brainplotlib is a Python package that plots data on cortical surface.
It's designed to have minimal requirements --- only NumPy and matplotlib.
The package can be installed with pip:
pip install brainplotlibSee the examples gallery for all code examples with detailed explanations.
import numpy as np
from brainplotlib import brain_plot
## Generate some random data
# In this case it's icoorder3 resolution (642 vertices per hemisphere), and
# the non-cortical vertices have been masked out (588 and 587 remaining
# vertices for the left and right hemisphere, respectively).
rng = np.random.default_rng(0)
v = rng.random((1175, ))
img, scale = brain_plot(v, vmax=1, vmin=0, cmap='viridis', return_scale=True)The rendered image is a NumPy array.
It can be rendered using matplotlib:
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(img.shape[1] / 200, img.shape[0] / 200), dpi=200)
plt.imshow(img)
plt.axis('off')
cbar = plt.colorbar(scale, shrink=0.8, aspect=30)
plt.savefig('random_data_with_colorbar.png', bbox_inches='tight')
plt.show()Alternatively, the high-resolution image can be saved directly using OpenCV.
import cv2
cv2.imwrite(
'random_data.png',
np.round(img[:, :, [2, 1, 0]] * 255).astype(np.uint8))If you use this software in your publications, please cite it
@software{brainplotlib,
author = {Ma Feilong and Guo Jiahui and M. Ida Gobbini and James V. Haxby},
title = {brainplotlib: plotting brain data on cortical surface},
month = feb,
year = 2022,
publisher = {Zenodo},
doi = {10.5281/zenodo.5979819},
url = {https://doi.org/10.5281/zenodo.5979819}
}