quickbrain

Source:

quickstart

The quickbrain Python package provides a compact Python API for creating beautiful brain images quickly and easily.

When to use quickbrain¶

• useful both for quick & dirty analyses and for publication-quality images

• to provide a comprehensive, interpretable overview of whole-brain activation patterns

• including the cerebellum (often omitted in other visualizations)

When to not use quickbrain¶

• If you want high-resolution surface projections, and don’t care about the outline contour and the cerebellum, use the nilearn.surface.plot_surf_stat_map function.

• If you want precise localization, don’t use surface projection-based visualizations; use volumetric visualizations instead, e.g. nilearn.plotting.plot_stat_map.

Install¶

pip install "quickbrain @ git+https://github.com/pni-lab/quickbrain.git"

Dependencies¶

quickbrain keeps its runtime dependencies intentionally small:

• matplotlib

• nibabel

• nilearn

• numpy

• scipy

• svgpath2mpl

The documentation site is built with MyST Markdown in GitHub Actions; MyST is installed there with npm and is not a Python package dependency of quickbrain.

Example¶

import nibabel as nib
from quickbrain import plot_brain
image = nib.load("path/to/your/image.nii.gz")
plot_brain(image)

Source:

quickstart

More examples¶

Open quickstart for a notebook walkthrough, then see quick API Documentation for the API generated from package docstrings.

Under the hood¶

The quickbrain package is built on top of the nilearn package, which provides a comprehensive set of tools for neuroimaging data analysis. The trick is that we don’t need a high-resolution surface if we only want an overview of the whole-brain pattern, instead of detailed localization. Thus, the quickbrain package uses a custom-built low-resolution mesh (including the cerebellum!) and the nilearn.surface.vol_to_surf and the nilearn.surface.plot_surf_stat_map functions to project the statistical map onto the brain surface and plot the brain surface. This makes it lightning fast. But, low resolution means less details. So we put back the details by adding beautiful contour overlays, to guide the eye across sulci and gyri.

Developers, contributors and contact¶