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, example_data # The example_data is icoorder5 resolution (10242 vertices per hemisphere), # and the non-cortical vertices have been masked out (9372 and 9370 remaining # vertices for the left and right hemisphere, respectively). img, scale = brain_plot( example_data, vmax=10, vmin=-10, cmap='seismic', 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('example_data_with_colorbar.png', bbox_inches='tight') plt.show()Alternatively, the high-resolution image can be saved directly using OpenCV.
import cv2 cv2.imwrite( 'example_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} }