMotor" twice.
 1. For the first loading it hides values darker than +4, and clips values greater than +4 to +4, it also sets this layer to be 50% translucent.
 2. For the second loading, it hides values brighter than -4, and clips values darker than -4 to -4. It sets this overlay to have the blue color scheme:

import gl
#open background image
#open overlay: show positive regions
gl.minmax(1, 4, 4)
#open overlay: show negative regions
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")

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rossisl Aug 13, 2020
RE: datasets generated with AFNI
Chris Rorden Aug 13, 2020