It looks like a customized look up table will work for your case. You can simply select "Lookup table" as the colormap and load your own lookup table. To create your own look up table, you can refer to the content of FreeSurferColorLUT.txt file in your freesurfer installation directory.

Best,
Ruopeng

Hi all, 

I’m wondering whether there’s a way to create a custom color map in Freeview that would operate as a alternative to the preset Greyscale, Heatmap, NIH, PET, Jet and GE Color options. 

Ideally, I could assign each number value a given color, e.g. every “0” value in an .nii file is black, every “1” value is red, every “2” value is blue, every “3" is green and so on. I already have the RGB values worked out for each number value; I just need to know how to format this information and where to put it so that I can my custom colormap as an option in Freeview. 

For my purposes, there would be no need to adjust the assigned colors based on the overall range of values. For instance, there would be no need to assign a different color value to a “1” value depending on whether the highest value in the overall .nii file is 1 or 100. 

I did try reading the related conversation here but I can’t seem to find the file it references, annotval2surfoverlay.m, in the Freesurfer directory. 

Thanks very much for your help! 

Anna 

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