3.7. List of all AFNI colorbars

This is a list of all AFNI colorbars at present, showing both the colorbar itself and an image that has a full overlay spectrum displaying the colorbar. (The image isn’t meant to look meaningful for every colorbar, it’s just an example.) Some of these apply as SUMA colorbars, as well. Order is reverse alphabetical.

You can set your default overlay colorbar in with the AFNI_COLORSCALE_DEFAULT environment variable in your “~/.afnirc” file. Otherwise, you can select session-by-session in the AFNI GUI by right-clicking on the colorbar when you have an overlay displayed.

We might add more over time.

Reference images, shown as ulays: the dsets viewed as overlay/underlays below to exemplify colorbar properties in a couple different scenarios. The range of nonzero voxel values in the ROI case is [1, 256].

anatomical dset

ROI dset
../_images/FIG_ref_anat.axi.png ../_images/FIG_ref_rois.axi.png

3.7.1. Colorbars (<=256 colors) and example images

Cbar name

Cbar

anatomical (opacity=9)

ROIs (opacity=5)

cbar range: [0, 98%ile]

cbar range: [0, 256]

Viridis

 ../_images/Viridis.png ../_images/tt_cbar_Viridis.axi.png ../_images/mm_cbar_Viridis.axi.png

Spectrum:yellow_to_red

 ../_images/Spectrum:yellow_to_red.png ../_images/tt_cbar_Spectrum:yellow_to_red.axi.png ../_images/mm_cbar_Spectrum:yellow_to_red.axi.png

Spectrum:yellow_to_cyan

 ../_images/Spectrum:yellow_to_cyan.png ../_images/tt_cbar_Spectrum:yellow_to_cyan.axi.png ../_images/mm_cbar_Spectrum:yellow_to_cyan.axi.png

Spectrum:yellow_to_cyan+gap

 ../_images/Spectrum:yellow_to_cyan+gap.png ../_images/tt_cbar_Spectrum:yellow_to_cyan+gap.axi.png ../_images/mm_cbar_Spectrum:yellow_to_cyan+gap.axi.png

Spectrum:red_to_blue

 ../_images/Spectrum:red_to_blue.png ../_images/tt_cbar_Spectrum:red_to_blue.axi.png ../_images/mm_cbar_Spectrum:red_to_blue.axi.png

Spectrum:red_to_blue+gap

 ../_images/Spectrum:red_to_blue+gap.png ../_images/tt_cbar_Spectrum:red_to_blue+gap.axi.png ../_images/mm_cbar_Spectrum:red_to_blue+gap.axi.png

ROI_i64

 ../_images/ROI_i64.png ../_images/tt_cbar_ROI_i64.axi.png ../_images/mm_cbar_ROI_i64.axi.png

ROI_i32

 ../_images/ROI_i32.png ../_images/tt_cbar_ROI_i32.axi.png ../_images/mm_cbar_ROI_i32.axi.png

ROI_i256

 ../_images/ROI_i256.png ../_images/tt_cbar_ROI_i256.axi.png ../_images/mm_cbar_ROI_i256.axi.png

ROI_i128

 ../_images/ROI_i128.png ../_images/tt_cbar_ROI_i128.axi.png ../_images/mm_cbar_ROI_i128.axi.png

ROI_glasbey_256

 ../_images/ROI_glasbey_256.png ../_images/tt_cbar_ROI_glasbey_256.axi.png ../_images/mm_cbar_ROI_glasbey_256.axi.png

Reds_and_Blues_w_Green

 ../_images/Reds_and_Blues_w_Green.png ../_images/tt_cbar_Reds_and_Blues_w_Green.axi.png ../_images/mm_cbar_Reds_and_Blues_w_Green.axi.png

Reds_and_Blues_Inv

 ../_images/Reds_and_Blues_Inv.png ../_images/tt_cbar_Reds_and_Blues_Inv.axi.png ../_images/mm_cbar_Reds_and_Blues_Inv.axi.png

Reds_and_Blues

 ../_images/Reds_and_Blues.png ../_images/tt_cbar_Reds_and_Blues.axi.png ../_images/mm_cbar_Reds_and_Blues.axi.png

RedBlueGreen

 ../_images/RedBlueGreen.png ../_images/tt_cbar_RedBlueGreen.axi.png ../_images/mm_cbar_RedBlueGreen.axi.png

red_monochrome

 ../_images/red_monochrome.png ../_images/tt_cbar_red_monochrome.axi.png ../_images/mm_cbar_red_monochrome.axi.png

Plasma

 ../_images/Plasma.png ../_images/tt_cbar_Plasma.axi.png ../_images/mm_cbar_Plasma.axi.png

Magma

 ../_images/Magma.png ../_images/tt_cbar_Magma.axi.png ../_images/mm_cbar_Magma.axi.png

inverted_gray_circle

 ../_images/inverted_gray_circle.png ../_images/tt_cbar_inverted_gray_circle.axi.png ../_images/mm_cbar_inverted_gray_circle.axi.png

inverted_amber_circle

 ../_images/inverted_amber_circle.png ../_images/tt_cbar_inverted_amber_circle.axi.png ../_images/mm_cbar_inverted_amber_circle.axi.png

green_monochrome

 ../_images/green_monochrome.png ../_images/tt_cbar_green_monochrome.axi.png ../_images/mm_cbar_green_monochrome.axi.png

gray_scale

 ../_images/gray_scale.png ../_images/tt_cbar_gray_scale.axi.png ../_images/mm_cbar_gray_scale.axi.png

gray_circle

 ../_images/gray_circle.png ../_images/tt_cbar_gray_circle.axi.png ../_images/mm_cbar_gray_circle.axi.png

GoogleTurbo

 ../_images/GoogleTurbo.png ../_images/tt_cbar_GoogleTurbo.axi.png ../_images/mm_cbar_GoogleTurbo.axi.png

FreeSurfer_Seg_i255

 ../_images/FreeSurfer_Seg_i255.png ../_images/tt_cbar_FreeSurfer_Seg_i255.axi.png ../_images/mm_cbar_FreeSurfer_Seg_i255.axi.png

CytoArch_ROI_i256_gap

 ../_images/CytoArch_ROI_i256_gap.png ../_images/tt_cbar_CytoArch_ROI_i256_gap.axi.png ../_images/mm_cbar_CytoArch_ROI_i256_gap.axi.png

CytoArch_ROI_i256

 ../_images/CytoArch_ROI_i256.png ../_images/tt_cbar_CytoArch_ROI_i256.axi.png ../_images/mm_cbar_CytoArch_ROI_i256.axi.png

Color_circle_ZSS

 ../_images/Color_circle_ZSS.png ../_images/tt_cbar_Color_circle_ZSS.axi.png ../_images/mm_cbar_Color_circle_ZSS.axi.png

Color_circle_AJJ

 ../_images/Color_circle_AJJ.png ../_images/tt_cbar_Color_circle_AJJ.axi.png ../_images/mm_cbar_Color_circle_AJJ.axi.png

cb_spiral35

 ../_images/cb_spiral35.png ../_images/tt_cbar_cb_spiral35.axi.png ../_images/mm_cbar_cb_spiral35.axi.png

cb_spiral

 ../_images/cb_spiral.png ../_images/tt_cbar_cb_spiral.axi.png ../_images/mm_cbar_cb_spiral.axi.png

blue_monochrome

 ../_images/blue_monochrome.png ../_images/tt_cbar_blue_monochrome.axi.png ../_images/mm_cbar_blue_monochrome.axi.png

amber_redtop_bluebot

 ../_images/amber_redtop_bluebot.png ../_images/tt_cbar_amber_redtop_bluebot.axi.png ../_images/mm_cbar_amber_redtop_bluebot.axi.png

amber_monochrome

 ../_images/amber_monochrome.png ../_images/tt_cbar_amber_monochrome.axi.png ../_images/mm_cbar_amber_monochrome.axi.png

amber_circle

 ../_images/amber_circle.png ../_images/tt_cbar_amber_circle.axi.png ../_images/mm_cbar_amber_circle.axi.png

Add_Edge

 ../_images/Add_Edge.png ../_images/tt_cbar_Add_Edge.axi.png ../_images/mm_cbar_Add_Edge.axi.png

3.7.2. Colorbars (>256 colors) and example images

Sometimes one wants to use a colorbar that has more than 256 colors in it. This might occur when overlaying an atlas with a loooot of ROIs, or one with with laaaarge ROI values.

To correctly load a colorbar with more than (the default) 256 colors, you must start the AFNI GUI using the -XXXnpane .. option, providing the appropriate number of colors available in the colorbar (which is typically knowable from the name). For example, you could use the following to load the ROI_glasbey_512 colorbar, which has 512 colors:

afni -XXXnpane 512

When using @chauffeur_afni to make images/montages/movies (see examples here), you also use that option, e.g.,:

@chauffeur_afni -XXXnpane 512 ...

Below is a list of current colorbars in AFNI that contain more than 256 colors.

Cbar name

Cbar

ROIs (opacity=9)

cbar range: [0, Nroi]

ROI_glasbey_512

 ../_images/ROI_glasbey_512.png ../_images/xx_cbar_ROI_glasbey_512.axi.png

ROI_glasbey_2048

 ../_images/ROI_glasbey_2048.png ../_images/xx_cbar_ROI_glasbey_2048.axi.png

ROI_glasbey_1024

 ../_images/ROI_glasbey_1024.png ../_images/xx_cbar_ROI_glasbey_1024.axi.png