Okay, my mistake. I've successfully made the 128-color pal file, but now I just can't make it read into AFNI. The input file I used is just:
1 0 0
1 1 0
0 1 0
0 1 1
0 0 1
with tabs instead of spaces (obviously, these are just test colors). Then I did the command:
MakeColorMap -f ~/cmap/Fiducials.txt -nc 128 -sl -ah test128 > test128.pal
Then, I set the # of colors in AFNI to '**', right clicked on 'Intensity' and selected 'Read In Pallette.' But when I select test128.pal, I get a message box saying 'can't use the colorscale you selected.' This is the same error I was getting before when I tried to use my 17-color scale as continuous. Thanks.