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, roi256, roi64or if the colormap is in a .pal file:
MakeColorMap -cmapdb Palfile -cmap MapName
Usage4: MakeColorMap <-fscolut lbl0 lbl1>
[<-fscolutfile FS_COL_LUT>]Create AFNI/SUMA colormaps of FreeSurfer colors indexed between lbl0 and lbl1.
- -fscolut lbl0 lbl1: Get colors indexed between
- lbl0 and lbl1, non existing integer labels are given a gray color. Use -fscolut -1 -1 to get all the colors and labels.
- -fscolutfile FS_COL_LUT: Use color LUT file FS_COL_LUT
- Default is to use $FREESURFER_HOME/FreeSurferColorLUT.txt
-show_fscolut: Show all of the LUT
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...
- -ahc prefix: optional, Afni Hex format, ready to go into.
- pbardefs.h
-h or -help: displays this help message.
- -flipud\ : Flip the map upside down. If the colormap is being
- created for interactive loading into SUMA with the ‘New’ button from the ‘Surface Controller’ you will need to flip it upside down.
- -usercolutfile USER_COL_LUT: A user’s own color lookup file.
The format of the file is similar to FreeSurfer’s ColorLUT.txt It is an ascii file whith each line containing the following:
Key R G B A LabelWith Key being an integer color/region identifier, Label is the string identifier and R,G,B,A are the colors and alpha values either between 0 and 1, or 0 and 255. Alpha values are ignored at the moment, but they must be in the file.
-suma_cmap: write colormap in SUMA’s format
- -sdset DSET: Add colormap to surface-based dataset DSET, making it a
- Labeled data set, which gets special treatment in SUMA. A labeled data set can only have one value per node.
- -sdset_prefix DSET_PREF: Prefix of dset for writing labeled version
- of DSET. Without it, the new name is based on DSET’s name
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
Say you have your own color lookup table formatted much like FreeSurfer’s color lookup files. The content of this sample colut.txt file is:
- #integer label String Label R G B A
- 1 Big_House 0.3 0.1 1 1 2 Small_Face 1 0.2 0.4 1 3 Electric 1 1 0 1 4 Atomic 0.1 1 0.3 1
You can attach the colormap to a surface-based datatset with ConvertDset’s -labelize option, or you can also do it here in one pass with:
- MakeColorMap -usercolutfile colut.txt -suma_cmap toylut
- -sdset you_look_marvellous.niml.dset
Adding a new colormap into AFNI: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)
- [-novolreg]: Ignore any Rotate, Volreg, Tagalign,
- or WarpDrive transformations present in the Surface Volume.
[-noxform]: Same as -novolreg
- [-setenv “‘ENVname=ENVvalue’”]: Set environment variable ENVname
to be ENVvalue. Quotes are necessary.
- Example: suma -setenv “‘SUMA_BackgroundColor = 1 0 1’”
- See also options -update_env, -environment, etc in the output of ‘suma -help’
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.
-HELP: Extreme help, same as -help in majority of cases.
-h_view: Open help in text editor. AFNI will try to find a GUI editor
- -hview\ : on your machine. You can control which it should use by
- setting environment variable AFNI_GUI_EDITOR.
-h_web: Open help in web browser. AFNI will try to find a browser.
- -hweb\ : on your machine. You can control which it should use by
- setting environment variable AFNI_GUI_EDITOR.
- -h_find WORD: Look for lines in this programs’s -help output that match
- (approximately) WORD.
-h_raw: Help string unedited
-h_spx: Help string in sphinx loveliness, but do not try to autoformat
-h_aspx: Help string in sphinx with autoformatting of options, etc.
- -all_opts\ : Try to identify all options for the program from the
- output of its -help option. Some options might be missed and others misidentified. Use this output for hints only.
Dec 16 2015
Ziad S. Saad & Rick R. Reynolds SSCC/NIMH/NIH saadz@mail.nih.gov Tue Apr 23 14:14:48 EDT 2002