Load a Python colormap to FSLeyes

Note

You can directly pass the name of an matplotlib colormap to FSLeyes on the command line, for example:

fsleyes sub-001_T2w_rootlets.nii.gz -cm Jet

Thanks to Joshua for bringing this to my attention.

Get RGB colors, one per line, for a given Python colormap. In the script below, we get RGB colors for the jet matplotlib colormap.

import matplotlib.pyplot as plt
import numpy as np

# Generate the jet colormap
cmap = plt.cm.get_cmap('jet')

# Retrieve the RGB values for specific points in the colormap
colors = []
for i in np.linspace(0, 1, 20):
    color = cmap(i)[:3]  # Extract RGB values
    colors.append(color)

# Print the RGB values in the desired format
for color in colors:
    print(f"{color[0]:.6f} {color[1]:.6f} {color[2]:.6f}")

The script above returns the following RGB colors:

0.000000 0.000000 0.500000
0.000000 0.000000 0.731729
0.000000 0.000000 0.963458
0.000000 0.127451 1.000000
0.000000 0.331373 1.000000
0.000000 0.550980 1.000000
0.000000 0.754902 1.000000
0.060089 0.974510 0.907653
0.224541 1.000000 0.743201
0.401645 1.000000 0.566097
0.566097 1.000000 0.401645
0.743201 1.000000 0.224541
0.907653 1.000000 0.060089
1.000000 0.828613 0.000000
1.000000 0.639797 0.000000
1.000000 0.436456 0.000000
1.000000 0.247640 0.000000
0.963458 0.044299 0.000000
0.731729 0.000000 0.000000
0.500000 0.000000 0.000000

Save the RGB colors above as a text file, for example, jet_matplotlib.txt.

Then, open FSLeyes and load the custom colormap through the overlay display panel. The colormap will be saved to $HOME/.fsleyes/colourmaps directory.

Sources:

valosekj/load_python_colormap_to_fsleyes.md

Load a Python colormap to FSLeyes