Hi. As I posted before, I've been trying to make a customized continuous color map for AFNI. I've tried doing this in two ways: with MakeColorMap and by editing .afnirc (by the process explained at [afni.nimh.nih.gov]).

With MakeColorMap, I tried the following command:

MakeColorMap -f ~/cmap/Fiducials.txt -nc 17 -ah test1 > test1.pal

where ~/cmap/Fiducuals.txt is a list of about 5 color codes formatted as the help section prescribes. This worked, but I could only load the .pal file when I had the # of colors in "define overlay" set to 17. When I did "read in palette" and selected my file while the color mode was set to continuous, I got an error message saying "can't read the file you selected." I also tried setting # of colors to both 1 and a couple of very large numbers, but it still wouldn't read these in as continuous, and there was no way to load them in as non-continuous since the menu in AFNI only ranges from 2 to 20 colors.

I also tried pasting the contents of the .pal file into .afnirc (down where it contains a posgray20 scale that looks like the same format). I can then right click Intensity and select my colorscale in the pulldown Set Pal menu, but as far as I can tell nothing actually changes when I do that. The terminal also shows some error messages on startup about the scale having too many colors (even when it's 128 colors, which as I understand it is the # of colors in a continuous scale).

Finally, I tried using the process outlined on that webpage I mentioned in the first paragraph. I added the following line to the environment section of afnirc:

AFNI_COLORSCALE_01 = custom_colormap

where custom_colormap is in my home directory and follows the first format shown on that webpage (5 colors with both the numbers to indicate spacing, and the 6-digit color codes). As far as I can tell, this does nothing at all (I get no error messages, and I couldn't find the colorscale listed anywhere within AFNI).

I would really appreciate it if somebody could help me make this work. Thanks.