Colormaps

Authors: Francois Tadel

From CTF

Colormap configuration

• Open a 2D sensor cap view, and play with colors.

• Brainstorm keeps track of many user-defined colormaps: anatomy, EEG, MEG, sources, stat, time, time-frequency, etc. You can go to the Colormaps menu in the main window to see this list. Usually, you will use only popup menus from specific figures to edit the colormaps.
• If you modify a colormap, the changes will be applied to all the figures, saved in your user preferences and available the next time you start Brainstorm.
• You are going to manipulate only with the MEG colormap, but the others work exactly the same way.

• Right-click on you 2D sensor cap figure > Colormap.

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• Colormap: You can change the colors that are used to represent the recorded MEG values. You can create your own colormaps with the Matlab colormap editor, clicking on the last option Custom.

• Absolute values: Display the absolute values of the recordings, instead of the original values.

  • This is the default for Anatomy, Sources and Stat colormaps, but it is not very useful for recordings: for EEG and MEG, the sign of the values is very important.

  Fig.1: Relative values; Fig.2: Absolute values

• Maximum: How is the maximum of the colorbar estimated, for the color correspondence.

  • Global: The bounds of the colormap are set to the maximum value across the whole time window. Eg. if you use the rbw colormap and the min and max values are [-100ft, +100ft], the colors will be mapped in the following way: -100ft is blue, +100ft is red, 0ft is white. The display is identical for each time sample. If you select this option at t=-49ms, the 2D topography figure will turn almost white because the values are low before the stimulus.

  • Local: It uses the local min and max values at the current time frame AND for each figure, instead of the global min and max. Eg. at t=-49ms, the extrema values are roughly [-25ft, +25ft]. So the colors will be mapped in order to have: -25ft = blue, and +25ft = red.

  • Custom: You can set manually the minimum/maximum bounds of the colorbar. It does not have to be symmetrical around zero. If you set the values to [-100, 200] ft, the white colors would correspond to values ~50ft, hence values around 0ft would be displayed in blue.

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  Fig.1: Local max; Fig.2: Global max; Fig.3: Custom [-100,300]

  • You can usually keep this option to Local when looking at recordings, it makes things nicer. But keep in mind that it is not because you see flashy colors that you have strong effects. It's always a matter of colormap configuration.

  • Remember that when you change this option, it is saved in your user preferences. If you close Brainstorm and start it again, the colormap configuration stays the same.

• Range: Use symmetrical or non-symmetrical colormaps.

  • [-max, max]: Symmetrical colorbar around the absolute value of the maximum. Eg. at t=47ms, the range is [-80ft, +100ft], and the colorbar used is [-100ft, +100ft], white is zero.

  • [min, max]: Uses the real min and max. Eg. at t=47ms, the colorbar used is [-80ft, +100ft], white is NOT zero.

  • This option is ignored when the option "Maximum: Custom" is selected.

    

  Fig.1: [-max,max]; Fig.2: [min,max]

• Contrast and Brightness:

  • Brightness moves the center of the colormap up and down.
  • Contrast saturate/desaturate the colors.

    

  Fig.1: High brightness; Fig.2: High contrast

  • The words brightness/contrast may not be adapted for colormaps such as rbw, jet or hsv. It makes more sense for colormaps with only one tint that varies in intensity, such as the grey colormap.

  • You can also modify those values by clicking directly on the color bar in the figures. Hold the mouse button, and move up/down to change the brightness and left/right to change the contrast. Even if the sliders do not work, you can modify the colormaps.

• Display colorbar: Just in case you want to hide the color bar...

• Permanent menu: Open a window that displays this colormap sub-menu. Might be useful when you do a lot of colormap adjustments.

• Restore defaults: Click on it now so all your experiments will be discarded.

  • You can also reset the colormap by double-clicking on the color bar.