AFNI program: MakeColorMap

Usage1: 
MakeColorMap <-fn Fiducials_Ncol> [-pos] [-ah prefix] [-h/-help]
    Creates a colormap of N colors that contains the fiducial colors.
    -fn Fiducials_Ncol: Fiducial colors and their indices in the color
                        map are listed in file Fiducials_Ncol.
       Each row contains 4 tab delimited values:
       R G B i
       R G B values are between 0 and 1 and represent the 
       i-th color in the colormap. i should be between 0 and
       N-1, N being the total number of colors in the colormap.

Usage2: 
MakeColorMap <-f Fiducials> <-nc N> [-sl] [-ah prefix] [-h/-help]
    Creates a colormap of N colors that contains the fiducial colors.
    -f Fiducials:  Fiducial colors are listed in an ascii file Fiducials. 
       Each row contains 3 tab delimited R G B values between 0 and 1.
    -nc N: Total number of colors in the color map.
    -sl: (optional, default is NO) if used, the last color in the Fiducial 
       list is omitted. This is useful in creating cyclical color maps.

Usage3: 
MakeColorMap <-std MapName>
    Returns one of SUMA's standard colormaps. Choose from:
    rgybr20, ngray20, gray20, bw20, bgyr19, 
    matlab_default_byr64, roi128, roi64

Common options to all usages:
    -ah prefix: (optional, Afni Hex format.
                 default is RGB values in decimal form)
       use this option if you want a color map formatted to fit 
       in AFNI's .afnirc file. The colormap is written out as 
      prefix_01 = #xxxxxxx 
      prefix_02 = #xxxxxxx
       etc...
    -h or -help: displays this help message.

Example Usage 1: Creating a colormap of 20 colors that goes from 
Red to Green to Blue to Yellow to Red.

   The file FidCol_Nind contains the following:
   1 0 0 0
   0 1 0 5
   0 0 1 10
   1 1 0 15
   1 0 0 19

   The following command will generate the RGB colormap in decimal form:
   MakeColorMap -fn FidCol_Nind 

   The following command will generate the colormap and write it as 
   an AFNI color palette file:
   MakeColorMap -fn FidCol_Nind -ah TestPalette > TestPalette.pal

Example Usage 2: Creating a cyclical version of the colormap in usage 1:

   The file FidCol contains the following:
   1 0 0
   0 1 0
   0 0 1
   1 1 0
   1 0 0

   The following command will generate the RGB colormap in decimal form:
   MakeColorMap -f FidCol -sl -nc 20 

Example Usage 3: MakeColorMap -std ngray20 

To read in a new colormap into AFNI, either paste the contents of 
TestPalette.pal in your .afnirc file or read the .pal file using 
AFNI as follows:
1- run afni
2- Define Function --> right click on Inten (over colorbar) 
   --> Read in palette (choose TestPalette.pal)
3- set the #colors chooser (below colorbar) to 20 (the number of colors in 
   TestPalette.pal).
  Common Debugging Options:
   [-trace]: Turns on In/Out debug and Memory tracing.
             For speeding up the tracing log, I recommend 
             you redirect stdout to a file when using this option.
             For example, if you were running suma you would use:
             suma -spec lh.spec -sv ... > TraceFile
             This option replaces the old -iodbg and -memdbg.
   [-TRACE]: Turns on extreme tracing.
   [-nomall]: Turn off memory tracing.
   [-yesmall]: Turn on memory tracing (default).
  NOTE: For programs that output results to stdout
    (that is to your shell/screen), the debugging info
    might get mixed up with your results.
 
++ SUMA version 2.5000, June 10 2004

Compile Date:
   Aug  3 2004

    Ziad S. Saad & Rick R. Reynolds SSCC/NIMH/NIH ziad@nih.gov    Tue Apr 23 14:14:48 EDT 2002