help > RE: Custom Color Map
Nov 29, 2018  05:11 PM | Mingrui Xia
RE: Custom Color Map

I wrote a small function to help generate the color map you need. This function can adjust an original continuous color map by adding a blank corresponding to your need. Then this adjusted color map can be input as the custom colormap in GUI.

For example, in your case: 

First, generate the same colormap as in the image (without the white part):
original_color_map = [linspace(22,208,5),ones(1,5)*255;linspace(22,208,5),linspace(208,22,5);ones(1,5)*255,linspace(208,22,5)]'/255;

then, use the attached function to adjust this colormap with your values:
adjusted_color_map = BrainNet_GenColormap(-11,-3,3,4,original_color_map);

I need more time to add this function to the GUI, possibly with the next release. 


Originally posted by Renante Rondina:

I have been using BrainNet for some time now, and am comfortable with the GUI, but I am not very proficient at coding. I had a question about customizing the color map.

I am interested in displaying node data that ranges from negative to positive values (e.g., -11 to +4), with a gradient to the color map so that nodes with more extreme values are either more saturated or have a different hue (e.g., warmer vs. cooler). I also need to threshold my data so that nodes with mid-range values (e.g., -3 to +3) do not appear on the brain map. Ideally, the colors corresponding to those mid-range values would appear as white or colorless on the color map, similar to the colormap shown on the right side of this image:

However, there is nothing similar in the preset options when selecting nodal color. Currently, I am using a Jet scale and have removed data points with mid-range values from the input file. Please see attached file for an example output image. Note that this image does not contain any nodes with mid-range values, which would correspond to colors from yellow to redish-orange on the color map. However, this creates a problem when interpreting multiple images with different scales as the colors corresponding to mid-range values changes in the color map from image to image.

Are there any available patches or custom-made maps that would be suitable for my purposes?
Please let me know,
Thank you in advance

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Renante Rondina Nov 21, 2018
RE: Custom Color Map
Mingrui Xia Nov 29, 2018