https://github.com/feilong/brainplotlib
A lightweight package to plot brain surfaces with Python.
https://github.com/feilong/brainplotlib
brain fmri neuroimaging plotting python visualization
Last synced: about 1 month ago
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A lightweight package to plot brain surfaces with Python.
- Host: GitHub
- URL: https://github.com/feilong/brainplotlib
- Owner: feilong
- License: bsd-3-clause
- Created: 2022-01-25T15:26:11.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2023-07-25T15:32:11.000Z (over 2 years ago)
- Last Synced: 2026-01-04T03:00:46.072Z (about 2 months ago)
- Topics: brain, fmri, neuroimaging, plotting, python, visualization
- Language: Python
- Homepage: https://feilong.github.io/brainplotlib/
- Size: 86.4 MB
- Stars: 44
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
- Citation: CITATION.bib
- Zenodo: .zenodo.json
Awesome Lists containing this project
README
[](https://pypi.org/project/brainplotlib/)
[](https://pepy.tech/project/brainplotlib)
[](https://doi.org/10.5281/zenodo.5979819)
`brainplotlib` is a Python package that plots data on cortical surface.
It's designed to have minimal requirements --- only `NumPy` and `matplotlib`.
## Installation
The package can be installed with pip:
```bash
pip install brainplotlib
```
## Example usage
**See the [examples gallery](https://feilong.github.io/brainplotlib/examples/index.html) for all code examples with detailed explanations.**
```Python
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`:
```Python
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`.
```Python
import cv2
cv2.imwrite(
'example_data.png',
np.round(img[:, :, [2, 1, 0]] * 255).astype(np.uint8))
```
## Citation
If you use this software in your publications, please cite it [](https://doi.org/10.5281/zenodo.5979819)
```bibtex
@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}
}
```