Dear Chris, 

I have already read the information that you had about ussing custom atlases but the atlas I am trying to add gives still some issues.

I have two atlases (Yeo 2011 for the cerebrum and Buckner 2011 for the cerebellum) loaded as Atlases to use in MRICroGL. What I would like to do it is to change the colors for each network assigned automatically to match the colors that they have in their original atlases:
  1     Visual    120  18 134
  2     Sensorimotor    70 130 180
  3     DorsalAttention   0 118  14 
  4     VentralAttention 196  58 250 
  5     Limbic 220 248 164 
  6     Executive 230 148  34
  7     Default 205  62  78

For this I have created a .lut file using python, with the same name as the atlas and filled in the first 7 rows (with the colors mentioned above) and padded the rest of the 256 rows with zeros. However when I try to load the atlas with the lut file it only shows some random regions in red. Am I missing something important I had to add to the lut file?

Thanks in advance!

Hello,

  You could certainly follow that approach. However, if you are just starting this now, it might be worth developing an atlas to work with NiiVue rather than MRIcroGL. As NiiVue has been adopted by many teams (AFNI, FSL, FreeSurfer, OpenNeuro), this can ease sharing. 

The relevant description of the NiiVue labels is here:

https://github.com/niivue/niivue/blob/main/docs/development-notes/colormaps.md#atlases-and-labeled-images

The live demo lets you apply your own colormap by inserting it into the text entry on the web page:

https://niivue.github.io/niivue/features/segment.html

A nice feature of NiiVue, is that it supports both voxels and labels, so your solution will work for both representations.