.. _edu_afni_cbars: .. comment: This file was auto-generated by: afni_doc/python_help_scripts/make_file_of_all_afni_cbars.py See afni_doc/do_doc_build_and_copy.tcsh for how it was run ****************************** **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. .. list-table:: 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]. :header-rows: 1 :align: center :widths: 35 35 * - anatomical dset - ROI dset * - .. image:: media/cbar_refs/FIG_ref_anat.axi.png :align: center - .. image:: media/cbar_refs/FIG_ref_rois.axi.png :align: center | Colorbars (<=256 colors) and example images ====================================================================== .. list-table:: :header-rows: 1 :widths: 15 8 36 36 * - Cbar name - Cbar - anatomical (opacity=9) - ROIs (opacity=5) * - - - cbar range: [0, 98%ile] - cbar range: [0, 256] * - Viridis - .. image:: media/cbars/Viridis.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Viridis.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Viridis.axi.png :align: center * - Spectrum:yellow_to_red - .. image:: media/cbars/Spectrum:yellow_to_red.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Spectrum:yellow_to_red.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Spectrum:yellow_to_red.axi.png :align: center * - Spectrum:yellow_to_cyan - .. image:: media/cbars/Spectrum:yellow_to_cyan.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Spectrum:yellow_to_cyan.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Spectrum:yellow_to_cyan.axi.png :align: center * - Spectrum:yellow_to_cyan+gap - .. image:: media/cbars/Spectrum:yellow_to_cyan+gap.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Spectrum:yellow_to_cyan+gap.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Spectrum:yellow_to_cyan+gap.axi.png :align: center * - Spectrum:red_to_blue - .. image:: media/cbars/Spectrum:red_to_blue.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Spectrum:red_to_blue.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Spectrum:red_to_blue.axi.png :align: center * - Spectrum:red_to_blue+gap - .. image:: media/cbars/Spectrum:red_to_blue+gap.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Spectrum:red_to_blue+gap.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Spectrum:red_to_blue+gap.axi.png :align: center * - ROI_i64 - .. image:: media/cbars/ROI_i64.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_ROI_i64.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_ROI_i64.axi.png :align: center * - ROI_i32 - .. image:: media/cbars/ROI_i32.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_ROI_i32.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_ROI_i32.axi.png :align: center * - ROI_i256 - .. image:: media/cbars/ROI_i256.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_ROI_i256.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_ROI_i256.axi.png :align: center * - ROI_i128 - .. image:: media/cbars/ROI_i128.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_ROI_i128.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_ROI_i128.axi.png :align: center * - ROI_glasbey_256 - .. image:: media/cbars/ROI_glasbey_256.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_ROI_glasbey_256.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_ROI_glasbey_256.axi.png :align: center * - Reds_and_Blues_w_Green - .. image:: media/cbars/Reds_and_Blues_w_Green.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Reds_and_Blues_w_Green.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Reds_and_Blues_w_Green.axi.png :align: center * - Reds_and_Blues_Inv - .. image:: media/cbars/Reds_and_Blues_Inv.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Reds_and_Blues_Inv.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Reds_and_Blues_Inv.axi.png :align: center * - Reds_and_Blues - .. image:: media/cbars/Reds_and_Blues.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Reds_and_Blues.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Reds_and_Blues.axi.png :align: center * - RedBlueGreen - .. image:: media/cbars/RedBlueGreen.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_RedBlueGreen.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_RedBlueGreen.axi.png :align: center * - red_monochrome - .. image:: media/cbars/red_monochrome.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_red_monochrome.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_red_monochrome.axi.png :align: center * - Plasma - .. image:: media/cbars/Plasma.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Plasma.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Plasma.axi.png :align: center * - Magma - .. image:: media/cbars/Magma.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Magma.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Magma.axi.png :align: center * - inverted_gray_circle - .. image:: media/cbars/inverted_gray_circle.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_inverted_gray_circle.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_inverted_gray_circle.axi.png :align: center * - inverted_amber_circle - .. image:: media/cbars/inverted_amber_circle.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_inverted_amber_circle.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_inverted_amber_circle.axi.png :align: center * - green_monochrome - .. image:: media/cbars/green_monochrome.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_green_monochrome.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_green_monochrome.axi.png :align: center * - gray_scale - .. image:: media/cbars/gray_scale.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_gray_scale.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_gray_scale.axi.png :align: center * - gray_circle - .. image:: media/cbars/gray_circle.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_gray_circle.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_gray_circle.axi.png :align: center * - GoogleTurbo - .. image:: media/cbars/GoogleTurbo.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_GoogleTurbo.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_GoogleTurbo.axi.png :align: center * - FreeSurfer_Seg_i255 - .. image:: media/cbars/FreeSurfer_Seg_i255.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_FreeSurfer_Seg_i255.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_FreeSurfer_Seg_i255.axi.png :align: center * - CytoArch_ROI_i256_gap - .. image:: media/cbars/CytoArch_ROI_i256_gap.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_CytoArch_ROI_i256_gap.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_CytoArch_ROI_i256_gap.axi.png :align: center * - CytoArch_ROI_i256 - .. image:: media/cbars/CytoArch_ROI_i256.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_CytoArch_ROI_i256.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_CytoArch_ROI_i256.axi.png :align: center * - Color_circle_ZSS - .. image:: media/cbars/Color_circle_ZSS.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Color_circle_ZSS.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Color_circle_ZSS.axi.png :align: center * - Color_circle_AJJ - .. image:: media/cbars/Color_circle_AJJ.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Color_circle_AJJ.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Color_circle_AJJ.axi.png :align: center * - cb_spiral35 - .. image:: media/cbars/cb_spiral35.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_cb_spiral35.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_cb_spiral35.axi.png :align: center * - cb_spiral - .. image:: media/cbars/cb_spiral.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_cb_spiral.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_cb_spiral.axi.png :align: center * - blue_monochrome - .. image:: media/cbars/blue_monochrome.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_blue_monochrome.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_blue_monochrome.axi.png :align: center * - amber_redtop_bluebot - .. image:: media/cbars/amber_redtop_bluebot.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_amber_redtop_bluebot.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_amber_redtop_bluebot.axi.png :align: center * - amber_monochrome - .. image:: media/cbars/amber_monochrome.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_amber_monochrome.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_amber_monochrome.axi.png :align: center * - amber_circle - .. image:: media/cbars/amber_circle.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_amber_circle.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_amber_circle.axi.png :align: center * - Add_Edge - .. image:: media/cbars/Add_Edge.png :height: 3in :align: center - .. image:: media/cbars/IMGS/tt_cbar_Add_Edge.axi.png :align: center - .. image:: media/cbars/IMGS_MULTI/mm_cbar_Add_Edge.axi.png :align: center 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: .. code-block:: none afni -XXXnpane 512 When using ``@chauffeur_afni`` to make images/montages/movies (see examples :ref:`here `), you also use that option, e.g.,: .. code-block:: none @chauffeur_afni -XXXnpane 512 ... Below is a list of current colorbars in AFNI that contain more than 256 colors. .. list-table:: :header-rows: 1 :widths: 15 8 36 * - Cbar name - Cbar - ROIs (opacity=9) * - - - cbar range: [0, Nroi] * - ROI_glasbey_512 - .. image:: media/cbars/CBARS_XXXnpane/ROI_glasbey_512.png :height: 3in :align: center - .. image:: media/cbars/IMGS_XXXnpane/xx_cbar_ROI_glasbey_512.axi.png :height: 3in :align: center * - ROI_glasbey_2048 - .. image:: media/cbars/CBARS_XXXnpane/ROI_glasbey_2048.png :height: 3in :align: center - .. image:: media/cbars/IMGS_XXXnpane/xx_cbar_ROI_glasbey_2048.axi.png :height: 3in :align: center * - ROI_glasbey_1024 - .. image:: media/cbars/CBARS_XXXnpane/ROI_glasbey_1024.png :height: 3in :align: center - .. image:: media/cbars/IMGS_XXXnpane/xx_cbar_ROI_glasbey_1024.axi.png :height: 3in :align: center