quick API Documentation

quickbrain – fast brain surface plotting.

quickbrain.plotting¶

quickbrain.plotting – Python package for one-call brain surface visualisation.

plot_brain¶

plot_brain(stat_map=None, *, bg_map: 'Union[str, float, np.ndarray, None]' = 'curvature', threshold: 'float | None' = None, hemi: 'str' = 'left', view: 'str' = 'lateral', surf_type: 'str' = 'pial', res: 'Union[int, str]' = 'low', vol_to_surf_radius: 'float' = 3.0, overlay: 'str | Path | None' = 'default', overlay_linewidth: 'float' = 1.0, background: 'str' = 'white', post_blur: 'float' = 3.0, axes: 'Axes | None' = None, figure: 'Figure | None' = None, title: 'str | None' = None, colorbar: 'bool' = True, output_file: 'str | Path | None' = None, **kwargs) -> 'Figure'

Plot a statistical map on the MNI152 brain surface.

Parameters¶

• stat_map : array-like, path-like, or nibabel image, optional Per-vertex data, a path to a NIfTI volume, or a loaded nibabel image. Volumes are projected with nilearn.surface.vol_to_surf. If None, only the background (curvature) is shown.

• bg_map : "curvature" | float | ndarray | None, default "curvature" Background map. "curvature" uses the curvature map. A float in [0, 1] produces a uniform grey background.

• threshold : float or None, default None Stat-map values whose absolute value is below threshold are transparent.

• hemi : "left" or "right", default "left"

• view : "lateral" or "medial", default "lateral"

• surf_type : "pial" or "inflated", default "pial" Volume-to-surface projection is always done on the pial geometry.

Advanced options:¶

• res : 1 | 10 | "high" | "low", default "low" 1 / "high" = fine mesh; 10 / "low" = coarse (faster).

• vol_to_surf_radius : float, default 3.0

• overlay : "default", path, or None, default "default" SVG contour overlay. Looks for overlays/{surf_type}/{side}_{view}.svg first, then overlays/{side}_{view}.svg.

• overlay_linewidth : float, default 1.0 Multiplier for the SVG stroke widths. Values > 1 make the contours thicker, < 1 thinner.

• background : "white" or "transparent", default "white"

• post_blur : float, default 3.0 Pixel-space Gaussian blur (sigma in px) applied to the brain bounding box after rendering but before the SVG overlay. Title and colorbar are never blurred. Set to 0 to disable.

• axes : matplotlib Axes or None Existing 3-D axes to draw into. The composited result replaces the axes content.

• figure : matplotlib Figure or None

• title : str or None

• colorbar : bool, default True

• output_file : path-like or None

• **kwargs Forwarded to nilearn.plotting.plot_surf_stat_map. Forbidden: surf_mesh, engine, title.

Returns¶

• matplotlib.figure.Figure

Example¶

from quickbrain import load_example_image, plot_brain
image = load_example_image("pain_response")
plot_brain(image, hemi="left", view="lateral", threshold=0.01)

load_example_image¶

load_example_image(name: 'ExampleImage' = 'pain_response')

Load a bundled example NIfTI image.

Parameters¶

• name : "pain_response" or "left_hippocampus" Example image to load.

Returns¶

• nibabel.spatialimages.SpatialImage Loaded NIfTI image.

Example¶

from quickbrain import load_example_image, plot_brain
image = load_example_image("pain_response")
plot_brain(image, hemi="left", view="lateral", threshold=0.01)